Contacts of the strand formed by residues 31 - 37 (chain B) in PDB entry 1XSK
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 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B GLN* 3.5 0.3 - - - -
28B GLN* 2.6 42.4 + - + +
29B ASP 3.1 1.0 + - - -
30B ASN* 1.3 91.0 + - - +
32B MET* 1.3 58.3 + - - +
56B ARG* 2.8 49.6 + - + +
57B PHE 3.5 6.1 - - - +
58B PHE* 3.5 30.1 - - + +
88B GLN* 5.4 3.6 - - - +
94B ILE* 3.4 10.0 - - - +
103B PHE* 4.2 0.2 - - - -
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Residues in contact with MET 32 (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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25B VAL* 4.1 17.5 - - + -
26B GLU 3.7 4.7 - - - +
27B GLN* 4.5 0.7 - - - +
31B GLU* 1.3 73.3 - - - +
33B VAL* 1.3 66.2 + - - +
34B VAL* 4.3 9.9 - - + -
56B ARG* 3.4 1.7 - - - -
57B PHE* 2.8 47.7 + - + -
94B ILE* 3.2 31.1 - - + +
95B GLU 4.4 1.3 - - - +
101B ALA* 4.1 17.7 - - - +
102B GLU 2.8 50.0 - - - +
103B PHE* 3.5 18.6 - - + +
110B ALA 5.7 0.4 - - - +
112B VAL* 6.1 0.7 - - - -
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Residues in contact with VAL 33 (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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24B GLU 4.0 0.3 - - - +
25B VAL* 3.4 4.3 - - - +
26B GLU* 2.7 45.3 + - + +
28B GLN* 3.0 32.5 - - + +
32B MET* 1.3 76.6 - - - +
34B VAL* 1.3 65.4 + - - +
35B TYR* 3.5 35.6 - - + +
54B THR* 3.9 16.8 - - + -
55B LEU 3.3 8.3 - - - +
56B ARG* 3.6 27.4 - - + +
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Residues in contact with VAL 34 (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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22B VAL* 4.1 32.8 - - + -
24B GLU 3.6 3.1 - - - +
25B VAL* 4.5 9.6 - - + -
32B MET* 4.3 15.0 - - + -
33B VAL* 1.3 79.4 - - - +
35B TYR* 1.3 66.9 + - - +
54B THR 3.7 0.2 - - - -
55B LEU* 2.7 50.1 + - + +
57B PHE* 4.0 24.2 - - + -
101B ALA* 4.7 1.8 - - + -
112B VAL* 4.4 15.9 - - + -
118B TRP* 4.7 9.4 - - + -
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Residues in contact with TYR 35 (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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353A LYS* 3.8 39.9 + - + -
22B VAL* 3.7 3.6 - - - +
23B PHE* 2.8 33.4 + - + +
24B GLU* 2.9 50.1 + - + +
26B GLU* 4.6 15.2 + - + -
28B GLN* 4.5 8.8 + - - -
33B VAL* 3.5 25.7 - - + +
34B VAL* 1.3 72.6 - - - +
36B ALA* 1.3 60.8 + - - +
52B LEU* 3.8 20.9 - - + -
53B PHE 3.3 5.4 - - - -
54B THR* 3.8 30.4 - - + +
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Residues in contact with ALA 36 (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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19B PRO* 3.5 20.2 - - + -
21B GLN 3.1 13.0 - - - +
34B VAL 3.9 0.4 + - - -
35B TYR* 1.3 75.0 - - - +
37B ALA* 1.3 61.1 + - - +
52B LEU* 3.2 6.7 - - - +
53B PHE* 2.8 35.8 + - - +
55B LEU* 4.3 7.2 - - + -
118B TRP* 3.4 30.1 - - + -
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Residues in contact with ALA 37 (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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313A PHE* 5.5 1.6 - - + -
18B HIS 4.3 0.9 - - - -
19B PRO* 4.4 0.7 - - - -
20B LEU 2.8 28.7 + - - -
21B GLN* 2.9 16.4 + - + +
23B PHE* 4.9 1.7 - - + +
36B ALA* 1.3 73.2 - - - +
38B PRO* 1.3 63.2 - - + +
39B ARG 3.2 21.3 + - - +
41B VAL* 3.6 29.4 - - + -
50B THR* 5.3 0.2 - - - +
51B PRO 4.8 0.9 - - - +
52B LEU* 3.8 12.3 - - + +
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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