Contacts of the strand formed by residues 117 - 128 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151F THR 5.4 3.4 - - - +
152F GLN* 6.4 2.2 - - + -
112G LYS 3.8 0.2 - - - +
113G THR* 3.2 5.9 - - - -
114G LYS 3.0 32.8 + - - +
115G ASP* 3.9 9.6 - - + +
116G GLY* 1.3 85.3 - - - +
118G VAL* 1.3 75.6 + - - +
119G GLU* 4.0 6.9 + - + +
141G LYS* 3.9 27.8 - - + -
142G TYR 3.3 15.7 - - - +
143G THR* 4.4 15.0 - - + +
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Residues in contact with VAL 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G TRP* 4.5 9.2 - - + -
97G VAL* 6.5 0.2 - - + -
111G VAL* 4.0 26.5 - - + -
112G LYS 3.5 5.6 - - - +
113G THR* 4.0 9.9 - - + -
117G VAL* 1.3 72.0 - - - +
119G GLU* 1.3 62.6 + - - +
120G ILE* 4.1 11.6 + - + +
140G ARG 3.7 0.9 - - - +
141G LYS* 3.3 7.4 - - - -
142G TYR* 2.9 37.8 + - + +
144G LEU* 3.5 41.5 - - + -
153G VAL* 4.6 4.7 - - + -
165G VAL* 4.3 13.5 - - + -
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Residues in contact with GLU 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G THR 3.6 1.4 - - - +
111G VAL* 3.4 5.5 - - - +
112G LYS* 2.7 61.9 + - + +
114G LYS* 4.9 17.2 - - + +
117G VAL* 4.8 7.6 - - + +
118G VAL* 1.3 74.8 - - - +
120G ILE* 1.3 62.2 + - - +
121G THR* 4.0 6.2 + - - +
139G THR* 4.4 13.5 - - + +
140G ARG 3.6 3.1 - - - +
141G LYS* 4.0 34.2 + - + -
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Residues in contact with ILE 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G VAL* 5.0 2.9 - - + -
99G LEU* 4.1 28.7 - - + -
109G LEU* 5.2 4.3 - - + -
110G THR 3.5 7.9 - - - +
111G VAL* 4.3 10.3 - - + -
118G VAL* 4.4 12.6 - - + +
119G GLU* 1.3 75.3 - - - +
121G THR* 1.3 64.0 + - - +
138G PHE* 3.6 12.7 - - + -
139G THR* 3.4 1.6 - - - -
140G ARG* 2.9 42.6 + - + +
142G TYR* 4.4 24.9 - - + -
163G LEU* 3.7 23.3 - - + -
165G VAL* 3.9 23.8 - - + -
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Residues in contact with THR 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G GLU 3.8 1.1 - - - +
109G LEU* 3.3 6.5 - - - +
110G THR* 3.0 47.3 + - - +
112G LYS* 6.0 1.9 - - - +
119G GLU* 4.0 7.7 + - - +
120G ILE* 1.3 75.2 + - - +
122G GLY* 1.3 69.1 + - - +
123G LYS* 5.1 5.6 - - + -
138G PHE* 3.4 12.3 - - - +
139G THR* 3.3 23.6 + - - +
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Residues in contact with GLY 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G PHE* 3.5 8.1 - - - -
108G GLU 3.4 7.9 - - - -
109G LEU* 3.9 7.4 - - - -
121G THR* 1.3 77.3 - - - +
123G LYS* 1.3 63.6 + - - +
137G CYS* 3.3 1.2 - - - +
138G PHE* 3.0 53.5 + - - +
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Residues in contact with LYS 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G PHE* 3.4 6.8 - - - -
108G GLU* 3.1 29.7 + - - +
121G THR* 5.1 6.5 - - + -
122G GLY* 1.3 77.0 - - - +
124G HIS* 1.3 65.6 + - - +
125G GLU* 4.3 19.6 + - - +
136G ARG 3.4 13.2 - - - +
137G CYS* 4.3 12.3 - - + -
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Residues in contact with HIS 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G HIS 3.9 7.2 - - - -
104G PHE* 3.8 22.7 - + + -
108G GLU* 3.0 33.2 - - - +
123G LYS* 1.3 75.9 - - - +
125G GLU* 1.3 72.1 + - - +
127G ARG* 3.6 31.2 + - + +
134G ILE* 3.2 27.4 - - + -
135G SER* 3.5 14.6 - - - -
136G ARG* 3.1 54.0 + - + +
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Residues in contact with GLU 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G GLU* 4.7 2.4 + - - -
123G LYS* 4.3 20.9 + - + +
124G HIS* 1.3 92.5 + - - +
126G GLU* 1.3 73.6 + - - +
127G ARG* 3.3 5.0 + - - +
135G SER* 4.0 2.8 - - - -
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Residues in contact with GLU 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G GLU* 1.3 82.4 + - - +
127G ARG* 1.3 62.7 + - - +
133G TYR* 3.7 31.4 - - + +
134G ILE 3.4 13.0 - - - +
135G SER* 3.7 12.7 - - - +
139H THR* 5.4 2.0 - - - +
141H LYS* 3.0 42.5 + - - +
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Residues in contact with ARG 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G HIS* 2.5 35.7 + - - +
104G PHE* 5.0 0.2 - - - +
105G ALA* 5.1 2.6 - - - +
108G GLU* 3.9 10.7 + - - -
124G HIS* 3.6 40.3 + - + +
125G GLU 4.0 1.8 - - - +
126G GLU* 1.3 77.7 - - - +
128G GLN* 1.3 69.2 + - - +
129G ASP* 6.0 1.1 - - + +
133G TYR* 3.3 7.2 - - - -
134G ILE* 2.9 41.2 + - + +
136G ARG* 3.9 9.9 - - - +
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Residues in contact with GLN 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G ARG* 1.3 81.8 - - - +
129G ASP* 1.3 74.4 + - - +
132G GLY* 3.2 16.5 - - - +
133G TYR* 3.6 33.2 + - + -
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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