Contacts of the helix formed by residues 85 - 103 (chain A) in PDB entry 3H8E
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 GLY 85 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA 3.8 1.8 + - - -
84A LEU* 1.3 77.9 - - - +
86A ASP* 1.3 67.3 + - - -
87A ARG 3.3 2.9 - - - -
88A THR* 3.3 10.1 + - - -
89A TRP* 3.0 21.9 + - - +
117A VAL* 4.6 0.4 - - - -
118A ASN* 4.5 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLY* 1.3 71.2 - - - +
87A ARG* 1.3 66.9 + - - +
89A TRP* 3.7 4.1 - - - +
90A ARG* 2.9 30.1 + - - +
117A VAL* 3.7 7.7 - - - +
118A ASN 4.4 4.1 + - - +
120A ARG* 2.8 44.0 + - - +
129A LEU* 3.4 20.9 - - + +
408A LYS 4.7 0.5 - - - +
411A ASP* 3.9 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLY 3.3 0.8 - - - -
86A ASP* 1.3 81.6 - - - +
88A THR* 1.3 61.7 + - - +
90A ARG* 3.4 15.6 + - - +
91A LYS* 2.8 64.0 + - - +
411A ASP* 2.8 45.1 + - - -
413A ARG* 3.7 9.9 - - - +
422B GLU* 3.5 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO* 3.5 33.3 - - + +
84A LEU* 3.7 26.0 - - + -
85A GLY* 3.3 12.6 + - - -
86A ASP 3.3 0.4 - - - -
87A ARG* 1.3 78.7 - - - +
89A TRP* 1.3 61.3 + - - +
91A LYS* 3.3 9.6 + - - +
92A LEU* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.9 12.2 - - + +
85A GLY 3.0 17.3 + - - +
86A ASP 3.7 2.2 - - - +
88A THR* 1.3 78.1 - - - +
90A ARG* 1.3 64.7 + - + +
92A LEU* 3.2 24.2 + - + +
93A VAL* 3.1 29.6 + - + +
112A LEU* 4.1 14.1 - - + -
115A VAL* 3.7 31.9 - - + -
117A VAL* 3.5 33.6 - - + +
126A LYS* 2.9 53.3 + - + -
129A LEU* 4.0 21.3 - - + -
130A LEU* 3.6 41.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASP 2.9 20.4 + - - +
87A ARG* 3.9 14.5 - - - +
89A TRP* 1.3 73.5 - - + +
91A LYS* 1.3 58.8 + - + +
93A VAL* 3.4 7.3 + - - +
94A ALA* 2.9 28.6 + - - +
129A LEU* 3.7 31.5 + - + +
132A GLU* 3.6 38.8 + - - +
133A THR* 2.8 34.8 + - + +
410A ALA 4.2 4.9 + - - -
411A ASP* 2.9 49.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLY* 5.5 1.1 - - - -
87A ARG* 2.8 54.5 + - + +
88A THR* 3.7 8.3 - - + +
89A TRP 3.2 0.2 - - - -
90A ARG* 1.3 78.2 - - + +
92A LEU* 1.3 57.2 + - - +
94A ALA* 3.4 6.7 + - - +
95A SER* 2.9 34.5 + - - +
425B GLU* 5.6 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PRO* 5.8 0.4 - - + -
56A PRO* 5.1 2.8 - - + +
57A GLY* 4.3 16.2 - - - +
76A VAL* 3.8 28.0 - - + -
77A GLY 3.4 20.9 - - - +
78A SER* 4.0 11.9 - - - -
84A LEU* 4.0 23.3 - - + -
88A THR 2.9 14.0 + - - +
89A TRP* 3.2 29.6 + - + +
91A LYS* 1.3 74.8 - - - +
93A VAL* 1.3 67.8 + - - +
95A SER* 3.1 4.9 + - - -
96A VAL* 3.0 32.9 + - + +
112A LEU* 4.3 10.8 - - + -
115A VAL* 4.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TRP* 3.1 29.0 + - + +
90A ARG* 3.6 9.2 - - - +
92A LEU* 1.3 79.8 - - + +
94A ALA* 1.4 57.6 + - - +
96A VAL* 3.2 8.2 + - + +
97A ALA* 2.9 26.4 + - + +
110A LEU* 5.7 3.8 - - + -
112A LEU* 5.1 1.6 - - + -
130A LEU* 3.7 59.9 - - + +
133A THR* 3.9 13.7 - - + -
134A LEU* 4.3 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG 2.9 18.2 + - - +
91A LYS* 3.7 7.6 - - - +
92A LEU 3.3 0.2 - - - -
93A VAL* 1.4 78.1 - - - +
95A SER* 1.3 56.1 + - - +
97A ALA* 3.7 7.5 - - - +
98A GLY* 2.9 25.8 + - - -
101A LYS* 4.7 2.6 + - - -
133A THR* 4.0 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLY* 3.6 33.1 + - - -
59A THR* 5.1 2.9 - - - -
76A VAL* 5.2 0.4 - - - -
91A LYS* 2.9 20.7 + - - +
92A LEU 3.4 9.0 - - - -
94A ALA* 1.3 73.1 - - - +
96A VAL* 1.3 66.4 + - - +
98A GLY* 3.3 3.0 + - - -
99A VAL* 3.2 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 4.0 25.4 - - + -
59A THR* 5.4 0.7 - - - -
74A LEU* 4.2 9.6 - - + -
76A VAL* 3.8 35.0 - - + -
92A LEU* 3.0 23.0 + - + +
93A VAL* 3.5 9.2 - - + +
95A SER* 1.3 77.2 - - - +
97A ALA* 1.3 64.3 + - - +
99A VAL* 3.1 5.2 + - - +
100A LEU* 3.0 41.0 + - + +
110A LEU* 4.8 14.1 - - + -
112A LEU* 5.3 3.1 - - + -
134A LEU* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A VAL 2.9 19.0 + - - +
94A ALA* 3.7 9.0 - - - +
95A SER 3.3 0.2 - - - -
96A VAL* 1.3 74.9 - - - +
98A GLY* 1.3 51.8 + - - +
100A LEU* 3.3 10.2 + - - +
101A LYS* 2.8 55.1 + - + +
133A THR 5.8 1.3 - - - +
134A LEU* 3.9 29.6 - - + +
137A GLY* 6.4 1.6 - - - -
138A GLU* 5.7 1.3 - - - +
154A LEU* 5.8 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ALA 2.9 14.9 + - - -
95A SER* 3.7 4.0 - - - -
96A VAL 3.2 0.6 - - - -
97A ALA* 1.3 73.8 - - - +
99A VAL* 1.3 65.4 + - - +
101A LYS* 3.5 24.0 + - - +
102A GLY* 3.5 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A THR* 4.2 27.8 - - + +
61A LEU* 4.7 10.1 - - + -
74A LEU* 4.0 25.8 - - + -
95A SER 3.2 13.1 + - - +
96A VAL 3.1 7.0 + - - +
98A GLY* 1.3 75.8 - - - +
100A LEU* 1.3 65.0 + - - +
102A GLY* 3.1 12.5 + - - -
103A LEU* 3.3 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 3.7 37.5 - - + +
19A VAL* 4.4 8.7 - - + -
74A LEU* 4.6 5.8 - - + -
96A VAL* 3.0 35.1 + - + +
97A ALA* 3.7 9.0 - - - +
99A VAL* 1.3 74.5 - - - +
101A LYS* 1.3 63.5 + - - +
103A LEU* 3.2 28.5 + - + +
105A GLY 5.3 0.9 - - - +
108A ALA* 3.7 24.0 - - + -
110A LEU* 4.9 4.7 - - + -
134A LEU* 5.6 3.6 - - + -
154A LEU* 4.1 36.8 + - + +
157A VAL* 4.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ALA* 4.7 2.6 + - - +
97A ALA* 2.8 36.5 + - + +
98A GLY* 3.7 24.9 - - - +
99A VAL 3.2 0.4 - - - -
100A LEU* 1.3 76.7 - - - +
102A GLY* 1.3 59.3 + - - +
103A LEU 3.7 4.9 + - - +
137A GLY* 3.4 31.6 + - - -
138A GLU* 5.0 9.2 - - - +
152A ARG* 3.9 55.5 - - - +
153A ALA 5.3 0.3 + - - -
154A LEU* 5.5 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLY 3.5 5.8 + - - -
99A VAL 3.1 8.8 + - - -
101A LYS* 1.3 80.0 - - - +
103A LEU* 1.3 63.8 + - - +
104A ASN 4.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 3.7 26.0 - - + +
61A LEU* 3.9 25.1 - - + -
72A ARG* 3.9 21.3 - - - +
99A VAL* 3.3 29.8 - - + +
100A LEU* 3.2 26.2 + - + +
101A LYS 4.0 4.3 - - - +
102A GLY* 1.3 85.0 - - - +
104A ASN* 1.3 59.8 + - - +
105A GLY* 3.1 13.4 + - - +
153A ALA* 3.8 11.4 + - - +
154A LEU 5.1 0.2 + - - -
----------------------------------------------------------
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