Contacts of the strand formed by residues 56 - 62 (chain B) in PDB entry 5IHB
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 VAL 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B PHE* 4.3 12.8 - - + -
45B HIS* 5.0 4.5 - - + +
54B SER 4.3 1.6 - - - +
55B PRO* 1.3 73.8 - - + +
57B HIS* 1.3 68.8 + - - +
76B ASN* 3.1 19.2 + - - -
96B PRO* 3.4 28.4 - - + +
97B SER* 3.7 33.8 + - - +
120B MET* 4.7 6.5 - - + -
121B GLU 3.5 7.0 - - - +
122B ARG* 3.7 39.0 - - + +
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Residues in contact with HIS 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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55B PRO* 4.1 32.1 - - + +
56B VAL* 1.3 79.5 + - - +
58B GLY* 1.3 58.9 + - - +
59B TYR* 3.6 24.4 - - + +
76B ASN* 3.4 13.8 + - - +
77B LYS* 3.8 40.9 - - + +
120B MET* 3.4 4.2 - - - +
121B GLU* 2.8 50.7 + - + +
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Residues in contact with GLY 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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57B HIS* 1.3 71.8 - - - +
59B TYR* 1.3 63.5 + - - -
75B THR* 2.9 30.3 + - - -
76B ASN* 2.8 13.8 + - - +
92B LEU* 3.5 11.5 - - - +
96B PRO* 4.1 5.5 - - - +
118B PHE* 3.6 17.7 - - - -
119B ARG 3.3 7.0 - - - -
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Residues in contact with TYR 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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57B HIS* 3.6 20.7 - - + +
58B GLY* 1.3 73.0 - - - -
60B TRP* 1.3 60.1 + - - +
61B PHE* 3.3 27.5 + + + -
72B PRO* 4.2 14.1 - - + -
74B ALA 3.5 4.3 - - - -
75B THR* 3.4 26.2 - - - -
77B LYS* 3.2 26.0 - - + +
80B GLN* 4.0 19.7 + - + -
117B PHE 3.9 0.2 - - - +
118B PHE* 3.2 10.5 - - - -
119B ARG* 2.6 61.0 + - + +
121B GLU* 2.9 45.4 + - + -
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Residues in contact with TRP 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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23B LEU* 5.2 1.6 - - + -
25B VAL* 4.9 8.5 - - + -
39B VAL* 6.3 0.4 - - + -
41B CYS* 3.8 21.5 - - + -
59B TYR* 1.3 71.5 - - - +
61B PHE* 1.3 59.7 - - - +
72B PRO* 3.0 7.4 - - - +
73B VAL* 2.9 41.7 + - + -
74B ALA* 3.0 14.1 + - + +
92B LEU* 3.7 19.1 - - + +
101B CYS 3.0 29.1 + - - -
103B LEU* 3.8 36.3 - - + +
116B TYR* 3.9 28.5 - - + -
117B PHE* 3.4 28.5 - - - -
118B PHE* 3.5 27.4 - + + -
134B LEU* 4.2 22.4 - - + -
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Residues in contact with PHE 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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59B TYR* 3.3 35.0 - + + -
60B TRP* 1.3 75.6 - - - +
62B ARG* 1.3 62.9 + - - +
65B ALA* 3.7 18.4 - - + -
67B ILE* 3.5 45.1 - - + -
70B ASP 3.8 14.8 - - - -
71B SER 4.1 1.6 - - - -
72B PRO* 3.6 37.2 - - + -
73B VAL* 4.6 0.7 - - - +
80B GLN* 6.4 0.2 - - - -
116B TYR* 3.1 12.6 - - - +
117B PHE* 2.9 60.6 + + + -
119B ARG* 4.2 5.8 - - + -
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Residues in contact with ARG 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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61B PHE* 1.3 75.0 - - - +
63B GLU* 1.3 70.2 + - - +
64B GLY 3.3 0.2 + - - -
65B ALA* 3.0 26.4 + - + +
73B VAL* 4.1 15.8 - - + +
83B GLN* 5.9 2.2 - - + -
111B ARG 3.4 17.1 + - - -
113B ASN 2.7 29.5 + - - -
114B GLY* 4.3 2.2 - - - -
115B SER 3.7 8.7 - - - +
116B TYR* 3.3 40.2 + - + -
117B PHE* 3.3 5.0 - - - -
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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