Contacts of the strand formed by residues 117 - 128 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A GOL 4.1 25.4 - - - -
112B LYS 3.7 0.9 - - - +
113B THR* 3.4 4.4 - - - +
114B LYS* 3.1 32.5 + - - +
115B ASP* 3.8 9.2 - - + +
116B GLY* 1.3 84.3 - - - +
118B VAL* 1.3 74.9 + - - +
119B GLU* 3.8 4.9 + - + +
141B LYS* 4.2 23.3 - - + -
142B TYR 3.4 14.8 - - - +
143B THR* 4.3 7.6 - - + -
144B LEU* 4.5 1.3 - - - +
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Residues in contact with VAL 118 (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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95B TRP* 4.4 9.0 - - + -
111B VAL* 3.9 26.2 - - + -
112B LYS 3.6 4.0 - - - +
113B THR* 3.8 11.9 - - - +
117B VAL* 1.3 72.4 - - - +
119B GLU* 1.3 61.4 + - - +
120B ILE* 4.2 15.3 - - + -
140B ARG 3.8 0.3 - - - +
141B LYS* 3.2 5.7 - - - -
142B TYR* 3.0 44.9 + - + +
144B LEU* 3.6 37.7 - - + -
153B VAL* 4.9 3.4 - - + -
165B VAL* 4.2 14.4 - - + -
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Residues in contact with GLU 119 (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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110B THR 3.6 1.7 - - - +
111B VAL* 3.5 3.1 - - - -
112B LYS* 2.8 46.9 + - + +
117B VAL* 3.8 4.8 + - + +
118B VAL* 1.3 73.8 - - - +
120B ILE* 1.3 64.3 + - - +
121B THR* 4.0 13.6 + - - +
139B THR* 4.0 21.7 - - + +
140B ARG 3.5 1.8 - - - -
141B LYS* 3.5 30.3 + - + -
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Residues in contact with ILE 120 (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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97B VAL* 5.6 0.2 - - + -
99B LEU* 4.3 15.3 - - + -
109B LEU* 5.0 2.9 - - + -
110B THR 3.4 8.3 - - - +
111B VAL* 4.2 11.2 - - + -
118B VAL* 4.2 10.1 - - + -
119B GLU* 1.3 75.9 - - - +
121B THR* 1.3 65.4 + - - +
138B PHE* 4.0 21.1 - - + -
139B THR* 3.4 4.0 - - - +
140B ARG* 2.7 46.2 + - + +
142B TYR* 3.7 31.0 - - + -
163B LEU* 3.8 23.6 - - + -
165B VAL* 4.1 22.4 - - + -
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Residues in contact with THR 121 (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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108B GLU 3.9 0.2 - - - +
109B LEU* 3.3 7.0 - - - +
110B THR* 3.0 48.0 + - - +
119B GLU* 4.0 17.7 + - - +
120B ILE* 1.3 75.8 + - - +
122B GLY* 1.3 67.9 + - - +
123B LYS* 5.4 2.9 - - + -
138B PHE* 3.5 12.6 - - - +
139B THR* 4.1 13.2 + - - +
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Residues in contact with GLY 122 (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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104B PHE* 3.8 7.6 - - - -
108B GLU 3.3 9.0 - - - -
109B LEU* 4.0 4.9 - - - -
121B THR* 1.3 78.6 - - - +
123B LYS* 1.3 65.3 + - - +
137B CYS* 3.3 2.6 - - - +
138B PHE* 3.0 51.4 + - - +
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Residues in contact with LYS 123 (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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104B PHE* 3.7 5.4 - - - -
108B GLU* 3.1 30.7 + - - +
121B THR* 5.4 4.3 - - + -
122B GLY* 1.3 76.8 - - - +
124B HIS* 1.3 67.1 + - - +
125B GLU* 6.5 1.1 - - + -
136B ARG 3.4 13.9 - - - +
137B CYS* 4.4 10.8 - - + -
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Residues in contact with HIS 124 (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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103B HIS 3.5 18.6 + - - -
104B PHE* 3.6 23.1 - + + -
108B GLU* 3.2 17.9 - - - +
123B LYS* 1.3 77.9 - - - +
125B GLU* 1.3 80.7 + - - +
127B ARG* 3.1 33.5 - - + +
134B ILE* 3.5 22.4 - - + -
135B SER* 3.7 5.0 - - - -
136B ARG* 3.2 68.5 + - + +
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Residues in contact with GLU 125 (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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108B GLU* 4.7 0.8 + - - -
123B LYS* 6.5 1.3 - - + -
124B HIS* 1.3 93.8 + - - +
126B GLU* 1.3 72.2 - - - +
127B ARG* 3.2 9.5 + - - +
135B SER* 4.0 2.7 - - - -
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Residues in contact with GLU 126 (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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139A THR* 5.3 5.1 - - - +
141A LYS* 2.6 43.0 + - - +
125B GLU* 1.3 77.8 - - - +
127B ARG* 1.3 63.8 + - - +
133B TYR* 3.8 36.8 - - + +
134B ILE 3.3 15.0 - - - +
135B SER* 3.8 12.8 + - - +
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Residues in contact with ARG 127 (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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103B HIS 3.1 23.0 + - - -
104B PHE* 4.3 0.8 - - - +
105B ALA* 5.2 0.6 - - - +
108B GLU* 2.8 43.2 + - - -
124B HIS* 3.1 26.9 + - + +
125B GLU* 3.6 12.0 + - - +
126B GLU* 1.3 76.6 - - - +
128B GLN* 1.3 71.1 - - - +
129B ASP* 6.3 0.4 - - + -
133B TYR* 4.1 8.1 - - - -
134B ILE* 3.0 38.2 + - + +
136B ARG* 5.9 0.4 - - - +
76I ALA 5.2 13.4 - - - +
77I LEU* 4.3 14.9 - - - +
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Residues in contact with GLN 128 (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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127B ARG* 1.3 82.5 - - - +
129B ASP* 1.3 63.2 + - - +
132B GLY* 3.3 10.2 - - - +
133B TYR* 3.5 46.8 + - + -
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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