Contacts of the strand formed by residues 59 - 68 (chain B) in PDB entry 4BHT
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 ARG 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B PRO* 3.2 1.4 - - - +
58B GLU* 1.3 83.0 - - + +
60B VAL* 1.3 64.7 + - - +
61B ILE* 4.1 20.2 - - + -
81B ARG 4.6 0.2 - - - -
83B GLN* 2.6 68.9 + - - +
91B TYR* 3.4 27.0 + - - -
157B HIS* 5.6 2.5 - - - -
162B THR* 5.5 4.4 - - - +
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Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PRO* 4.0 24.0 - - + -
59B ARG* 1.3 80.9 - - - +
61B ILE* 1.3 75.2 - - - +
62B GLN* 4.1 2.9 + - + +
80B TRP* 4.2 7.4 - - + -
81B ARG 3.5 9.6 - - - +
82B VAL* 4.0 18.2 - - + -
103B LEU* 3.8 33.4 - - + -
107B LYS* 5.2 2.0 - - + -
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Residues in contact with ILE 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 ARG* 4.1 17.0 - - + -
60B VAL* 1.3 76.9 - - - +
62B GLN* 1.3 65.7 + - - +
63B PHE* 3.8 19.8 - - + -
80B TRP* 3.2 6.9 - - - +
81B ARG* 3.0 40.5 + - + +
83B GLN* 4.1 19.7 - - - +
153B GLU* 4.6 4.5 - - - +
157B HIS* 3.5 57.0 - - + +
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Residues in contact with GLN 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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60B VAL* 4.0 3.9 + - + +
61B ILE* 1.3 77.6 - - - +
63B PHE* 1.3 66.2 + - - +
78B ARG* 3.4 51.0 + - + +
79B ALA 3.4 4.5 - - - -
80B TRP* 3.8 24.3 - - + +
103B LEU* 5.8 4.0 - - - +
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Residues in contact with PHE 63 (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 ILE* 3.8 19.5 - - + -
62B GLN* 1.3 83.3 - - - +
64B ARG* 1.3 71.1 + - - +
65B VAL* 3.8 4.2 + - + -
78B ARG* 3.7 5.9 - - - +
79B ALA* 3.0 61.7 + - + -
80B TRP* 3.9 13.7 - - - -
81B ARG 4.2 1.1 - - - -
95B MET* 5.7 0.2 - - + -
150B LEU* 3.7 30.3 - - + -
153B GLU* 3.3 32.3 - - + +
154B LEU* 4.0 28.7 - - + -
157B HIS* 5.9 0.4 - + - -
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Residues in contact with ARG 64 (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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185A LYS* 5.0 11.6 + - - +
63B PHE* 1.3 80.3 - - - +
65B VAL* 1.3 65.3 + - - +
66B VAL* 3.2 30.7 - - + +
76B VAL* 4.0 17.9 - - + +
77B ASN 3.7 4.5 - - - -
78B ARG* 5.2 0.4 - - - +
149B ALA 5.5 0.5 - - - +
153B GLU* 5.2 1.7 - - - +
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Residues in contact with VAL 65 (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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63B PHE* 4.1 13.2 - - + +
64B ARG* 1.3 78.8 - - - +
66B VAL* 1.3 62.8 + - - +
67B TRP* 3.8 4.2 - - + -
75B GLN 3.6 1.6 - - - +
76B VAL* 3.6 1.3 - - - -
77B ASN* 2.8 42.3 + - - +
79B ALA* 3.8 29.4 - - + +
146B PHE* 3.7 27.6 - - + -
149B ALA* 3.8 15.9 - - + +
150B LEU* 3.7 31.6 - - + +
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Residues in contact with VAL 66 (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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64B ARG* 3.2 38.6 - - + +
65B VAL* 1.3 73.5 - - - +
67B TRP* 1.3 62.5 + - - +
74B ILE* 3.4 32.8 - - + -
75B GLN 3.4 5.4 - - - +
76B VAL* 4.5 12.6 - - + -
149B ALA* 3.5 15.2 - - - +
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Residues in contact with TRP 67 (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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65B VAL* 3.8 10.5 - - + -
66B VAL* 1.3 75.9 - - - +
68B VAL* 1.3 81.7 + - - +
69B ASP* 3.7 28.0 - - + -
74B ILE* 3.5 4.5 - - - +
75B GLN* 2.8 61.3 + - + +
77B ASN* 2.9 21.7 + - - -
133B PHE* 3.5 22.7 - + - -
138B LYS* 3.7 27.6 - - + -
142B GLU* 3.8 29.8 - - + -
145B ARG* 4.5 6.1 - - + +
146B PHE* 3.8 26.5 - + + +
149B ALA* 4.3 13.0 - - + -
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Residues in contact with VAL 68 (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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144A MET* 4.5 22.2 - - + -
145A ARG* 5.9 6.3 - - + +
67B TRP* 1.3 87.6 - - - +
69B ASP* 1.3 65.2 + - - +
72B ASN* 3.6 43.5 - - - +
73B GLN 3.5 3.6 - - - +
74B ILE* 4.2 16.4 - - + -
145B ARG* 2.9 37.0 + - - +
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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