Contacts of the strand formed by residues 117 - 128 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112D LYS 3.8 0.7 - - - +
113D THR* 3.3 5.0 - - - +
114D LYS* 2.9 33.2 + - - +
115D ASP* 3.6 11.2 - - + +
116D GLY* 1.3 84.5 - - - +
118D VAL* 1.3 75.7 + - - +
119D GLU* 4.0 2.4 + - + +
141D LYS* 3.9 26.7 - - + -
142D TYR 3.3 14.8 - - - +
143D THR* 4.9 7.9 - - + +
144D LEU 4.6 0.7 - - - +
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Residues in contact with VAL 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D TRP* 4.6 7.0 - - + -
111D VAL* 3.8 27.1 - - + -
112D LYS 3.5 4.9 - - - +
113D THR* 3.8 11.7 - - - +
117D VAL* 1.3 74.8 - - - +
119D GLU* 1.3 61.7 + - - +
120D ILE* 4.2 14.1 - - + -
140D ARG 3.8 0.5 - - - +
141D LYS* 3.2 6.4 - - - -
142D TYR* 3.0 43.8 + - + +
144D LEU* 3.5 39.3 - - + -
153D VAL* 4.8 7.2 - - + -
165D VAL* 4.2 10.5 - - + -
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Residues in contact with GLU 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D THR 3.6 1.6 - - - +
111D VAL* 3.4 5.2 - - - -
112D LYS* 2.8 50.9 + - + +
117D VAL* 4.0 3.1 + - + +
118D VAL* 1.3 75.3 - - - +
120D ILE* 1.3 62.9 + - - +
121D THR* 4.0 16.6 + - + +
139D THR* 3.9 25.8 - - + +
140D ARG 3.5 3.4 - - - +
141D LYS* 4.2 22.2 + - + -
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Residues in contact with ILE 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D VAL* 5.5 0.7 - - + -
99D LEU* 4.5 14.4 - - + -
109D LEU* 5.1 2.2 - - + -
110D THR 3.4 9.2 - - - +
111D VAL* 4.2 8.7 - - + -
118D VAL* 4.2 12.3 - - + -
119D GLU* 1.3 77.8 - - - +
121D THR* 1.3 67.0 + - - +
138D PHE* 3.8 21.2 - - + -
139D THR* 3.3 2.9 - - - +
140D ARG* 2.8 44.0 + - + +
142D TYR* 3.8 30.5 - - + -
163D LEU* 3.7 24.9 - - + -
165D VAL* 3.9 23.6 - - + -
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Residues in contact with THR 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D GLU 3.8 0.5 - - - +
109D LEU* 3.4 5.3 - - - +
110D THR* 2.7 54.1 + - - +
119D GLU* 4.0 19.5 - - + +
120D ILE* 1.3 80.0 - - - +
122D GLY* 1.3 60.8 + - - +
138D PHE* 3.4 10.5 - - - -
139D THR* 3.5 26.2 - - + +
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Residues in contact with GLY 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D PHE* 3.6 9.6 - - - -
108D GLU 3.2 9.6 - - - -
109D LEU* 4.0 4.7 - - - -
121D THR* 1.3 76.4 - - - +
123D LYS* 1.3 64.1 + - - +
137D CYS* 3.3 3.3 - - - +
138D PHE* 3.1 49.8 + - - +
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Residues in contact with LYS 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D PHE* 3.5 5.5 - - - -
108D GLU* 3.1 29.3 + - - +
122D GLY* 1.3 75.6 - - - +
124D HIS* 1.3 65.9 + - - +
125D GLU* 4.1 19.2 + - - +
136D ARG 3.5 11.4 - - - +
137D CYS* 4.4 11.2 - - + -
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Residues in contact with HIS 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D HIS 3.6 18.4 + - - -
104D PHE* 3.6 22.7 - + + -
108D GLU* 3.3 32.5 - - - +
123D LYS* 1.3 75.9 - - - +
125D GLU* 1.3 83.5 + - - +
127D ARG* 3.6 19.8 + - + +
134D ILE* 3.3 24.9 - - + -
135D SER* 3.5 13.9 - - - -
136D ARG* 3.2 57.6 + - + +
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D GLU* 4.8 1.8 + - - -
123D LYS* 4.1 22.4 - - - +
124D HIS* 1.3 97.6 + - - +
126D GLU* 1.3 71.9 + - - +
127D ARG* 3.3 7.5 + - - +
135D SER* 3.9 4.0 - - - -
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Residues in contact with GLU 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B THR* 5.9 2.4 - - - +
139C THR* 5.1 5.7 - - - +
141C LYS* 2.9 49.1 + - - +
125D GLU* 1.3 79.6 + - - +
127D ARG* 1.3 62.7 + - - +
133D TYR* 3.9 29.1 - - + +
134D ILE* 3.6 13.0 - - - +
135D SER* 3.8 15.3 + - - +
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Residues in contact with ARG 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D HIS 3.2 24.9 + - - -
104D PHE* 4.8 0.6 - - - +
105D ALA* 4.9 4.2 - - - +
108D GLU* 2.5 37.0 + - - -
124D HIS* 3.6 21.9 + - + +
125D GLU 3.5 9.7 + - - +
126D GLU* 1.3 80.5 - - - +
128D GLN* 1.3 74.7 - - - +
129D ASP* 5.0 0.2 - - - +
132D GLY 3.4 1.0 - - - +
133D TYR* 3.3 7.6 - - - -
134D ILE* 2.8 35.7 + - - +
77J LEU* 5.1 19.5 - - - +
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Residues in contact with GLN 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B VAL 4.1 4.5 - - - +
112B LYS* 3.6 35.2 + - + +
113B THR* 2.9 45.9 + - - +
114B LYS* 5.3 3.2 - - - +
150B PRO 5.3 0.7 - - - +
127D ARG* 1.3 85.1 - - - +
129D ASP* 1.3 62.2 - - - +
132D GLY* 3.4 9.3 - - - +
133D TYR* 3.2 52.0 + - + +
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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