Contacts of the strand formed by residues 49 - 58 (chain B) in PDB entry 6W4E
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 GLU 49 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B SER* 5.5 5.4 - - - +
2B THR* 2.6 30.5 + - - +
4B TYR* 3.7 3.1 + - - -
45B VAL* 4.1 3.4 - - - -
46B ILE 2.9 11.5 + - - +
47B ASP* 3.4 2.8 - - + +
48B GLY* 1.3 80.8 - - - +
50B THR* 1.3 65.6 + - - +
51B CYS* 3.0 23.6 - - - -
164B ARG* 2.7 31.0 + - - +
167B LYS* 5.8 1.7 + - - -
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Residues in contact with THR 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B SER* 2.8 39.1 + - - +
2B THR 3.6 5.0 + - - -
43B GLN* 3.7 37.5 - - + +
44B VAL 3.4 7.2 - - - +
45B VAL* 4.3 13.6 - - + +
48B GLY 4.3 0.2 + - - -
49B GLU* 1.3 79.8 - - - +
51B CYS* 1.3 57.7 + - - +
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Residues in contact with CYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B SER 4.3 1.8 - - - +
2B THR 3.3 4.0 - - - -
4B TYR* 3.5 29.8 - - + -
42B LYS 3.7 0.7 - - - +
43B GLN* 3.4 6.4 - - - +
44B VAL* 2.8 43.3 + - - +
46B ILE* 3.6 31.6 - - - -
49B GLU* 3.0 19.1 - - - +
50B THR* 1.3 75.6 - - - +
52B LEU* 1.3 61.5 - - - +
53B LEU* 3.9 3.8 + - + -
164B ARG* 3.4 14.1 - - - +
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B SER 4.8 5.1 - - - +
2B THR 2.8 14.7 + - - +
3B GLU* 3.4 27.1 - - + +
4B TYR* 2.9 27.5 + - - -
41B ARG* 4.4 22.0 - - + -
42B LYS 3.5 24.5 - - - +
43B GLN* 4.5 10.8 - - + +
51B CYS* 1.3 71.2 - - - +
53B LEU* 1.3 62.2 + - - +
54B ASP* 3.6 0.6 + - + -
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B TYR* 3.7 10.5 - - + -
6B LEU* 4.0 14.8 - - + -
23B LEU* 4.6 20.9 - - + -
40B TYR 3.4 1.6 - - - +
41B ARG* 3.3 11.4 - - - +
42B LYS* 2.7 43.6 + - + +
44B VAL* 3.6 31.9 - - + -
46B ILE* 4.2 4.7 - - + -
51B CYS* 4.8 2.0 - - + -
52B LEU* 1.3 75.0 - - - +
54B ASP* 1.3 60.7 + - - +
55B ILE* 3.5 15.0 - - + -
156B PHE* 4.9 8.1 - - + -
157B TYR* 5.4 2.0 - - + -
160B VAL* 3.6 30.5 - - + -
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Residues in contact with ASP 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B GLU* 4.0 24.3 - - + +
4B TYR 2.8 16.1 + - - +
5B LYS* 3.4 22.5 + - - +
6B LEU 2.8 26.2 + - - +
7B VAL* 5.8 0.2 - - - +
39B SER* 6.0 0.2 - - - -
40B TYR 3.8 2.0 - - - -
41B ARG* 2.7 40.2 + - + +
52B LEU 3.6 0.8 + - - -
53B LEU* 1.3 70.7 - - - +
55B ILE* 1.3 57.8 + - - +
56B LEU* 3.9 3.8 + - - +
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Residues in contact with ILE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 3.2 17.3 - - + +
8B VAL* 3.7 25.6 - - + -
20B THR* 3.8 21.8 - - + -
23B LEU* 4.0 26.2 - - + -
24B ILE* 4.0 20.6 - - + -
39B SER* 3.3 5.0 - - - -
40B TYR* 2.8 42.0 + - + +
42B LYS* 5.0 0.7 - - + -
53B LEU* 4.1 22.0 - - + -
54B ASP* 1.3 76.0 - - - +
56B LEU* 1.3 64.1 + - - +
57B ASP 4.3 0.2 - - - -
156B PHE* 4.2 15.3 - - + -
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU 3.0 12.4 + - - +
7B VAL* 3.8 13.8 - - + +
8B VAL* 3.1 26.8 + - - +
37B GLU* 3.6 26.9 - - + +
38B ASP 3.3 19.7 - - - +
39B SER* 3.8 14.8 - - - +
54B ASP* 4.9 5.2 - - - +
55B ILE* 1.3 76.7 - - - +
57B ASP* 1.3 59.7 + - - +
58B THR* 3.8 14.2 + - + -
71B TYR* 4.0 36.1 - - + -
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Residues in contact with ASP 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 4.1 5.0 - - + +
16B LYS* 3.2 40.8 + - - +
17B SER* 2.6 8.5 + - - +
20B THR* 4.8 12.1 - - + +
35B THR* 2.8 15.6 + - + +
37B GLU* 3.5 1.2 - - - -
38B ASP* 2.8 40.0 + - + +
40B TYR* 4.9 8.4 - - + -
55B ILE* 4.3 1.4 - - - +
56B LEU* 1.3 70.6 - - - +
58B THR* 1.3 59.9 + - - +
201B GSP 3.6 0.8 + - - -
202B MG 1.5 38.4 - - - -
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Residues in contact with THR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL* 4.6 0.3 - - - +
8B VAL 3.7 10.9 + - - -
9B VAL* 4.5 2.3 - - - +
16B LYS* 2.6 29.7 + - - +
35B THR* 3.5 5.3 - - - +
36B ILE 3.6 13.5 - - - +
37B GLU* 4.0 17.5 - - + +
56B LEU* 3.8 10.7 + - + -
57B ASP* 1.3 82.0 + - - +
59B ALA* 1.3 63.7 + - - +
67B MET* 4.6 2.9 - - + -
71B TYR* 3.0 55.8 + - + -
201B GSP 5.1 1.4 + - - -
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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