Contacts of the strand formed by residues 44 - 51 (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 44 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ARG 3.8 0.2 - - - +
39E GLN* 3.3 12.2 - - - -
40E ALA* 3.0 31.2 + - - +
41E PRO 4.8 1.6 + - - -
42E GLU 3.9 0.2 - - - -
43E LYS* 1.3 79.8 - - - +
45E LEU* 1.3 64.0 + - - -
46E GLU* 3.7 5.7 + - - +
228E TYR* 4.3 20.6 - - - -
241E ALA 5.0 0.7 - - - -
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Residues in contact with LEU 45 (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* 4.5 10.8 - - + -
38E ARG 3.5 1.1 - - - -
39E GLN* 3.5 37.0 - - + +
43E LYS 5.3 0.3 - - - +
44E GLY* 1.3 74.2 - - - -
46E GLU* 1.3 67.8 + - - +
95E TYR* 4.3 11.7 - - + -
111E TRP* 4.6 10.5 - - + -
177E PHE* 5.2 4.5 - - + -
179E GLN* 5.0 0.4 - - - +
185E PRO* 4.7 12.1 - - + -
228E TYR* 3.8 41.8 - - + -
239E PHE* 3.6 50.2 + - + +
240E GLY 5.1 2.9 + - - +
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Residues in contact with GLU 46 (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* 3.0 2.6 - - - +
38E ARG* 2.5 78.7 + - + +
40E ALA* 5.8 1.6 - - - -
43E LYS* 3.7 35.8 + - + +
44E GLY 4.4 5.8 - - - +
45E LEU* 1.3 80.1 - - - +
47E TRP* 1.3 63.2 + - - +
239E PHE* 3.6 6.1 - - - -
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Residues in contact with TRP 47 (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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35E HIS* 3.2 24.8 + - + -
36E TRP 4.2 4.9 - - - -
37E VAL* 4.4 11.4 - - + -
46E GLU* 1.3 76.2 - - - +
48E VAL* 1.3 63.6 + - - +
49E ALA* 3.3 11.5 + - - -
50E TYR* 3.3 29.6 - - + -
59E TYR* 3.8 16.2 - - + -
60E TYR 3.6 16.8 - - - -
61E ALA* 3.4 36.8 - - + +
108E PHE* 4.8 0.9 - + - -
235E TYR* 3.8 10.5 - + - -
236E PRO* 3.4 25.6 - - + -
237E LEU* 3.5 55.2 + - + +
238E THR* 5.6 0.2 - - - +
239E PHE* 3.2 20.7 - + + -
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Residues in contact with VAL 48 (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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36E TRP* 3.0 20.6 + - + +
37E VAL 3.9 2.0 - - - -
38E ARG* 3.2 51.8 - - + +
47E TRP* 1.3 78.3 - - - +
49E ALA* 1.3 71.6 + - + +
60E TYR* 3.9 0.2 - - - -
61E ALA* 2.9 32.4 + - - +
64E VAL* 4.1 19.5 - - + +
68E PHE* 4.3 18.2 - - + -
81E LEU* 5.4 5.2 - - + -
94E TYR* 4.3 8.7 - - + -
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Residues in contact with ALA 49 (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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35E HIS* 3.2 4.5 - - - -
36E TRP* 2.9 32.4 + - + -
47E TRP* 3.3 18.6 + - - -
48E VAL* 1.3 89.3 - - + +
50E TYR* 1.3 58.3 + - - +
59E TYR 3.5 9.6 - - - +
60E TYR* 4.2 12.8 - - + -
68E PHE* 6.5 0.4 - - + -
70E ILE* 3.4 26.2 - - + -
81E LEU* 5.3 1.6 - - + -
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Residues in contact with TYR 50 (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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11A ALA* 4.5 9.7 - - + +
14A GLU* 5.1 3.3 + - - -
33E GLY* 4.0 7.0 - - - -
34E MET 3.0 28.5 - - - -
35E HIS* 3.2 35.7 - + + +
47E TRP* 3.3 11.2 - - + -
49E ALA* 1.3 75.4 - - - +
51E ILE* 1.3 73.0 + - - +
52E SER* 3.9 26.5 + - - -
53E SER 4.7 0.7 + - - -
57E THR 4.7 0.2 - - - -
58E ILE* 3.7 8.0 - - - +
59E TYR* 3.2 51.1 + + + +
70E ILE* 4.2 3.4 - - - -
99E SER* 4.0 0.4 - - - -
101E TYR* 3.8 27.7 - + - -
235E TYR* 3.8 15.7 - + + -
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Residues in contact with ILE 51 (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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33E GLY* 3.4 0.2 - - - -
34E MET* 2.9 58.8 + - + +
36E TRP* 5.5 0.9 - - + -
50E TYR* 1.3 79.4 - - - +
52E SER* 1.3 77.7 + - - +
54E GLY 4.7 7.0 - - - +
55E SER* 6.1 0.7 - - - -
56E GLY 5.4 0.4 - - - +
58E ILE* 3.7 32.1 - - + -
70E ILE* 3.8 32.7 - - + +
72E ARG* 3.9 22.4 - - + +
79E LEU* 3.8 17.3 - - + -
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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