Contacts of the helix formed by residues 69 - 84 (chain B) in PDB entry 1VE3
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 69 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ASP* 2.9 15.0 + - - -
68B ILE* 1.3 81.2 - - - +
70B GLU* 1.3 63.6 + - - +
71B ASP* 3.4 10.6 + - - +
72B MSE 3.1 25.5 + - - +
73B ILE* 3.0 28.5 + - - +
91B VAL* 4.8 0.4 - - - -
301B SAM 3.4 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE 3.6 3.8 + - - +
69B SER* 1.3 72.4 + - - +
71B ASP* 1.3 60.3 + - - +
73B ILE* 3.2 2.6 + - - +
74B ARG* 2.7 46.7 + - - +
77B ARG* 5.9 0.2 + - - -
91B VAL* 2.8 43.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LYS* 5.0 13.9 - - + +
69B SER* 3.3 8.1 + - - +
70B GLU* 1.3 77.9 - - - +
72B MSE 1.3 68.6 + - + +
74B ARG* 2.7 39.7 + - - +
75B LYS* 3.1 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 5.4 10.3 - - + -
13B TYR 4.5 2.2 - - - +
14B THR* 3.9 22.0 - - + -
48B GLY* 3.1 42.3 - - - +
49B VAL* 3.8 12.0 - - + +
67B ASP* 3.8 5.4 - - - +
69B SER* 3.1 30.1 + - - +
71B ASP* 1.3 79.6 - - + +
73B ILE* 1.3 58.4 + - - +
75B LYS* 3.3 36.4 + - - +
76B ALA* 2.9 27.2 + - - +
301B SAM 3.6 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B CYS* 4.0 14.4 - - - -
48B GLY 4.6 0.7 - - - +
67B ASP* 3.5 33.0 - - + +
69B SER 3.0 16.2 + - - +
70B GLU 3.8 2.9 - - - +
72B MSE 1.3 72.2 - - - +
74B ARG* 1.3 65.7 + - - +
76B ALA* 3.3 3.6 + - - +
77B ARG* 3.0 61.0 + - - +
89B PHE* 4.0 13.0 - - + -
90B ILE 3.5 18.4 - - - +
91B VAL* 3.6 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLU* 2.7 39.4 + - - +
71B ASP* 2.7 42.4 + - - +
73B ILE* 1.3 72.3 - - - +
75B LYS* 1.3 65.0 + - + +
77B ARG* 3.4 10.2 + - - +
78B GLU* 3.1 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B THR* 4.7 15.7 - - - +
49B VAL* 3.9 15.5 - - + -
71B ASP* 3.1 28.7 + - - +
72B MSE 3.3 35.4 - - - +
74B ARG* 1.3 75.8 - - + +
76B ALA* 1.3 59.7 + - - +
78B GLU* 3.1 21.9 + - - +
79B TYR* 2.9 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLY 4.0 2.9 - - - +
49B VAL* 3.3 34.7 + - - +
54B PHE* 3.5 6.4 - - - -
72B MSE 2.9 15.1 + - - +
73B ILE* 3.3 7.6 + - - +
75B LYS* 1.3 75.0 - - - +
77B ARG* 1.3 58.3 + - - +
79B TYR* 3.3 1.4 + - - -
80B ALA* 2.8 27.9 + - - +
89B PHE* 3.9 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 3.0 38.8 + - + +
74B ARG* 3.7 8.8 - - - +
75B LYS 3.2 0.2 - - - -
76B ALA* 1.3 74.3 - - - +
78B GLU* 1.3 60.9 + - + +
80B ALA* 3.2 8.9 + - - +
81B LYS* 2.9 34.0 + - - +
89B PHE* 2.8 40.7 + - + +
90B ILE* 4.0 6.9 - - - +
91B VAL* 4.5 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ARG* 3.1 40.4 + - - +
75B LYS* 3.1 25.1 + - - +
77B ARG* 1.3 76.7 - - - +
79B TYR* 1.3 63.9 + - + +
81B LYS* 3.1 30.0 + - - +
82B SER* 3.2 14.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B THR 3.3 23.2 + - - -
15B ASP* 3.6 9.5 + - - -
16B ILE* 3.3 46.2 + - + -
17B ASN* 3.8 23.0 + - - -
49B VAL* 3.7 14.4 - - + -
54B PHE* 3.6 16.4 - - + -
75B LYS* 2.9 30.2 + - + +
76B ALA 3.6 5.8 - - - +
78B GLU* 1.3 77.7 - - + +
80B ALA* 1.3 61.1 + - - +
82B SER* 2.9 24.6 + - - -
83B ARG* 3.1 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B PHE* 3.6 21.7 - - + -
76B ALA 2.8 16.6 + - - +
77B ARG* 3.2 9.8 + - - +
79B TYR* 1.3 76.0 - - - +
81B LYS* 1.3 58.2 + - - +
84B GLU* 2.8 25.6 + - - -
85B SER* 2.8 25.9 + - - +
87B VAL 5.2 3.4 - - - +
89B PHE* 4.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ARG* 2.9 15.9 + - - +
78B GLU* 3.1 23.4 + - - +
80B ALA* 1.3 77.8 - - - +
82B SER* 1.3 61.7 + - - +
84B GLU* 3.2 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLU 3.2 6.7 + - - -
79B TYR* 2.9 28.9 + - - -
81B LYS* 1.3 79.5 - - - +
83B ARG* 1.3 63.9 + - - +
84B GLU* 3.4 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 3.4 31.9 + - - +
17B ASN* 3.8 17.0 + - - -
22B ARG* 5.8 3.8 - - - +
51B GLY 5.4 1.4 + - - -
54B PHE* 3.8 40.8 - - + +
58B ASP* 5.5 3.8 + - - -
79B TYR* 3.1 26.0 + - - +
80B ALA 4.1 2.5 - - - +
82B SER* 1.3 81.9 + - - +
84B GLU* 1.3 69.7 + - - +
85B SER* 3.0 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ALA 2.8 7.2 + - - -
81B LYS* 3.2 13.2 + - - +
82B SER 4.9 3.1 - - - +
83B ARG* 1.3 80.4 - - - +
85B SER* 1.3 64.9 + - - +
86B ASN* 3.8 12.0 + - - +
----------------------------------------------------------
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