Contacts of the helix formed by residues 85 - 109 (chain X) in PDB entry 1V7M
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with CYS 85 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25X ARG 5.5 0.7 - - - -
28X GLN* 4.2 12.3 - - - -
29X CYS* 2.1 57.9 - - + -
30X PRO* 4.6 8.3 - - + -
84X THR* 1.3 79.0 - - - +
86X LEU* 1.3 62.4 + - - +
87X SER 3.2 1.6 - - - -
88X SER* 2.7 28.7 + - - -
89X LEU* 3.0 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26X LEU* 4.7 15.3 - - + -
29X CYS* 3.5 11.2 - - - -
31X GLU 5.0 3.6 - - - +
32X VAL* 4.6 19.1 - - + -
33X HIS* 4.7 8.7 - - + +
35X LEU* 4.9 5.4 - - + -
81X LEU* 4.0 19.1 - - + -
84X THR* 3.7 4.9 + - - +
85X CYS* 1.3 79.5 - - - +
87X SER* 1.3 51.4 + - - +
89X LEU* 2.9 8.2 + - + +
90X LEU* 2.8 59.8 + - + -
124X PRO* 3.9 32.3 - - + -
128X PHE* 5.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78X ARG* 2.6 61.8 + - - +
81X LEU* 3.9 13.2 + - - -
82X GLY 3.4 25.3 + - - -
83X PRO* 5.0 2.2 - - - +
84X THR* 3.6 7.8 + - - -
85X CYS 3.2 0.4 - - - -
86X LEU* 1.3 77.1 - - - +
88X SER* 1.3 68.8 + - - +
90X LEU* 4.2 7.2 - - - -
91X GLY 3.3 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78X ARG* 4.7 2.6 + - - +
83X PRO* 5.3 0.6 - - - +
84X THR 3.6 16.6 + - - -
85X CYS* 2.7 24.2 + - - -
87X SER* 1.3 81.3 - - - +
89X LEU* 1.3 66.0 + - - +
91X GLY* 3.3 6.2 + - - -
92X GLN* 2.4 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22X LEU* 3.4 39.6 - - + +
25X ARG* 3.6 19.3 - - + +
26X LEU* 3.6 32.3 - - + +
29X CYS* 5.8 2.7 - - - -
85X CYS* 3.0 8.2 + - - +
86X LEU* 2.9 9.9 + - + +
88X SER* 1.3 82.0 + - - +
90X LEU* 1.3 67.2 + - - +
91X GLY 3.2 2.0 - - - -
92X GLN* 3.2 33.5 + - - +
93X LEU* 3.3 12.8 + - - +
128X PHE* 4.3 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35X LEU* 5.8 0.4 - - + -
74X VAL* 3.6 10.3 - - + +
77X ALA* 3.7 29.8 - - + -
78X ARG* 4.0 22.4 + - + +
81X LEU* 5.2 2.5 - - + -
86X LEU* 2.8 37.2 + - + +
87X SER* 4.1 3.1 - - - +
88X SER 3.4 0.2 - - - -
89X LEU* 1.3 77.1 - - - +
91X GLY* 1.3 54.8 + - - +
92X GLN 3.3 0.4 - - - -
93X LEU* 3.5 7.2 - - + +
94X SER* 3.2 26.9 + - - -
124X PRO* 5.0 4.0 - - + +
127X ILE* 3.2 33.9 - - + -
128X PHE* 3.6 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 91 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78X ARG* 3.3 30.5 - - - +
87X SER 3.3 9.5 + - - -
88X SER 3.3 2.7 + - - -
89X LEU 3.2 0.8 - - - -
90X LEU* 1.3 72.7 - - - +
92X GLN* 1.3 63.9 + - - +
94X SER* 3.0 18.5 + - - -
95X GLY* 3.4 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 92 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22X LEU* 3.6 35.1 - - + +
88X SER* 2.4 31.7 + - - +
89X LEU* 3.2 27.4 + - - +
91X GLY* 1.3 77.5 - - - +
93X LEU* 1.3 59.4 + - - +
95X GLY* 3.2 4.8 + - - +
96X GLN* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19X SER* 5.5 5.4 - - - +
22X LEU* 3.9 9.8 - - + +
70X LEU* 5.2 0.7 - - + -
74X VAL* 4.1 17.9 - - + -
89X LEU 3.3 9.3 + - - +
90X LEU* 3.5 11.0 - - - +
92X GLN* 1.3 74.0 - - - +
94X SER* 1.3 57.0 + - - +
96X GLN* 2.6 31.9 + - + +
97X VAL* 2.9 18.0 + - + +
127X ILE* 3.4 42.2 - - + +
128X PHE* 3.9 31.2 - - + +
131X PHE* 3.7 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71X LEU* 4.6 2.5 - - - -
74X VAL* 4.0 17.0 - - - +
75X MET* 4.6 10.9 - - - -
78X ARG* 4.7 2.6 + - - -
90X LEU 3.2 10.1 + - - -
91X GLY* 3.0 21.7 + - - -
93X LEU* 1.3 77.4 - - - +
95X GLY* 1.3 65.2 + - - -
97X VAL* 3.1 11.6 + - - +
98X ARG* 3.0 49.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 95 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91X GLY 3.4 8.6 + - - -
92X GLN* 3.2 8.9 + - - -
93X LEU 3.0 2.0 + - - -
94X SER* 1.3 82.6 + - - +
96X GLN* 1.3 61.9 + - - +
98X ARG* 3.5 17.3 + - - +
99X LEU* 3.5 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 96 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14X LYS* 6.3 1.3 - - - -
15X LEU* 3.8 22.6 - - + +
18X ASP* 3.1 31.1 + - - +
19X SER* 3.1 32.1 + - - -
22X LEU* 3.4 25.3 - - - +
92X GLN 3.0 7.6 + - - +
93X LEU* 2.6 19.5 + - - +
95X GLY* 1.3 73.1 - - - -
97X VAL* 1.3 58.3 + - - +
99X LEU* 3.3 22.9 + - + +
100X LEU* 3.8 2.9 + - - +
131X PHE* 4.2 20.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67X VAL* 3.8 18.8 - - + -
70X LEU* 3.5 36.1 - - + -
71X LEU* 3.8 24.9 - - + -
74X VAL* 4.9 3.1 - - + -
93X LEU* 2.9 28.7 + - + +
94X SER* 3.1 8.7 + - - +
96X GLN* 1.3 71.9 - - - +
98X ARG* 1.3 55.4 + - - +
99X LEU 3.0 5.4 - - - -
100X LEU* 2.9 19.9 + - - +
101X LEU* 2.9 12.4 + - + +
131X PHE* 4.2 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I THR* 3.8 11.1 + - - +
30I SER* 5.8 1.4 + - - -
31I ASP* 3.1 39.3 + - - +
55I VAL* 3.2 26.3 - - + +
71X LEU* 3.2 25.1 - - + +
75X MET* 3.6 24.4 - - - +
94X SER* 3.0 38.2 + - - +
95X GLY* 3.7 12.6 - - - +
96X GLN 3.4 0.6 - - - -
97X VAL* 1.3 74.2 - - - +
99X LEU* 1.3 58.8 + - + +
100X LEU 3.4 0.2 - - - -
101X LEU* 3.9 12.0 - - + +
102X GLY 3.1 19.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I VAL* 5.0 8.7 - - + -
11X VAL* 6.0 0.7 - - - +
15X LEU* 4.5 18.6 - - + -
95X GLY 3.5 20.6 - - - +
96X GLN* 3.3 13.4 + - + +
97X VAL 3.0 0.8 - - - -
98X ARG* 1.3 80.2 - - + +
100X LEU* 1.3 62.4 + - - +
102X GLY* 3.7 1.7 + - - -
103X ALA* 3.3 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11X VAL* 5.4 2.5 - - + -
15X LEU* 4.3 24.1 - - + +
67X VAL* 3.2 37.0 - - + -
96X GLN 3.8 3.0 + - - +
97X VAL* 2.9 11.9 + - - +
99X LEU* 1.3 75.2 - - - +
101X LEU* 1.3 69.0 - - - +
103X ALA* 3.1 8.7 + - + +
104X LEU* 3.1 43.3 + - + +
131X PHE* 4.5 14.1 - - + -
134X LEU* 5.6 2.2 - - + -
135X LEU* 4.3 9.9 - - + -
139X VAL* 4.4 25.6 - - + -
143X MET* 5.0 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I ASP* 4.8 13.9 - - - +
55I VAL* 5.6 5.6 - - + -
101I TRP* 4.7 9.6 - - + -
64X LEU* 4.1 3.1 - - + -
67X VAL* 4.1 14.2 - - + +
68X THR* 3.0 44.9 - - + -
71X LEU* 4.7 19.3 - - + -
97X VAL* 2.9 14.9 + - + +
98X ARG* 4.0 12.1 - - + +
100X LEU* 1.3 76.9 - - - +
102X GLY* 1.3 64.1 + - - +
104X LEU* 3.5 4.1 + - - +
105X GLN* 2.9 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I VAL* 4.3 14.1 - - - -
56I ASN* 3.1 21.2 - - - +
98X ARG 3.1 18.9 + - - -
99X LEU* 3.9 2.5 - - - -
100X LEU 3.3 0.2 - - - -
101X LEU* 1.3 76.8 - - - +
103X ALA* 1.3 55.5 + - - +
105X GLN* 4.3 4.3 - - - -
106X SER* 3.1 26.2 + - - -
151X CYS 5.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11X VAL* 5.1 11.0 - - + -
99X LEU 3.3 13.1 + - - +
100X LEU* 3.1 15.7 + - + +
102X GLY* 1.3 71.2 - - - +
104X LEU* 1.3 68.2 + - + +
106X SER* 3.3 4.5 + - - -
107X LEU* 2.9 24.9 + - - +
150X LEU* 5.1 12.1 - - + -
151X CYS* 4.3 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60X ALA* 4.4 23.8 - - + +
63X ILE* 3.3 32.5 - - + -
64X LEU* 3.7 28.7 - - + -
67X VAL* 3.7 15.9 - - + -
100X LEU* 3.1 27.8 + - + +
101X LEU 3.7 2.5 - - - +
103X ALA* 1.3 77.0 - - + +
105X GLN* 1.3 57.8 + - - +
107X LEU* 3.0 11.8 + - + +
108X LEU* 2.9 34.5 + - + +
142X LEU* 5.1 10.8 - - + -
150X LEU* 6.1 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 105 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I ASP 5.1 0.5 - - - +
33I TRP* 3.6 17.5 + - + -
53I SER* 4.6 1.2 + - - -
55I VAL* 5.8 0.3 - - - +
56I ASN* 3.0 21.4 + - - +
101I TRP* 4.3 0.2 - - - -
64X LEU* 3.6 16.6 - - + +
68X THR* 4.3 2.4 - - - +
101X LEU* 2.9 60.6 + - - +
102X GLY 3.9 3.1 + - - +
104X LEU* 1.3 73.3 - - - +
106X SER* 1.3 52.4 + - - +
108X LEU 4.6 0.2 - - - +
109X GLY* 2.8 29.6 + - - -
110X THR 3.5 25.5 + - - +
111X GLN* 2.8 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 106 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I ARG* 4.7 14.4 + - - +
56I ASN* 3.9 10.3 + - - -
102X GLY 3.1 19.1 + - - -
103X ALA* 3.7 5.6 - - - -
104X LEU 3.2 0.2 - - - -
105X GLN* 1.3 74.1 - - - +
107X LEU* 1.3 67.8 + - - +
108X LEU 3.4 0.2 + - - -
109X GLY* 3.5 8.7 + - - -
151X CYS 5.4 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57X GLU* 6.5 0.4 - - + -
60X ALA* 4.3 24.5 - - + -
103X ALA 2.9 14.3 + - - +
104X LEU* 3.5 12.6 - - + +
106X SER* 1.3 76.8 + - - +
108X LEU* 1.3 68.0 + - + +
109X GLY 3.8 0.2 + - - -
142X LEU* 5.1 10.3 - - + -
147X GLY* 5.3 9.9 - - - -
148X SER* 3.4 39.5 - - - +
149X THR 4.8 4.9 - - - +
150X LEU* 5.9 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90M ARG 5.2 4.3 - - - +
57X GLU* 4.0 44.7 - - + +
60X ALA* 4.0 15.9 - - + +
61X GLN* 3.8 34.8 - - + +
64X LEU* 3.7 26.9 - - + -
104X LEU* 2.9 17.5 + - + +
105X GLN 4.2 2.0 - - - +
107X LEU* 1.3 89.2 - - + +
109X GLY* 1.3 60.5 + - - +
110X THR* 3.1 20.6 + - + +
112X LEU* 4.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 109 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I TRP* 3.6 7.1 - - - -
52I ARG* 4.2 13.5 - - - -
90M ARG 5.5 1.8 - - - -
93M TYR* 3.4 10.3 + - - -
95M ARG* 3.2 24.7 + - - -
105X GLN 2.8 13.6 + - - -
106X SER 3.5 9.0 + - - -
107X LEU 3.8 0.2 + - - -
108X LEU* 1.3 74.5 - - - +
110X THR* 1.3 62.0 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il