Contacts of the strand formed by residues 104 - 111 (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 SER 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A TRP* 3.5 5.4 - - - +
101A GLY* 2.9 23.3 + - - +
102A HIS 3.7 0.6 - - - -
103A PHE* 1.3 81.8 - - - +
105A THR* 1.3 69.0 + - - +
106A VAL* 4.5 3.8 - - - +
121A LYS* 3.5 28.0 - - - +
122A VAL 3.3 14.6 - - - -
123A VAL* 3.8 11.2 - - - +
124A LYS* 4.4 7.8 - - - +
1702A SO4 2.9 18.5 + - - -
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Residues in contact with THR 105 (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* 4.1 20.4 + - + +
99A GLY 3.6 12.6 - - - +
100A TRP* 4.3 9.6 - - + +
104A SER* 1.3 76.7 + - - +
106A VAL* 1.3 66.5 + - - +
107A TRP* 3.3 37.9 - - + +
120A MET 3.6 2.1 - - - +
121A LYS* 3.6 0.4 - - - -
122A VAL* 2.9 36.0 + - - -
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LYS* 3.7 4.2 - - - -
98A LEU* 2.9 45.3 + - + -
99A GLY 2.8 18.4 + - - +
104A SER* 4.5 7.6 - - - +
105A THR* 1.3 79.0 - - - +
107A TRP* 1.3 64.6 + - - +
119A ALA* 4.1 16.6 - - + -
120A MET 3.6 6.7 - - - +
121A LYS* 4.4 15.3 - - + -
800A PVB 4.0 53.8 - - + +
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Residues in contact with TRP 107 (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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81A PRO* 6.4 0.7 - - + -
82A VAL* 3.6 43.8 - - + +
83A LYS 4.9 0.2 - - - -
84A ILE* 4.2 23.8 - - + -
94A VAL* 3.5 24.7 - - + -
96A ARG 3.5 17.5 - - - +
97A LYS* 3.4 45.3 - - + -
98A LEU* 4.2 4.3 - - - -
105A THR* 3.3 32.5 - - + +
106A VAL* 1.3 75.5 - - - +
108A LEU* 1.3 61.2 + - - +
109A CYS* 3.5 6.9 + - - -
119A ALA* 3.4 2.3 - - - -
120A MET* 2.8 58.6 + - + +
122A VAL* 4.2 14.0 - - + +
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Residues in contact with LEU 108 (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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94A VAL* 3.8 1.0 - - - +
95A ILE* 2.8 39.8 + - + +
96A ARG* 2.8 25.1 + - + +
98A LEU* 3.9 23.6 - - + +
107A TRP* 1.3 68.8 - - - +
109A CYS* 1.3 60.1 - - - +
117A PHE* 4.2 26.7 - - + -
118A VAL 3.6 5.4 - - - +
179A VAL* 3.5 39.7 - - + -
240A VAL* 4.5 7.6 - - + +
243A MET* 4.9 11.7 - - - +
244A ALA* 4.3 22.0 - - + +
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Residues in contact with CYS 109 (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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92A TYR* 4.1 14.8 - - + -
93A HIS 3.1 11.9 - - - +
94A VAL* 3.8 17.7 - - - -
95A ILE* 4.2 4.9 - - - -
107A TRP* 3.8 9.4 - - - -
108A LEU* 1.3 78.8 - - - +
110A TRP* 1.3 57.4 + - - +
117A PHE* 3.4 9.7 - - - -
118A VAL* 2.8 47.3 + - + +
120A MET* 3.5 38.1 - - - -
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Residues in contact with TRP 110 (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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91A ARG 3.1 4.2 - - - +
92A TYR* 4.5 1.3 - - - -
93A HIS* 2.6 51.4 + + + +
95A ILE* 4.0 14.0 - - + +
109A CYS* 1.3 72.2 - - - +
111A ASP* 1.3 71.1 + - - +
112A MET* 3.5 22.8 + - - +
115A LYS* 3.4 38.1 - - + +
116A ARG* 3.3 28.7 - - - -
117A PHE* 3.5 39.0 - + + -
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Residues in contact with ASP 111 (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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91A ARG* 2.9 45.7 + - - +
92A TYR* 3.5 26.5 - - + -
109A CYS 4.1 1.4 + - - -
110A TRP* 1.3 73.4 + - - +
112A MET* 1.3 62.1 + - - +
113A GLN 3.4 4.7 + - - -
114A GLY* 3.1 18.0 + - - -
115A LYS* 3.0 25.8 + - - -
116A ARG* 3.0 25.9 + - - +
118A VAL* 4.2 12.2 - - + +
160A ILE* 5.9 2.3 - - - +
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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