Contacts of the strand formed by residues 84 - 90 (chain B) in PDB entry 3Q2P
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 84 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 3.5 28.3 + - - -
14B ASN* 4.1 10.3 + - - +
15B LEU* 3.2 47.7 - - - +
18B PHE* 3.4 46.6 - - + +
75B ILE* 4.2 1.6 - - + -
76B SER 3.0 12.1 - - - +
77B GLU* 2.5 32.6 + - + +
82B ARG 4.1 5.1 + - - +
83B GLY* 1.3 77.9 - - - +
85B LYS* 1.3 68.1 + - - +
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Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PHE* 3.9 6.5 - - - -
22B GLU* 6.0 0.4 - - - -
75B ILE* 3.4 4.7 - - - +
76B SER* 3.0 48.9 + - - +
83B GLY 5.7 0.7 - - - -
84B ARG* 1.3 79.6 - - - +
86B LEU* 1.3 64.9 + - - +
87B LEU* 3.5 17.9 + - + +
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Residues in contact with LEU 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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18B PHE* 3.9 7.7 - - + -
19B ALA* 3.5 41.5 - - + +
22B GLU* 3.7 27.3 + - + +
23B GLU* 3.7 25.8 - - + +
26B ILE* 4.7 9.6 - - + -
74B ASP 3.6 9.9 - - - +
75B ILE* 4.4 3.4 - - + +
85B LYS* 1.3 74.9 - - - +
87B LEU* 1.3 63.3 + - - +
88B ARG 3.3 29.2 - - - +
89B PHE* 4.2 6.7 - - + -
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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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59B GLU* 4.1 22.7 - - - +
74B ASP* 2.8 28.4 + - - +
76B SER* 4.0 23.8 - - - +
85B LYS* 4.1 28.3 - - + +
86B LEU* 1.3 82.1 - - - +
88B ARG* 1.3 76.5 + - - +
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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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94A PRO* 3.6 46.1 + - + +
95A PRO 3.7 20.0 + - - -
96A PRO* 4.9 4.6 - - - +
59B GLU* 5.1 1.0 + - - -
61B GLN* 5.3 4.2 - - - +
72B ARG 4.3 0.7 - - - +
73B ALA* 3.3 3.8 - - - -
74B ASP* 2.7 68.4 + - + +
86B LEU* 3.3 9.6 - - - +
87B LEU* 1.3 96.0 + - - +
89B PHE* 1.3 60.5 + - - +
90B ASN* 3.9 17.9 - - - +
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Residues in contact with PHE 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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19B ALA* 4.0 25.1 - - + -
20B VAL* 4.0 25.4 - - + -
23B GLU* 3.3 30.2 - - + +
29B TYR* 3.5 22.1 + + - -
32B LEU* 3.8 27.6 - - + -
64B VAL* 4.4 4.9 - - + -
71B PHE* 3.5 40.2 - + + -
72B ARG 3.5 3.4 - - - -
73B ALA* 4.0 19.5 - - + -
86B LEU* 4.2 6.5 - - + -
88B ARG* 1.3 74.8 - - - +
90B ASN* 1.3 69.3 + - - +
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Residues in contact with ASN 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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29B TYR* 3.4 8.2 + - - +
71B PHE* 3.3 7.8 - - - -
72B ARG* 2.8 42.3 + - + +
88B ARG* 3.9 20.4 - - - +
89B PHE* 1.3 88.3 + - - +
91B GLY* 1.3 58.4 + - - +
93B VAL* 3.6 9.1 - - + +
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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