Contacts of the strand formed by residues 83 - 89 (chain B) in PDB entry 5ITY
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 GLY 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B GLY* 5.8 2.7 + - - -
79B PHE* 3.3 38.4 + - - +
81B MET 4.0 0.6 - - - -
82B SER* 1.3 78.5 - - - +
84B SER* 1.3 64.2 + - - -
114B PHE* 4.2 7.9 - - - -
115B VAL 3.2 9.4 - - - -
116B ASP* 4.0 4.3 - - - -
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Residues in contact with SER 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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79B PHE* 4.0 6.1 - - - -
82B SER 5.0 0.7 + - - -
83B GLY* 1.3 76.0 - - - -
85B PHE* 1.3 69.0 + - - +
86B GLN* 3.9 11.9 + - - -
114B PHE* 3.4 12.4 - - - -
115B VAL* 2.9 44.0 + - - +
244B TYR* 3.3 18.4 - - - -
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Residues in contact with PHE 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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10B ALA* 4.7 2.7 - - + +
13B PHE* 3.6 9.6 - - + -
14B VAL* 4.1 23.1 - - + -
56B LEU* 4.0 17.5 - - + -
58B LEU* 4.2 21.5 - - + -
77B PHE* 3.9 31.9 - + - -
79B PHE* 3.9 26.9 - + - -
84B SER* 1.3 76.6 - - - +
86B GLN* 1.3 68.8 + - - +
101B PHE* 4.4 9.9 - + - -
112B LEU* 4.1 16.2 - - + -
113B CYS 3.2 16.8 - - - -
114B PHE* 3.8 20.4 - + + -
244B TYR* 2.9 30.4 + - + +
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Residues in contact with GLN 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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13B PHE* 4.1 6.3 - - - -
84B SER* 3.9 12.8 + - - +
85B PHE* 1.3 81.6 - - - +
87B LEU* 1.3 60.1 + - - +
88B VAL* 4.0 15.9 - - + +
94B PRO* 3.5 19.0 - - - +
111B ALA 3.5 1.0 - - - +
112B LEU* 3.4 3.8 - - - +
113B CYS* 2.6 41.6 + - + +
115B VAL* 3.8 32.2 - - + +
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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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13B PHE* 4.0 20.9 - - + -
17B ALA* 4.0 20.0 - - + +
18B CYS* 5.1 1.3 - - - -
21B LEU* 3.8 27.1 - - + -
23B PHE* 4.8 4.5 - - + -
86B GLN* 1.3 73.2 - - - +
88B VAL* 1.3 64.0 + - - +
110B LEU* 4.1 27.8 - - + -
111B ALA 3.4 22.9 - - - +
112B LEU* 3.7 19.3 - - + +
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Residues in contact with VAL 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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86B GLN* 4.0 26.9 - - + +
87B LEU* 1.3 80.3 - - - +
89B PRO* 1.3 77.2 - - + +
92B GLU 3.5 21.3 - - - +
93B LEU* 4.1 4.3 - - + -
94B PRO* 4.2 10.3 - - + -
110B LEU* 3.2 11.7 - - - +
111B ALA* 2.7 51.6 + - + +
113B CYS* 3.9 18.6 - - - -
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Residues in contact with PRO 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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88B VAL* 1.3 92.9 - - + +
90B ARG* 1.3 56.8 + - - +
91B GLU* 3.0 2.9 - - + +
92B GLU* 2.6 66.4 + - + +
109B ARG 3.8 1.6 - - - +
110B LEU* 3.7 13.7 - - + -
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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