Contacts of the strand formed by residues 7 - 17 (chain W) in PDB entry 3MQT
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 ILE 7 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6W ASN* 1.3 74.5 - - - +
8W VAL* 1.3 62.2 + - - +
9W SER 3.8 4.5 - - - +
10W VAL* 4.5 1.8 - - + -
31W VAL* 3.5 28.3 - - + -
32W THR 3.8 3.8 - - - +
33W ASP* 4.1 1.3 - - - +
34W GLU* 5.3 0.4 - - - +
70W VAL* 3.4 31.2 - - + +
71W ILE* 3.6 23.9 - - + +
72W GLY* 2.7 28.2 + - - -
73W ARG* 2.9 24.2 + - + +
74W ASP 4.8 0.2 - - - -
75W PRO* 4.0 17.0 - - + -
81W ASN* 4.8 2.2 - - - +
109W LEU* 3.7 26.7 - - + -
112W LEU* 4.3 7.6 - - + -
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Residues in contact with VAL 8 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6W ASN 3.7 0.6 + - - -
7W ILE* 1.3 75.1 - - - +
9W SER* 1.3 66.8 + - - +
32W THR* 2.8 28.0 + - + +
33W ASP 3.6 20.2 - - - +
34W GLU* 4.5 13.7 - - + +
71W ILE* 3.7 17.5 - - + +
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Residues in contact with SER 9 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8W VAL* 1.3 85.1 - - - +
10W VAL* 1.3 70.4 + - - +
11W GLU* 4.3 3.0 + - - +
30W LYS 5.1 0.7 + - - -
31W VAL* 3.3 7.1 - - - +
32W THR* 3.0 48.3 + - - +
71W ILE* 3.6 6.5 - - - +
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Residues in contact with VAL 10 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9W SER* 1.3 80.5 - - - +
11W GLU* 1.3 63.9 - - - +
12W PHE* 3.9 22.9 - - + -
29W VAL* 4.2 8.1 - - + -
30W LYS 3.5 3.4 - - - -
31W VAL* 4.1 15.7 - - + -
67W LYS* 2.9 47.4 + - + +
70W VAL* 3.7 29.8 - - + -
71W ILE* 3.9 12.0 - - + +
105W ILE* 4.2 13.9 - - + -
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Residues in contact with GLU 11 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9W SER* 5.7 3.1 + - - +
10W VAL* 1.3 76.8 - - - +
12W PHE* 1.3 68.0 + - - +
13W ILE* 3.8 24.6 - - + +
28W ILE 3.3 5.0 - - - +
29W VAL* 3.4 3.3 - - - -
30W LYS* 3.0 53.0 + - + +
67W LYS* 4.4 2.0 - - - +
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Residues in contact with PHE 12 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10W VAL* 3.9 10.8 - - + -
11W GLU* 1.3 81.7 - - - +
13W ILE* 1.3 61.5 + - - +
14W PRO* 3.2 13.0 - - - +
27W VAL* 3.8 20.6 - - + -
28W ILE 3.5 2.9 - - - -
29W VAL* 3.8 23.6 - - + -
43W ALA* 4.4 6.5 - - + -
50W MET* 3.5 23.8 - - + -
51W LYS* 3.4 21.6 - - + +
54W SER* 3.5 34.3 + - - +
55W GLU* 5.0 2.3 + - - +
66W ILE* 5.0 1.1 - - + -
67W LYS* 4.6 2.5 - - - +
101W ALA* 3.8 41.3 - - + -
105W ILE* 3.8 20.6 - - + -
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Residues in contact with ILE 13 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11W GLU* 3.8 27.6 - - + +
12W PHE* 1.3 73.7 - - - +
14W PRO* 1.3 66.9 - - + +
15W VAL* 3.5 8.0 + - + +
27W VAL* 3.5 2.6 - - - +
28W ILE* 2.7 49.3 + - + +
30W LYS* 4.2 22.7 - - + -
378W VAL* 4.9 4.3 - - + -
382W THR* 3.6 31.9 - - + -
386W PHE* 4.2 26.7 - - + -
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Residues in contact with PRO 14 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12W PHE 3.2 11.9 - - - +
13W ILE* 1.3 85.4 - - + +
15W VAL* 1.3 62.8 + - - +
16W ASN* 4.0 3.7 + - + +
26W THR 3.9 6.3 - - - +
27W VAL* 4.6 2.4 - - + -
47W PRO* 3.8 30.5 - - + +
48W GLU* 3.6 26.5 - - - +
51W LYS* 3.7 26.0 - - + -
382W THR* 3.7 14.7 - - - +
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Residues in contact with VAL 15 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13W ILE* 3.6 10.5 - - + +
14W PRO* 1.3 79.1 - - - +
16W ASN* 1.3 58.4 + - - +
17W VAL* 5.1 2.2 - - + -
24W GLU 3.9 0.7 - - - +
25W ASN* 3.2 6.6 - - - +
26W THR* 3.1 43.3 + - + +
28W ILE* 3.7 25.4 - - + -
47W PRO* 4.5 0.8 - - - +
345W LEU* 3.9 26.5 - - + -
349W LEU* 5.0 5.8 - - + -
378W VAL* 4.8 3.6 - - + -
381W VAL* 4.6 17.3 - - + -
382W THR* 4.1 16.8 - - + +
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Residues in contact with ASN 16 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J GLU* 6.1 3.2 - - - +
14W PRO* 4.0 2.5 + - + -
15W VAL* 1.3 76.3 - - - +
17W VAL* 1.3 80.2 + - - +
18W ALA 4.0 1.4 + - - -
23W SER* 5.5 2.8 - - - -
24W GLU 3.8 3.1 + - - +
25W ASN* 3.2 30.5 + - - +
47W PRO* 4.3 12.7 - - + +
48W GLU* 6.1 2.9 - - - +
381W VAL* 4.7 15.4 + - - +
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Residues in contact with VAL 17 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15W VAL* 5.1 2.5 - - + -
16W ASN* 1.3 86.8 + - - +
18W ALA* 1.3 75.8 + - - +
23W SER* 5.1 2.9 - - - -
24W GLU* 3.0 36.3 + - + +
344W THR* 4.3 28.9 - - + +
345W LEU* 4.0 28.9 - - + -
377W PHE* 4.4 8.5 - - + -
381W VAL* 4.9 9.4 - - + -
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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