Contacts of the strand formed by residues 89 - 97 (chain A) in PDB entry 1JQP
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 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A PRO* 5.1 3.1 - - - +
85A VAL* 3.7 6.4 - - - +
86A LYS* 3.0 30.4 + - + +
88A SER* 1.3 96.3 - - - +
90A ALA* 1.3 67.3 + - - +
501A NAG 5.7 2.6 + - - -
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A PRO* 3.6 42.7 - - + +
83A TYR* 5.0 1.1 - - + -
84A GLU 3.2 15.7 - - - +
85A VAL* 3.9 3.6 - - - -
86A LYS* 4.0 4.9 - - - +
89A ARG* 1.3 84.1 - - - +
91A ILE* 1.3 67.4 + - - +
92A SER* 4.0 2.9 + - - -
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Residues in contact with ILE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A TYR* 3.2 5.4 - - - +
84A GLU* 2.7 54.0 + - + +
86A LYS* 4.0 20.0 - - + -
90A ALA* 1.3 76.1 - - - +
92A SER* 1.3 67.7 + - - +
93A TYR* 3.7 39.0 - - + +
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Residues in contact with SER 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A PRO 4.4 2.1 + - - -
4A ALA* 3.4 8.9 - - - -
5A ASN* 3.0 30.6 + - - +
6A CYS* 4.1 3.8 - - - -
82A LYS 3.7 4.9 - - - -
83A TYR* 4.5 0.9 - - - +
90A ALA 4.0 3.1 + - - -
91A ILE* 1.3 79.8 - - - +
93A TYR* 1.3 63.7 + - - +
94A CYS* 3.5 26.0 + - - -
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Residues in contact with TYR 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A CYS* 4.8 0.2 - - - -
82A LYS* 2.7 50.6 + - + +
83A TYR* 4.3 2.2 - - - -
84A GLU* 2.8 45.7 + - + -
91A ILE* 3.7 32.9 - - + +
92A SER* 1.3 72.3 - - - +
94A CYS* 1.3 56.1 + - - +
95A HIS 3.1 10.8 + - - -
96A GLU* 3.1 38.3 + - - +
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Residues in contact with CYS 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ASN 4.1 2.7 - - - -
6A CYS* 2.0 55.2 - - + -
10A ASP* 3.7 31.5 - - + +
15A TRP* 3.8 4.0 - - - -
81A PHE* 3.5 21.0 - - - -
92A SER* 3.5 18.6 + - - -
93A TYR* 1.3 72.4 - - - +
95A HIS* 1.3 66.9 + - + +
96A GLU 3.3 2.5 - - - -
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Residues in contact with HIS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASP* 3.8 16.2 + - + -
15A TRP* 3.6 9.4 - - - -
93A TYR 3.1 1.6 + - - -
94A CYS* 1.3 87.7 - - + +
96A GLU* 1.3 64.7 + - + +
116A LYS* 3.4 3.6 - - + +
117A LYS* 2.6 76.5 + - + +
118A MET 5.4 4.3 + - - -
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TRP* 4.1 0.6 - - - -
81A PHE* 3.7 11.3 - - - -
82A LYS* 3.2 55.7 + - + +
93A TYR* 3.1 24.7 + - - +
95A HIS* 1.3 88.6 - - + +
97A THR* 1.3 70.3 + - - +
114A VAL* 6.3 0.7 - - + -
115A GLY 3.2 11.9 - - - +
116A LYS* 4.1 23.1 - - + +
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Residues in contact with THR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TRP* 3.7 19.7 - - + -
17A PHE* 4.8 1.1 - - + -
68A PHE* 3.9 25.1 - - + -
79A ALA* 3.8 11.0 - - + +
80A PHE 3.4 13.7 - - - +
81A PHE* 5.3 0.4 - - - -
82A LYS* 3.6 18.8 - - - +
96A GLU* 1.3 82.3 - - - +
98A MET* 1.3 79.5 + - - +
113A PHE* 4.5 0.7 - - - -
114A VAL* 3.8 12.8 - - - +
115A GLY* 3.0 31.9 + - - +
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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