Contacts of the strand formed by residues 33 - 40 (chain E) in PDB entry 6VMS
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 33 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E PHE* 1.3 73.3 - - - +
34E MET* 1.3 71.6 + - - +
50E TYR* 4.0 13.5 - - - -
51E ILE 3.4 12.1 - - - -
52E SER 4.2 0.2 - - - -
53E SER* 3.9 12.0 - - - -
99E SER* 2.9 38.1 + - - +
100E ILE* 4.8 1.8 - - - +
101E TYR* 5.9 0.8 - - - -
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Residues in contact with MET 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E LEU* 4.7 8.1 - - + -
22E CYS* 4.7 0.9 - - - -
27E PHE* 4.8 0.2 - - + -
29E PHE* 3.4 40.2 - - + -
32E PHE* 4.4 3.4 - - - +
33E GLY* 1.3 87.6 - - - +
35E HIS* 1.3 64.9 + - - +
50E TYR* 3.0 8.0 - - - -
51E ILE* 2.9 39.9 + - + +
72E ARG* 3.6 11.2 - - - +
79E LEU* 3.5 16.2 - - + -
96E CYS* 3.5 25.1 - - - -
97E VAL 3.2 27.8 - - - +
98E ARG* 3.3 26.2 - - + +
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Residues in contact with HIS 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E MET* 1.3 79.3 - - - +
36E TRP* 1.3 66.0 + - - +
37E VAL* 4.4 6.1 - - + -
47E TRP* 3.2 21.1 + - - +
49E ALA 3.2 5.6 - - - +
50E TYR* 3.2 29.1 - + + +
95E TYR 3.6 1.7 - - - +
96E CYS* 3.6 2.9 - - - -
97E VAL* 2.9 39.9 + - + +
99E SER* 3.7 15.7 + - - -
101E TYR* 2.8 21.0 + - - -
108E PHE* 3.2 40.3 - + + -
235E TYR* 3.3 22.4 - + - -
237E LEU* 3.7 0.2 - - + -
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Residues in contact with TRP 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E GLU* 4.3 11.7 - - + -
20E LEU* 4.5 12.6 - - + -
21E SER 4.3 4.3 - - - -
22E CYS* 3.4 41.7 - - + -
35E HIS* 1.3 75.5 - - - +
37E VAL* 1.3 61.0 + - - +
47E TRP* 4.2 1.0 - - - -
48E VAL* 3.0 30.7 + - + +
49E ALA* 2.9 19.8 + - + +
51E ILE* 5.5 1.3 - - + -
70E ILE* 4.2 17.6 - - + +
79E LEU* 3.5 32.6 - - + +
80E PHE 4.9 0.6 + - - -
81E LEU* 3.2 55.1 - - + +
94E TYR* 4.2 18.8 - - + -
95E TYR 3.3 19.3 - - - -
96E CYS* 3.9 16.2 - - + -
115E THR* 6.3 0.2 - - - -
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Residues in contact with VAL 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E HIS* 4.4 11.2 - - + -
36E TRP* 1.3 79.3 - - - +
38E ARG* 1.3 64.4 + - - +
45E LEU* 4.5 8.1 - - + -
46E GLU 3.0 25.8 - - - +
47E TRP* 4.5 7.4 - - + -
48E VAL* 3.9 1.8 - - - -
93E MET 3.8 0.5 - - - +
94E TYR* 3.4 6.4 - - - -
95E TYR* 2.9 35.2 + - + +
97E VAL* 4.2 9.9 - - + -
108E PHE* 4.7 2.0 - - + -
111E TRP* 3.7 38.1 - - + -
239E PHE* 3.9 18.2 - - + -
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Residues in contact with ARG 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E VAL* 1.3 73.0 - - - +
39E GLN* 1.3 60.6 + - - +
40E ALA* 4.8 3.4 - - + +
43E LYS* 6.3 0.4 - - - +
44E GLY 3.8 0.2 - - - +
45E LEU* 3.4 1.4 - - - -
46E GLU* 2.5 70.5 + - + +
48E VAL* 3.2 20.5 - - + +
63E THR* 4.1 12.1 + - - -
64E VAL* 3.4 18.3 - - - +
67E ARG* 5.2 0.2 - - - +
68E PHE* 3.2 30.5 - - - -
89E GLU 4.8 9.4 + - - -
90E ASP* 2.6 32.9 + - - +
92E ALA* 3.7 19.7 - - + -
93E MET 3.7 4.0 - - - -
94E TYR* 3.2 22.9 + - + -
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Residues in contact with GLN 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ARG* 1.3 74.2 - - - +
40E ALA* 1.3 68.5 + - - +
41E PRO* 3.9 3.5 - - + +
44E GLY* 3.3 15.3 - - - +
45E LEU* 3.5 21.8 - - + +
92E ALA* 3.2 4.0 - - - +
93E MET* 2.9 46.5 + - + +
95E TYR* 2.9 38.8 + - + -
179E GLN* 2.9 31.7 + - - +
228E TYR* 3.8 10.1 + - - -
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Residues in contact with ALA 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ARG* 4.2 4.7 - - + +
39E GLN* 1.3 75.8 - - - +
41E PRO* 1.3 74.1 - - + +
42E GLU* 3.1 4.3 - - + +
43E LYS* 2.9 51.7 + - + +
44E GLY* 3.0 16.2 + - - +
46E GLU* 5.5 2.2 - - - +
89E GLU 6.0 1.1 - - - +
91E THR 4.5 9.0 - - - +
92E ALA* 4.2 4.5 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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