Contacts of the strand formed by residues 85 - 92 (chain B) in PDB entry 4PSQ
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 LYS 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B VAL 5.1 1.0 + - - -
7B SER 5.2 3.4 + - - -
9B PHE 4.2 9.4 + - - -
11B VAL* 3.9 22.2 - - + -
80B THR* 2.6 40.2 + - + +
82B ASP* 3.2 27.1 + - + +
83B PRO 3.5 0.2 - - - -
84B ALA* 1.3 80.7 - - - +
86B PHE* 1.3 62.6 + - - +
105B TRP* 3.5 56.6 - - + +
204B EDO 3.3 31.6 + - - +
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Residues in contact with PHE 86 (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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15B PHE* 3.7 20.0 - + - -
17B LYS* 4.1 16.8 - - + -
53B MET* 3.7 28.0 - - + -
77B PHE* 3.9 33.2 - - + -
78B THR 3.4 9.6 - - - +
79B ASP* 3.7 29.4 - - - -
80B THR* 4.6 2.4 - - - +
83B PRO* 3.2 28.0 - - + -
84B ALA 3.7 7.9 - - - -
85B LYS* 1.3 76.7 - - - +
87B LYS* 1.3 64.2 + - - +
103B ASP* 3.7 6.9 - - - +
104B HIS* 2.9 43.7 + + + +
105B TRP* 4.5 2.3 + - - -
106B ILE* 4.6 3.4 - - + -
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Residues in contact with LYS 87 (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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76B THR 3.5 2.6 - - - +
77B PHE* 3.4 2.5 - - - -
78B THR* 2.9 49.6 + - + +
80B THR* 4.9 9.9 - - + -
86B PHE* 1.3 74.6 - - - +
88B MET* 1.3 61.4 + - - +
89B LYS 3.6 1.2 + - - -
101B ASN* 4.1 27.9 + - - +
102B ASP 3.5 9.0 - - - +
103B ASP* 2.8 33.5 + - - +
206B EDO 4.8 9.5 + - - -
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Residues in contact with MET 88 (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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75B GLY* 4.3 4.7 - - - -
76B THR 3.6 3.8 - - - +
77B PHE* 3.4 37.0 - - + -
86B PHE 4.0 1.2 - - - -
87B LYS* 1.3 69.4 - - - +
89B LYS* 1.3 64.1 + - - +
90B TYR* 3.6 22.5 + - + -
101B ASN* 3.3 5.2 - - - -
102B ASP* 2.7 45.4 + - + +
104B HIS* 3.7 15.3 - - + +
133B TYR* 3.6 23.3 - - - +
201B 2WL 3.6 53.8 - - + +
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Residues in contact with LYS 89 (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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75B GLY* 3.4 1.2 - - - -
76B THR* 2.9 50.9 + - - +
87B LYS 3.6 2.4 + - - +
88B MET* 1.3 70.5 - - - +
90B TYR* 1.3 58.2 + - - +
91B TRP* 3.5 12.1 - - - -
99B LYS* 3.7 42.1 - - + +
100B GLY 3.4 10.8 - - - +
101B ASN* 3.7 14.5 - - + +
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Residues in contact with TYR 90 (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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73B MET* 4.8 4.3 - - - -
74B VAL 3.2 11.9 - - - +
88B MET* 3.7 25.8 - - + -
89B LYS* 1.3 75.2 - - - +
91B TRP* 1.3 69.0 + - - +
99B LYS* 3.3 2.4 - - - +
100B GLY* 2.7 65.4 + - - -
101B ASN 3.4 4.5 - - - -
102B ASP* 3.4 21.7 + - - -
121B ARG* 3.3 9.2 + - - -
201B 2WL 3.3 95.2 - + + -
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Residues in contact with TRP 91 (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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73B MET* 3.3 9.3 - - - +
74B VAL* 2.8 65.1 + - + +
76B THR* 3.7 23.8 - - + -
89B LYS* 3.5 36.1 - - - -
90B TYR* 1.3 94.6 - - - +
92B GLY* 1.3 76.6 + - - +
93B VAL* 4.2 3.1 - - - +
95B SER 4.2 0.7 - - - +
96B PHE* 3.7 21.7 - - + +
98B GLN 3.4 22.0 - - - +
99B LYS* 3.6 32.5 - - + -
201B 2WL 4.4 8.1 - - - -
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Residues in contact with GLY 92 (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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72B ASP 3.6 10.1 - - - -
73B MET* 4.3 8.0 - - - +
91B TRP* 1.3 77.1 - - - +
93B VAL* 1.3 66.6 + - - -
94B ALA 3.2 3.4 - - - -
95B SER* 3.1 17.6 + - - -
96B PHE 3.1 19.9 + - - -
201B 2WL 4.6 6.5 - - - -
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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