Contacts of the strand formed by residues 117 - 128 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133E TYR* 6.4 0.2 - - + -
112F LYS 3.9 0.2 - - - +
113F THR* 3.4 3.1 - - - -
114F LYS 3.0 33.7 + - - +
115F ASP* 3.8 9.2 - - + +
116F GLY* 1.3 84.2 - - - +
118F VAL* 1.3 73.4 + - - +
119F GLU* 3.9 4.1 + - + +
141F LYS* 3.9 26.9 - - + -
142F TYR 3.4 13.2 - - - +
143F THR* 5.0 10.8 - - + +
144F LEU* 4.5 0.2 - - - +
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Residues in contact with VAL 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F TRP* 4.5 8.3 - - + -
111F VAL* 4.0 22.0 - - + -
112F LYS 3.5 8.7 - - - +
113F THR* 4.0 11.0 - - - +
117F VAL* 1.3 73.6 - - - +
119F GLU* 1.3 60.5 + - - +
120F ILE* 4.2 14.1 - - + -
140F ARG 3.8 0.7 - - - +
141F LYS* 3.2 6.1 - - - -
142F TYR* 2.9 42.8 + - + +
144F LEU* 3.5 39.5 - - + -
153F VAL* 5.1 3.6 - - + -
165F VAL* 4.3 14.1 - - + -
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Residues in contact with GLU 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F THR* 3.6 1.6 - - - +
111F VAL* 3.4 4.7 - - - +
112F LYS* 2.8 50.6 + - + +
117F VAL* 3.9 4.2 + - + +
118F VAL* 1.3 72.1 - - - +
120F ILE* 1.3 64.2 + - - +
121F THR* 4.1 12.8 - - + +
139F THR* 3.9 24.3 - - + +
140F ARG 3.7 2.0 - - - -
141F LYS* 3.3 30.3 + - + -
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Residues in contact with ILE 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F VAL* 5.6 0.4 - - + -
99F LEU* 4.3 10.5 - - + -
109F LEU* 4.9 3.1 - - + -
110F THR 3.3 8.1 - - - +
111F VAL* 4.1 11.4 - - + -
118F VAL* 4.3 10.8 - - + -
119F GLU* 1.3 76.5 - - - +
121F THR* 1.3 65.0 + - - +
138F PHE* 3.8 23.3 - - + -
139F THR* 3.3 3.6 - - - +
140F ARG* 2.8 44.2 + - + +
142F TYR* 3.8 30.3 - - + -
163F LEU* 3.7 26.0 - - + -
165F VAL* 4.0 23.6 - - + -
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Residues in contact with THR 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F GLU 3.8 0.3 - - - +
109F LEU* 3.4 6.8 - - - +
110F THR* 2.9 51.5 + - + +
119F GLU* 4.1 17.9 - - + +
120F ILE* 1.3 77.3 - - - +
122F GLY* 1.3 58.7 + - - +
138F PHE* 3.4 10.3 - - - -
139F THR* 3.6 26.7 - - + +
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Residues in contact with GLY 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F PHE* 3.7 7.9 - - - -
108F GLU 3.3 10.3 - - - -
109F LEU* 4.0 4.5 - - - -
121F THR* 1.3 75.8 - - - +
123F LYS* 1.3 65.1 + - - +
137F CYS* 3.3 2.6 - - - +
138F PHE* 3.0 50.5 + - - +
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Residues in contact with LYS 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F PHE* 3.5 5.5 - - - -
108F GLU* 3.2 26.1 + - - +
122F GLY* 1.3 75.0 - - - +
124F HIS* 1.3 67.0 + - - +
125F GLU* 6.2 1.6 - - + -
136F ARG 3.4 13.2 - - - +
137F CYS* 4.2 17.7 - - + -
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Residues in contact with HIS 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F HIS 3.5 19.2 + - - -
104F PHE* 3.7 22.5 - + + -
108F GLU* 3.2 29.2 - - - +
123F LYS* 1.3 76.7 - - - +
125F GLU* 1.3 79.3 + - - +
127F ARG* 3.2 23.8 + - + +
134F ILE* 3.4 24.7 - - + -
135F SER* 3.7 11.5 - - - -
136F ARG* 3.2 59.0 + - + +
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Residues in contact with GLU 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F GLU* 4.5 2.8 + - - -
123F LYS* 6.2 2.2 - - + -
124F HIS* 1.3 93.9 + - - +
126F GLU* 1.3 70.9 + - - +
127F ARG* 3.3 8.9 + - - +
135F SER* 4.1 3.8 - - - -
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Residues in contact with GLU 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E THR* 5.4 3.5 - - - +
141E LYS* 2.7 44.7 + - - +
125F GLU* 1.3 78.4 - - - +
127F ARG* 1.3 64.1 + - - +
133F TYR* 4.0 34.2 - - + -
134F ILE* 3.4 16.4 - - - +
135F SER* 4.0 9.4 - - - +
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Residues in contact with ARG 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F HIS 3.0 22.6 + - - -
104F PHE* 4.5 0.6 - - - +
105F ALA 4.7 1.4 - - - +
108F GLU* 2.9 40.8 + - - -
124F HIS* 3.2 25.9 + - + +
125F GLU* 3.6 13.1 + - - +
126F GLU* 1.3 76.8 - - - +
128F GLN* 1.3 69.2 + - - +
129F ASP* 3.6 2.1 + - - +
133F TYR* 3.5 11.2 - - - -
134F ILE* 3.1 28.1 + - - +
76K ALA* 3.3 36.5 + - - +
77K LEU 5.4 0.6 + - - -
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Residues in contact with GLN 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F ARG* 1.3 79.2 - - - +
129F ASP* 1.3 65.0 + - - +
132F GLY* 3.4 14.4 - - - -
133F TYR* 3.4 48.7 + - + -
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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