Contacts of the helix formed by residues 80 - 103 (chain E) in PDB entry 2Q7M
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 GLN 80 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E GLY 3.9 2.4 - - - +
8E ASN* 3.5 25.4 - - + +
9E VAL* 2.8 25.7 + - - +
11E LEU* 2.6 62.6 - - - +
12E LEU* 3.6 17.6 - - + +
75E GLY* 3.6 16.3 + - - +
79E SER* 1.3 71.2 - - - +
81E VAL* 1.3 59.4 + - - +
84E ALA* 3.1 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E LEU* 5.5 4.3 - - + -
79E SER* 4.1 8.3 - - - -
80E GLN* 1.3 77.2 - - - +
82E PRO* 1.3 85.5 - - + +
83E ALA 3.2 0.9 - - - -
84E ALA* 3.2 3.9 + - - +
85E PHE* 2.9 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E SER* 2.8 35.9 - - - +
81E VAL* 1.3 105.7 - - + +
83E ALA* 1.3 52.1 + - - +
85E PHE* 3.0 6.2 + - + +
86E ALA* 2.8 36.4 + - - +
121E PHE* 4.2 9.2 - - + -
125E MET* 3.7 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E LEU* 4.0 2.7 - - + -
71E LEU* 3.2 20.0 - - - +
74E ALA* 3.0 31.6 - - + +
75E GLY* 3.4 15.5 - - - +
79E SER 3.3 9.4 - - - +
80E GLN 4.5 0.2 - - - -
82E PRO* 1.3 81.1 - - - +
84E ALA* 1.3 56.2 + - - +
87E GLY 3.0 22.7 + - - -
122E LEU* 3.8 3.6 - - - +
125E MET* 2.9 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E LEU* 3.4 35.2 - - + +
12E LEU* 4.0 7.8 - - + +
15E VAL* 4.1 10.6 - - + +
71E LEU* 4.4 3.8 - - - -
80E GLN 3.1 19.8 + - - +
81E VAL* 3.2 5.2 + - - +
83E ALA* 1.3 77.9 - - - +
85E PHE* 1.3 62.8 + - - +
87E GLY* 3.7 1.4 + - - -
88E LEU* 3.2 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E VAL* 2.9 18.6 + - + +
82E PRO* 3.7 6.5 - - + +
84E ALA* 1.3 73.7 - - - +
86E ALA* 1.3 63.6 - - + +
87E GLY 3.0 1.6 - - - -
88E LEU* 2.4 44.0 + - + +
89E MET* 3.0 45.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E PRO 2.8 10.2 + - - +
85E PHE* 1.3 80.2 - - + +
87E GLY* 1.3 61.8 + - - +
89E MET* 3.1 6.5 + - - +
90E TYR 3.1 18.2 + - - -
118E ILE* 3.2 18.6 - - + +
121E PHE* 3.0 41.5 - - + -
122E LEU* 3.3 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E VAL* 3.6 8.6 - - - +
67E PHE* 3.5 26.1 - - - -
71E LEU* 4.1 7.4 - - - -
83E ALA 3.0 16.7 + - - -
84E ALA 4.0 2.0 - - - -
85E PHE 3.0 1.2 - - - -
86E ALA* 1.3 77.0 - - - +
88E LEU* 1.3 60.1 + - - +
90E TYR* 3.5 2.1 - - - +
91E LEU* 3.3 28.6 + - - +
122E LEU* 4.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E VAL* 4.2 8.1 - - + -
18E ILE* 4.8 10.5 - - + -
84E ALA 3.2 13.7 + - - +
85E PHE* 2.4 34.4 + - + +
87E GLY* 1.3 69.9 - - - +
89E MET* 1.3 70.6 + - - +
91E LEU* 3.0 27.0 + - + +
92E PHE* 3.2 44.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E PHE* 3.0 53.9 + - + +
86E ALA* 3.4 4.9 - - - +
88E LEU* 1.3 79.6 - - - +
90E TYR* 1.3 59.2 + - - +
91E LEU 2.9 2.0 - - - -
92E PHE* 2.6 51.2 + - + +
93E VAL* 2.8 18.5 + - + +
118E ILE* 3.3 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E ALA* 2.8 40.7 + - - +
67E PHE* 3.4 46.9 - + + -
86E ALA 3.1 0.8 + - - +
87E GLY 3.5 11.7 - - - +
89E MET* 1.3 75.1 - - - +
91E LEU* 1.3 59.3 + - + +
93E VAL* 3.9 4.6 - - + +
94E ARG* 3.0 56.8 + - + +
114E PHE* 4.5 12.5 - + + -
115E GLY* 5.1 4.7 - - - -
118E ILE* 2.8 34.0 - - + +
119E ILE* 3.5 29.2 - - + -
506E 2CS 5.4 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E VAL* 3.2 30.1 - - + +
18E ILE* 2.9 35.9 - - + -
19E SER* 3.4 24.9 - - - +
22E GLN* 3.4 27.1 + - - +
67E PHE* 3.7 19.7 - - + -
87E GLY 3.3 11.6 + - - +
88E LEU* 3.0 16.9 + - + +
89E MET 2.9 1.0 - - - -
90E TYR* 1.3 81.7 - - + +
92E PHE* 1.3 64.1 + - + +
94E ARG* 4.0 4.7 - - - +
95E GLN* 3.4 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E LEU* 3.2 44.2 - - + -
89E MET* 2.6 42.9 + - + +
91E LEU* 1.3 74.7 - - + +
93E VAL* 1.3 56.0 + - + +
94E ARG 3.2 0.9 - - - -
95E GLN* 3.0 5.8 + - - +
96E LYS* 2.7 47.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E MET* 2.9 24.9 - - + +
90E TYR* 3.9 8.3 - - + +
92E PHE* 1.3 73.6 - - + +
94E ARG* 1.3 52.6 + - - +
96E LYS* 3.1 8.7 + - + -
97E TYR* 2.6 41.4 + - + +
114E PHE* 4.5 7.0 - - + -
115E GLY* 4.4 24.2 - - - +
118E ILE* 4.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 94 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E SER* 4.9 3.6 - - - -
22E GLN* 2.4 34.7 + - - +
23E ASN* 2.4 37.8 + - - +
26E PHE* 3.6 16.9 - - - -
60E CYS* 3.3 26.9 + - - -
64E TYR* 3.9 23.6 - - - +
67E PHE* 5.1 0.2 - - - -
90E TYR* 3.0 53.1 + - + +
91E LEU* 4.0 4.3 - - - +
93E VAL* 1.3 76.2 - - - +
95E GLN* 1.3 57.3 + - - +
97E TYR* 4.0 0.3 - - - +
98E PHE* 3.0 33.8 + - - +
114E PHE* 3.2 36.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E GLN* 3.9 7.0 + - - +
25E PHE* 4.2 19.1 - - - -
26E PHE* 3.0 30.1 - - - -
91E LEU 3.4 13.0 + - - +
92E PHE* 3.0 11.5 + - - +
94E ARG* 1.3 80.2 - - - +
96E LYS* 1.3 69.0 + - - +
98E PHE* 3.8 1.7 - - - -
99E VAL* 2.8 65.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E PHE* 2.7 39.7 + - + +
93E VAL* 3.7 10.8 - - + +
95E GLN* 1.3 103.6 + - - +
97E TYR* 1.3 59.2 + - - +
99E VAL* 3.9 12.9 - - + +
100E GLY* 3.4 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 97 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E ALA* 4.9 1.6 - - + -
59E ASN* 2.9 23.7 + - + +
60E CYS* 4.2 9.9 - - - -
93E VAL* 2.6 22.7 + - + +
94E ARG 4.0 0.4 - - - +
96E LYS* 1.3 72.3 - - - +
98E PHE* 1.3 58.4 + - - +
99E VAL 2.9 8.3 + - - -
100E GLY* 3.4 1.6 + - - -
101E TYR* 3.1 39.0 + + + +
110E PRO* 4.2 16.6 - - + -
111E GLY* 3.2 11.1 - - - -
112E TYR* 2.7 29.6 + - - -
113E ILE 4.9 3.8 - - - -
114E PHE* 3.0 58.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 98 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E PHE* 3.0 37.7 - + - -
26E PHE* 3.7 48.2 - + + -
29E LYS* 3.8 19.5 - - + -
53E VAL* 4.3 13.5 - - + -
56E ALA* 3.8 23.3 - - + -
57E ASN* 4.0 20.6 - - + -
60E CYS* 3.9 7.4 - - - -
94E ARG 3.0 17.7 + - - +
95E GLN* 4.4 4.7 - - - +
97E TYR* 1.3 77.9 - - - +
99E VAL* 1.3 61.6 + - + +
101E TYR* 4.2 2.8 + - - -
102E LEU* 3.7 19.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E PHE* 6.1 0.7 - - + -
95E GLN* 2.8 44.2 + - - +
96E LYS* 3.9 15.5 - - + +
97E TYR 2.9 0.6 - - - -
98E PHE* 1.3 79.4 - - + +
100E GLY* 1.3 63.8 + - - +
101E TYR 3.1 1.6 - - - -
102E LEU* 3.0 22.8 + - - +
103E GLY* 3.3 11.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 100 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E LYS 3.4 10.3 + - - -
97E TYR 3.4 2.0 + - - -
99E VAL* 1.3 80.8 - - - +
101E TYR* 1.3 57.1 + - - +
102E LEU 3.0 9.7 + - - -
103E GLY* 4.5 1.6 - - - -
104E GLU* 4.0 13.2 + - - -
105E ARG* 4.8 2.6 + - - +
108E SER* 4.6 7.6 + - - -
110E PRO* 5.6 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 101 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E ARG* 3.3 53.3 - - - +
55E THR* 3.7 14.6 - - + -
56E ALA* 3.3 35.2 - - + +
59E ASN* 3.7 19.3 - - - -
97E TYR* 3.1 24.7 + + + +
98E PHE* 4.4 1.1 - - - -
99E VAL 3.1 1.6 - - - -
100E GLY* 1.3 76.1 - - - +
102E LEU* 1.3 59.5 + - - +
104E GLU 4.7 0.7 - - - -
108E SER* 3.9 9.0 + - - -
110E PRO* 3.0 44.4 - - + -
111E GLY* 3.5 6.5 + - - -
40F ARG* 2.3 44.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E LYS* 6.1 2.9 - - + -
33E GLU* 5.8 0.9 - - + -
49E ALA* 4.5 8.2 - - + +
52E ARG* 4.7 5.6 - - + +
53E VAL* 3.1 36.1 - - + +
56E ALA* 5.7 0.2 - - + -
98E PHE* 3.7 19.5 - - + +
99E VAL* 3.0 10.7 + - - +
100E GLY 3.0 1.6 + - - -
101E TYR* 1.3 81.4 - - - +
103E GLY* 1.3 73.9 + - - +
104E GLU* 2.8 13.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E VAL 3.3 8.3 + - - -
100E GLY* 4.3 0.9 + - - -
102E LEU* 1.3 88.3 - - - +
104E GLU* 1.3 73.5 + - - +
----------------------------------------------------------
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