Contacts of the strand formed by residues 92 - 100 (chain A) in PDB entry 2X7G
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 TYR 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ASP 3.3 5.9 - - - +
87A LEU* 3.7 2.6 - - - +
88A PHE* 2.8 52.6 + - + +
89A ASN* 4.1 3.6 - - + -
91A ARG* 1.3 93.3 + - + +
93A HIS* 1.3 63.2 + - - +
94A VAL* 3.5 5.0 + - - +
109A CYS* 4.1 16.4 - - + -
110A TRP 3.7 2.0 - - - -
111A ASP* 3.5 31.9 - - + -
118A VAL* 3.8 20.0 - - + -
120A MET* 4.9 3.1 - - + -
160A ILE* 4.8 3.4 - - + +
161A ASP* 2.7 38.7 + - - +
163A PHE* 3.9 20.4 - + - -
176A VAL* 3.8 30.4 - - + +
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Residues in contact with HIS 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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85A GLY* 3.5 33.7 + - - -
86A ASP 3.4 5.2 + - - -
87A LEU* 4.0 3.4 - - - +
91A ARG 3.6 0.8 + - - -
92A TYR* 1.3 68.7 - - - +
94A VAL* 1.3 64.2 + - - +
95A ILE* 3.5 18.4 + - + +
109A CYS* 3.1 2.6 - - - -
110A TRP* 2.6 55.1 + + + +
112A MET* 3.8 33.0 - - + +
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 4.1 1.8 - - + -
83A LYS 3.6 20.9 - - - +
84A ILE* 4.2 4.9 - - - +
85A GLY* 2.9 27.9 + - - +
86A ASP 2.9 19.0 + - - +
88A PHE* 3.7 32.3 - - + -
92A TYR 4.0 0.9 - - - +
93A HIS* 1.3 71.8 + - - +
95A ILE* 1.3 64.1 + - - +
96A ARG 4.3 2.7 - - - +
107A TRP* 3.5 38.8 - - + -
109A CYS* 3.8 17.7 - - - -
120A MET* 4.1 4.3 - - + -
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Residues in contact with ILE 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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84A ILE* 3.7 18.3 - - - +
93A HIS* 3.7 27.6 - - + +
94A VAL* 1.3 76.5 - - - +
96A ARG* 1.3 64.7 + - + +
108A LEU* 2.8 31.3 + - + +
109A CYS 4.2 2.0 - - - -
110A TRP* 4.0 20.2 - - + +
117A PHE* 4.4 12.8 - - + -
244A ALA* 3.8 27.1 - - + +
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Residues in contact with ARG 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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84A ILE* 5.1 5.2 - - + -
94A VAL* 3.9 1.6 - - - +
95A ILE* 1.3 86.5 - - + +
97A LYS* 1.3 85.1 + - + +
98A LEU* 4.3 9.5 - - - +
107A TRP* 3.5 13.7 - - - -
108A LEU* 2.8 37.3 + - + +
243A MET* 3.9 41.4 + - - +
244A ALA* 5.7 1.6 + - - +
246A GLU* 3.9 29.5 - - - +
800A PVB 5.0 9.9 + - - -
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Residues in contact with LYS 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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84A ILE* 5.6 0.8 - - - +
96A ARG* 1.3 100.8 + - + +
98A LEU* 1.3 61.4 + - - +
99A GLY* 4.1 6.5 - - - +
100A TRP* 3.2 40.0 - - + +
105A THR* 4.1 15.6 + - + +
106A VAL 3.7 3.8 - - - -
107A TRP* 3.4 46.1 - - + -
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Residues in contact with LEU 98 (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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96A ARG* 3.8 11.0 + - - +
97A LYS* 1.3 74.6 - - - +
99A GLY* 1.3 58.5 + - - +
106A VAL* 2.9 33.4 + - + +
107A TRP 4.2 0.7 - - - -
108A LEU* 3.9 38.8 - - + +
119A ALA* 4.2 11.7 - - + -
179A VAL* 4.8 2.5 - - + -
243A MET* 3.9 28.0 - - + -
800A PVB 3.4 63.9 - - + +
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Residues in contact with GLY 99 (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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97A LYS* 3.4 7.1 - - - +
98A LEU* 1.3 83.5 - - - +
100A TRP* 1.3 76.0 + - - -
105A THR* 3.6 5.2 - - - +
106A VAL* 2.8 31.8 + - - +
800A PVB 3.8 10.9 - - - +
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Residues in contact with TRP 100 (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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97A LYS* 3.2 36.1 - - + +
99A GLY* 1.3 84.4 - - - -
101A GLY* 1.3 69.8 + - - +
104A SER 3.5 10.5 - - - +
105A THR* 4.3 8.3 - - - +
800A PVB 3.6 12.5 - - - +
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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