Contacts of the helix formed by residues 67 - 83 (chain E) in PDB entry 1VCB
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 SER 67 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D PHE* 3.7 17.4 - - - -
94D SER* 3.0 19.1 + - - -
23E SER* 3.3 8.8 + - - -
25E ASP* 2.4 40.3 + - - -
27E HIS* 2.9 15.7 + - - -
29E PHE* 4.2 6.0 - - - -
66E PRO* 1.3 70.0 - - - +
68E HIS* 1.3 61.5 + - - +
69E VAL 3.0 1.3 + - - -
70E LEU* 4.6 0.4 - - - +
71E SER* 3.0 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D PHE* 4.0 6.7 - - + +
94D SER* 2.7 42.9 + - - +
95D SER 3.9 13.7 - - - -
96D PRO* 3.3 33.3 - - + +
97D PRO* 4.8 0.4 - - + -
66E PRO* 3.3 28.6 - - + +
67E SER* 1.3 78.7 - - - +
69E VAL* 1.3 62.3 + - + +
71E SER* 3.6 12.3 + - - -
72E LYS* 4.3 5.5 - - - +
99E ILE* 3.8 33.0 - - + +
102E GLU* 3.1 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E ILE* 3.4 25.4 - - + -
66E PRO* 3.1 17.8 + - + +
67E SER 3.0 0.6 - - - -
68E HIS* 1.3 90.4 - - + +
70E LEU* 1.3 60.0 + - - +
71E SER 3.1 1.3 - - - -
72E LYS* 2.8 25.7 + - - +
73E VAL* 3.1 9.8 + - + -
99E ILE* 5.0 4.9 - - + +
102E GLU* 3.5 32.1 - - + +
103E LEU* 4.0 16.4 - - + +
106E ALA* 3.4 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E LEU* 4.1 16.2 - - + -
22E ILE 4.0 1.8 - - - -
23E SER* 3.9 28.0 - - - +
29E PHE* 4.0 24.9 - - + -
62E PHE* 4.0 25.4 - - + -
65E ILE* 3.8 17.0 - - + +
66E PRO 2.9 19.4 + - - +
67E SER 4.3 0.2 - - - +
69E VAL* 1.3 73.2 - - - +
71E SER* 1.3 61.6 + - - +
73E VAL* 3.8 24.0 - - + -
74E CYS* 3.1 33.3 + - - -
110E LEU* 5.5 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PHE* 3.9 5.9 - - - -
93D PHE* 3.7 37.0 - - - -
29E PHE* 4.1 11.1 - - - -
67E SER 3.0 19.0 + - - -
68E HIS* 3.6 10.6 + - - -
70E LEU* 1.3 77.1 - - - +
72E LYS* 1.3 63.2 + - - +
74E CYS* 3.5 3.6 + - - +
75E MET* 3.1 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D GLN 4.3 10.7 + - - -
68E HIS 4.3 11.0 - - - +
69E VAL 2.8 10.1 + - - +
71E SER* 1.3 79.1 + - - +
73E VAL* 1.3 60.6 + - - +
75E MET* 3.1 18.9 + - + +
76E TYR* 2.8 29.3 + - - +
93E PHE* 3.9 20.0 - - + -
94E PRO* 3.0 40.8 + - - +
95E ILE* 4.7 6.7 - - - +
96E ALA* 5.1 2.0 - - - +
99E ILE* 4.4 24.0 - - + -
103E LEU* 4.1 19.5 - - + -
158F LEU* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E ILE* 5.8 0.7 - - + -
65E ILE* 5.2 0.7 - - + -
69E VAL* 3.1 17.9 + - + +
70E LEU* 3.6 24.2 - - + +
72E LYS* 1.3 76.8 - - - +
74E CYS* 1.3 61.9 + - - +
76E TYR* 3.0 11.2 + - - +
77E PHE* 3.0 51.6 + - + -
103E LEU* 4.0 17.7 - - + -
106E ALA* 4.5 3.8 - - + -
110E LEU* 3.6 27.1 - - + -
112E CYS* 5.1 0.2 - - - -
158F LEU* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PHE* 3.6 28.5 - - + -
21E LEU* 3.9 19.3 - - - -
29E PHE* 3.9 17.0 - - - -
31E VAL* 3.6 27.8 - - + +
70E LEU* 3.1 21.8 + - - +
71E SER 3.8 0.2 - - - +
73E VAL* 1.3 79.3 - - - +
75E MET* 1.3 62.7 + - - +
77E PHE* 3.0 22.8 + - - +
78E THR* 3.3 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D MET* 4.0 29.8 - - + -
15D PHE* 3.9 14.4 - - + -
69D PRO 3.5 9.3 - - - +
70D GLN 3.7 21.8 - - - +
71D ALA* 4.7 1.8 - - - -
72D PRO* 3.9 13.7 - - + -
93D PHE* 5.6 1.8 - - + -
71E SER* 3.1 33.1 + - - +
72E LYS* 3.1 25.3 + - + +
74E CYS* 1.3 75.5 - - - +
76E TYR* 1.3 62.4 + - - +
78E THR* 3.2 11.1 + - - -
79E TYR* 3.1 22.5 + - - +
93E PHE* 4.1 6.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E THR* 4.5 8.7 - - + -
72E LYS 2.8 12.9 + - - +
73E VAL* 3.2 11.4 - - - +
75E MET* 1.3 74.3 - - - +
77E PHE* 1.3 74.0 + + - +
79E TYR* 3.3 22.1 - + - +
80E LYS* 2.8 55.3 + - + +
93E PHE* 3.6 24.4 - + + -
112E CYS* 3.6 16.6 + - + -
155F VAL* 4.1 1.9 + - - +
156F TYR 2.6 29.2 + - - -
157F THR* 3.1 10.6 - - - +
158F LEU* 3.4 39.0 - - + -
161F ARG* 5.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E LEU* 4.5 9.4 - - + -
31E VAL* 4.7 9.0 - - + -
35E HIS* 3.5 29.2 - - + +
36E ALA* 3.9 20.4 - - - -
38E THR* 3.9 21.1 - - + -
39E SER* 4.1 20.0 - - - -
42E ILE* 4.4 12.8 - - + -
73E VAL* 3.0 44.0 + - + -
74E CYS* 3.0 14.5 + - + +
76E TYR* 1.3 82.0 - + - +
78E THR* 1.3 62.6 + - + +
80E LYS* 3.9 3.0 - - - +
81E VAL* 3.0 29.6 + - - +
110E LEU* 4.9 0.7 - - + -
112E CYS* 4.1 19.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D PHE* 4.9 13.8 - - + +
15D PHE* 4.6 26.0 - - + -
16D THR 6.1 0.2 - - - +
69D PRO* 3.0 33.1 + - - +
72D PRO* 5.9 0.5 - - - +
31E VAL* 5.6 2.5 - - + -
35E HIS* 3.7 26.9 - - + +
74E CYS 3.3 12.9 + - - +
75E MET* 3.2 4.7 + - - -
77E PHE* 1.3 76.1 - - + +
79E TYR* 1.3 57.1 + - - +
81E VAL* 3.8 1.4 - - - +
82E ARG* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D PRO* 3.9 11.9 - - + -
70D GLN* 3.3 31.4 - - + +
75E MET 3.1 14.5 + - - +
76E TYR* 3.3 26.2 - + - +
78E THR* 1.3 77.0 + - - +
80E LYS* 1.3 64.1 + - - +
82E ARG* 3.3 0.9 + - - +
83E TYR* 3.0 52.9 + + - +
90E ILE* 3.5 14.4 - - + +
91E PRO* 2.6 28.1 + - + -
92E GLU* 4.4 0.2 - - - -
93E PHE* 3.8 35.0 + + + +
153F LEU* 5.2 1.6 - - - +
154F PRO 4.8 4.3 + - - -
155F VAL* 4.0 19.1 - - + -
156F TYR 5.1 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E THR* 4.2 25.1 + - + +
76E TYR* 2.8 50.7 + - + +
77E PHE* 3.9 4.3 - - - +
79E TYR* 1.3 71.7 - - - +
81E VAL* 1.3 71.5 + - - +
82E ARG 3.1 0.3 + - - -
84E THR* 3.1 60.7 + - + +
155F VAL* 4.2 12.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
34E GLU* 5.1 3.1 - - + +
35E HIS* 3.7 41.5 - - + +
38E THR* 4.0 18.6 - - - +
77E PHE 3.0 18.4 + - - +
78E THR 4.0 2.7 - - - +
80E LYS* 1.3 84.0 - - + +
82E ARG* 1.3 62.3 + - - +
84E THR* 4.6 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET* 5.9 6.9 - - - +
2D ASP* 5.7 3.6 + - - +
4D PHE* 4.0 26.4 - - + -
69D PRO* 3.9 22.4 - - + +
78E THR 2.9 18.8 + - - +
79E TYR 3.7 3.1 - - - +
81E VAL* 1.3 81.5 - - - +
83E TYR* 1.3 90.4 + - + +
84E THR 4.6 1.8 - - - +
86E SER* 4.2 8.7 + - - -
88E THR* 4.0 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ARG* 5.2 2.6 + - - -
69D PRO* 4.2 8.8 - - + +
70D GLN* 3.8 12.6 + - - -
79E TYR* 3.0 46.6 + + + +
82E ARG* 1.3 116.3 + - + +
84E THR* 1.3 69.8 + - - +
85E ASN 3.3 1.0 + - - -
86E SER* 3.1 18.6 + - - -
88E THR* 4.4 8.1 - - - -
89E GLU 4.4 7.2 - - - -
90E ILE* 3.7 35.4 - - + +
91E PRO* 3.5 38.0 - - + +
155F VAL* 3.7 7.6 - - + -
----------------------------------------------------------
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