Contacts of the strand formed by residues 82 - 91 (chain B) in PDB entry 4PN6
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 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B LYS* 3.6 9.7 - - - +
78B SER* 3.1 2.1 + - - -
79B SER* 2.8 48.3 + - - +
81B ASN* 1.4 86.3 - - - +
83B GLY* 1.3 67.9 + - - +
85B THR* 3.4 12.0 + - - -
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Residues in contact with GLY 83 (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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50B VAL* 4.1 18.4 - - - +
51B VAL 3.6 11.0 - - - -
52B LYS* 3.7 7.5 - - - +
77B GLU 3.7 4.3 - - - +
78B SER* 3.8 2.0 - - - -
82B SER* 1.3 79.5 + - - +
84B PRO* 1.4 76.0 - - - +
85B THR* 3.0 13.9 + - - -
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Residues in contact with PRO 84 (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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48B LEU* 3.8 31.1 - - + +
49B PRO 3.4 28.0 - - - +
50B VAL* 4.2 3.4 - - + -
51B VAL 3.8 7.4 - - - +
57B TRP* 3.7 37.9 - - + +
76B TYR* 4.2 9.0 - - + -
77B GLU 3.7 7.9 - - - +
78B SER* 3.9 3.8 - - - +
83B GLY* 1.4 79.5 - - - -
85B THR* 1.3 59.7 + - - +
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Residues in contact with THR 85 (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 TYR* 3.3 3.3 - - - -
77B GLU 2.9 32.8 + - - +
82B SER* 3.4 13.0 + - - -
83B GLY 3.0 13.3 + - - -
84B PRO* 1.3 72.2 + - - +
86B PHE* 1.3 72.8 + - - +
87B LEU* 3.7 9.4 + - + +
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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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74B SER* 4.0 4.5 - - - -
75B TYR 3.4 17.0 - - - -
76B TYR* 3.4 24.9 - + + -
85B THR* 1.3 82.1 - - - +
87B LEU* 1.3 66.4 + - - +
88B ARG* 3.3 39.9 - - - -
89B ALA* 3.8 5.8 - - + -
114B ASP 3.5 25.6 - - - -
115B ASN* 4.1 10.3 - - - -
116B SER 3.8 19.3 - - - -
117B THR* 4.8 11.4 - - - +
122B GLY 3.3 23.6 - - - +
123B GLY* 3.3 21.3 - - - -
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Residues in contact with LEU 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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75B TYR* 3.0 23.9 + - + +
77B GLU* 3.7 41.1 - - + +
85B THR* 4.1 11.9 - - + +
86B PHE* 1.3 83.3 - - - +
88B ARG* 1.3 82.4 + - - +
115B ASN 5.1 0.5 - - - +
117B THR* 3.5 22.6 - - - +
1003B NAG 5.8 1.4 - - - +
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Residues in contact with ARG 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 TYR* 2.9 54.6 + - + +
77B GLU* 5.2 1.8 + - - -
86B PHE* 3.3 10.9 - - - -
87B LEU* 1.3 107.1 - - + +
89B ALA* 1.3 58.6 + - - +
90B ILE* 3.6 28.5 - - + +
115B ASN* 3.5 11.2 - - - +
1003B NAG 4.3 33.9 - - - +
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Residues in contact with ALA 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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72B VAL* 4.1 11.1 - - + +
73B THR 3.4 9.0 - - - +
86B PHE* 4.4 4.9 - - + -
88B ARG* 1.3 70.4 - - - +
90B ILE* 1.3 63.4 + - - +
113B VAL* 3.9 32.5 - - + +
115B ASN* 2.7 24.2 + - + +
1003B NAG 3.3 29.9 + - - +
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Residues in contact with ILE 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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58B THR* 4.0 16.2 - - + +
72B VAL* 3.4 2.3 - - - -
73B THR* 2.7 52.8 + - - +
75B TYR* 3.8 26.9 - - + -
88B ARG* 3.6 40.1 + - + +
89B ALA* 1.3 73.7 - - - +
91B LEU* 1.3 63.9 + - - +
93B PHE* 4.8 14.4 - - + -
1003B NAG 5.4 0.7 - - - -
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Residues in contact with LEU 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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71B ASP* 3.6 24.0 - - + +
72B VAL* 3.9 14.4 - - + -
73B THR* 4.1 3.9 + - - -
89B ALA 4.2 0.2 + - - -
90B ILE* 1.3 77.8 - - - +
92B ASN* 1.3 60.4 + - - +
93B PHE* 3.3 46.4 + - + -
1003B NAG 5.1 10.9 - - + +
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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