Contacts of the strand formed by residues 117 - 128 (chain A) in PDB entry 6GJH
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 VAL 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A LYS 3.8 0.3 - - - +
113A THR* 3.3 4.2 - - - +
114A LYS* 2.9 33.5 + - - +
115A ASP* 3.9 10.5 - - + +
116A GLY* 1.3 84.9 - - - +
118A VAL* 1.3 72.6 + - - +
119A GLU* 3.8 4.2 + - + +
141A LYS* 3.8 27.8 - - + -
142A TYR 3.3 17.5 - - - +
143A THR* 4.4 13.9 - - + +
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Residues in contact with VAL 118 (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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95A TRP* 4.5 7.4 - - + -
111A VAL* 4.0 22.2 - - + -
112A LYS 3.4 7.9 - - - +
113A THR* 3.9 14.8 - - - +
117A VAL* 1.3 73.2 - - - +
119A GLU* 1.3 61.2 + - - +
120A ILE* 4.2 14.4 - - + -
140A ARG 3.8 0.7 - - - +
141A LYS* 3.2 6.8 - - - -
142A TYR* 2.9 43.2 + - + +
144A LEU* 3.7 32.5 - - + +
153A VAL* 4.3 10.1 - - + -
165A VAL* 4.3 11.7 - - + -
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Residues in contact with GLU 119 (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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110A THR* 3.6 1.6 + - - +
111A VAL* 3.5 4.3 - - - +
112A LYS* 2.6 65.6 + - + +
114A LYS* 6.1 1.8 - - + +
117A VAL* 3.8 4.5 + - + +
118A VAL* 1.3 72.9 - - - +
120A ILE* 1.3 62.5 + - - +
121A THR* 4.1 12.0 + - - +
139A THR* 3.8 25.3 - - + +
140A ARG 3.6 4.0 - - - +
141A LYS* 3.7 23.3 + - + +
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Residues in contact with ILE 120 (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 VAL* 5.4 1.1 - - + -
99A LEU* 4.2 26.5 - - + -
101A VAL* 5.5 0.2 - - + -
109A LEU* 5.0 3.4 - - + -
110A THR 3.4 8.1 - - - +
111A VAL* 4.4 8.5 - - + -
118A VAL* 4.3 12.1 - - + -
119A GLU* 1.3 76.4 - - - +
121A THR* 1.3 66.0 + - - +
138A PHE* 3.6 14.2 - - + -
139A THR* 3.3 3.0 - - - -
140A ARG 2.9 42.9 + - - +
142A TYR* 3.7 29.8 - - + -
163A LEU* 3.9 22.0 - - + -
165A VAL* 4.0 23.1 - - + -
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Residues in contact with THR 121 (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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108A GLU 3.9 0.3 - - - +
109A LEU* 3.3 9.3 - - - +
110A THR* 3.0 47.7 + - - +
112A LYS* 5.9 2.3 - - - +
119A GLU* 4.1 12.0 + - - +
120A ILE* 1.3 75.5 - - - +
122A GLY* 1.3 68.8 + - - +
123A LYS* 5.2 5.2 - - + -
138A PHE* 3.4 11.2 - - - +
139A THR* 3.4 21.3 + - - +
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Residues in contact with GLY 122 (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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104A PHE* 3.5 8.7 - - - -
108A GLU 3.3 8.7 - - - -
109A LEU* 3.9 5.4 - - - -
121A THR* 1.3 77.5 - - - +
123A LYS* 1.3 64.6 + - - +
137A CYS* 3.2 1.2 - - - +
138A PHE* 2.9 53.7 + - - +
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Residues in contact with LYS 123 (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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104A PHE* 3.4 5.9 - - - -
108A GLU* 3.1 27.7 + - - +
121A THR* 5.2 6.5 - - + -
122A GLY* 1.3 76.1 - - - +
124A HIS* 1.3 66.8 + - - +
125A GLU* 3.8 23.8 + - - +
136A ARG 3.4 12.6 - - - +
137A CYS* 4.4 10.1 - - + -
89H ARG* 5.7 0.5 + - - -
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Residues in contact with HIS 124 (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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103A HIS 3.9 7.6 - - - -
104A PHE* 3.7 23.8 - + + -
108A GLU* 3.3 33.7 - - - +
123A LYS* 1.3 74.7 - - - +
125A GLU* 1.3 80.8 + - - +
127A ARG* 3.4 30.4 + - + +
134A ILE 3.3 23.6 - - - -
135A SER* 3.5 13.5 - - - -
136A ARG* 3.2 58.9 + - + +
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Residues in contact with GLU 125 (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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108A GLU* 4.9 1.8 + - - -
123A LYS* 3.8 24.8 + - - +
124A HIS* 1.3 94.0 + - - +
126A GLU* 1.3 70.9 + - - +
127A ARG* 3.3 3.6 + - - +
135A SER* 3.9 4.6 - - - -
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Residues in contact with GLU 126 (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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125A GLU* 1.3 80.4 + - - +
127A ARG* 1.3 63.5 + - - +
133A TYR* 3.6 27.3 - - + +
134A ILE* 3.4 12.6 - - - +
135A SER* 3.8 10.3 - - - +
201A GOL 3.1 17.9 + - - -
139B THR* 5.7 1.4 - - - +
141B LYS* 3.2 40.8 + - - +
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Residues in contact with ARG 127 (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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103A HIS* 2.6 35.0 + - - +
105A ALA* 5.6 0.4 - - - +
108A GLU* 4.0 9.5 + - - -
124A HIS* 3.4 33.8 + - + +
125A GLU 4.1 5.2 - - - +
126A GLU* 1.3 76.2 - - - +
128A GLN* 1.3 69.7 + - - +
129A ASP* 6.0 2.4 - - + +
133A TYR* 3.3 7.5 - - - -
134A ILE* 3.0 39.3 + - + +
136A ARG* 3.8 18.0 - - - +
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Residues in contact with GLN 128 (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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127A ARG* 1.3 82.9 + - - +
129A ASP* 1.3 71.5 + - - +
132A GLY* 3.1 16.7 - - - +
133A TYR* 3.8 28.3 + - + -
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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