Contacts of the strand formed by residues 56 - 62 (chain B) in PDB entry 2H5X
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 SER 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B ILE* 4.4 3.7 + - - +
52B VAL* 3.5 1.4 - - - +
53B ARG* 2.8 55.3 + - - +
54B GLU 3.6 1.2 - - - -
55B ASP* 1.3 82.1 - - - +
57B MET* 1.3 63.1 + - - +
58B THR* 4.2 9.2 - - - -
52C VAL* 3.9 12.3 - - - +
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Residues in contact with MET 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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57A MET* 3.5 32.8 - - + +
50B MET* 4.6 6.7 - - + +
51B ILE 3.6 2.9 - - - -
52B VAL* 3.8 22.7 - - + -
53B ARG 6.1 0.7 - - - +
56B SER* 1.3 75.7 - - - +
58B THR* 1.3 62.7 + - - +
1C MET* 3.1 58.3 + - + +
50C MET* 5.4 2.7 - - - +
52C VAL* 4.1 21.6 - - + +
57C MET* 3.4 38.8 - - + +
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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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27B ARG* 5.5 3.1 - - + +
29B ASN* 3.2 26.5 - - - +
49B ALA 3.6 1.4 - - - +
50B MET* 3.3 6.9 - - - +
51B ILE* 2.9 37.5 + - - -
56B SER* 4.5 8.1 - - - -
57B MET* 1.3 81.9 + - - +
59B LEU* 1.3 78.3 + - - +
60B TYR* 3.6 25.0 + - + +
1C MET* 4.9 2.0 - - - +
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Residues in contact with LEU 59 (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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2B ILE* 3.8 20.9 - - + -
5B VAL* 4.1 12.8 - - + -
26B TYR* 3.8 34.5 - - + -
27B ARG 3.7 15.6 + - - +
28B VAL* 3.8 11.9 - - + -
29B ASN* 3.0 30.7 + - - +
48B THR* 3.5 26.2 - - - +
49B ALA 3.8 1.3 - - - -
50B MET* 4.0 17.7 - - + -
58B THR* 1.3 77.2 - - - +
60B TYR* 1.3 61.6 + - - +
1C MET* 3.8 25.2 - - + +
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Residues in contact with TYR 60 (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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29B ASN* 3.3 24.6 + - + +
48B THR* 3.1 5.1 - - - -
49B ALA 2.9 29.2 + - - +
51B ILE* 3.3 35.3 - - + +
58B THR* 3.6 32.9 + - + +
59B LEU* 1.3 73.9 - - - +
61B GLY* 1.3 60.2 + - - +
62B PHE* 3.1 16.4 - - + -
71B PHE* 3.6 20.6 - + + -
82B PRO* 3.3 28.9 - - + +
83B ARG* 4.9 4.4 + - - +
86B MET* 3.7 33.4 - - + -
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Residues in contact with GLY 61 (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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28B VAL* 3.6 19.7 - - - +
29B ASN 2.6 20.4 + - - +
30B ALA* 3.8 12.7 - - - +
34B THR* 4.3 1.4 + - - +
46B LEU* 3.9 10.1 - - - -
47B ILE 3.3 6.1 - - - -
48B THR* 4.0 4.5 - - - -
60B TYR* 1.3 72.1 - - - +
62B PHE* 1.3 78.5 + - - -
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Residues in contact with PHE 62 (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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31B THR* 5.6 4.7 - - + -
34B THR* 4.2 6.3 - - - -
46B LEU* 3.7 11.8 - - - +
47B ILE* 2.7 40.2 + - - +
49B ALA* 4.4 0.7 - - + -
60B TYR* 3.1 30.5 - - + -
61B GLY* 1.3 83.0 - - - -
63B PRO* 1.3 73.6 - - + +
64B ASP 3.4 3.8 + - - +
67B THR* 3.7 28.0 - - + -
68B ARG* 3.6 23.8 - - + +
71B PHE* 3.3 37.7 - + + -
86B MET* 4.2 11.7 - - + -
89B LEU* 3.8 23.6 - - + -
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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