Contacts of the strand formed by residues 133 - 143 (chain A) in PDB entry 2GH1
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 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A LYS* 3.8 9.3 - - - +
107A TYR* 3.5 11.4 - - + +
108A ASP 4.2 0.7 - - - +
109A ILE 4.8 0.2 - - - -
110A ALA* 3.3 27.8 - - + +
129A MSE 3.3 16.4 - - - +
130A ILE* 2.9 18.9 + - - +
131A HIS* 4.2 1.7 - - - +
132A SER* 1.3 80.7 - - - +
134A LYS* 1.3 71.1 + - - +
135A LYS* 4.0 3.6 + - - +
137A GLY* 3.6 16.2 - - - -
138A LYS 3.8 11.4 - - - +
139A ILE* 4.9 2.2 - - + -
291A ILE* 3.4 32.7 - - + +
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Residues in contact with LYS 134 (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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42A HIS* 5.8 3.0 + - - +
106A LYS* 3.7 40.3 + - + +
107A TYR 2.9 20.6 + - - +
108A ASP* 2.9 33.8 + - - +
132A SER 4.0 1.0 + - - -
133A VAL* 1.3 77.2 - - - +
135A LYS* 1.3 64.5 + - - +
136A GLY 5.4 0.2 - - - -
137A GLY* 2.7 32.8 + - - +
291A ILE* 4.0 2.9 - - - +
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Residues in contact with LYS 135 (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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133A VAL 5.2 2.5 + - - +
134A LYS* 1.3 81.2 - - - +
136A GLY* 1.3 59.4 + - - +
137A GLY 3.4 0.2 + - - -
291A ILE* 4.1 15.6 - - + +
292A GLU 3.2 24.2 - - - +
293A CYS* 3.5 19.6 - - + +
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Residues in contact with GLY 136 (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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134A LYS* 5.4 0.2 - - - -
135A LYS* 1.3 72.7 - - - +
137A GLY* 1.3 64.1 + - - +
138A LYS* 4.6 9.5 + - - +
290A GLU* 4.6 11.0 - - - +
291A ILE 2.9 18.5 + - - -
293A CYS* 3.6 19.3 - - - +
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Residues in contact with GLY 137 (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 ASP* 3.2 16.2 - - - -
133A VAL* 3.6 8.3 - - - -
134A LYS* 2.7 22.2 + - - +
135A LYS 3.1 1.0 + - - -
136A GLY* 1.3 81.9 - - - +
138A LYS* 1.3 64.4 + - - -
290A GLU* 3.3 4.9 - - - +
291A ILE 2.9 24.6 + - - -
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Residues in contact with LYS 138 (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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35A TRP* 4.2 31.4 - - + -
37A ILE* 4.5 11.5 - - + +
41A VAL* 5.3 6.5 - - - +
108A ASP* 2.9 9.7 + - - +
109A ILE* 3.2 30.3 - - + +
110A ALA 3.1 22.1 + - - -
133A VAL* 3.8 8.2 - - - +
136A GLY 4.6 8.1 + - - +
137A GLY* 1.3 78.6 - - - +
139A ILE* 1.3 62.0 + - - +
140A ILE* 4.2 15.9 - - + -
288A PHE* 5.9 0.7 - - + -
289A GLY 3.2 11.7 - - - +
290A GLU* 4.4 18.4 - - + -
291A ILE* 4.9 0.9 - - - +
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Residues in contact with ILE 139 (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 ALA* 3.3 14.4 - - + +
126A LEU* 3.9 26.2 - - + -
129A MSE 4.1 21.1 - - + -
130A ILE* 3.5 36.8 - - + +
133A VAL* 4.9 1.6 - - + -
138A LYS* 1.3 75.8 - - - +
140A ILE* 1.3 62.2 + - - +
141A CYS* 4.1 13.7 - - - -
194A LEU* 4.4 14.3 - - + +
199A VAL* 4.4 4.5 - - + -
288A PHE* 3.0 23.0 - - - +
289A GLY* 3.0 21.5 + - - +
291A ILE* 4.5 4.9 - - + -
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Residues in contact with ILE 140 (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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35A TRP* 3.6 40.8 - - + +
57A LEU* 6.1 0.7 - - + -
109A ILE* 3.7 12.6 - - + -
110A ALA 2.9 6.1 + - - +
111A ILE* 3.0 49.2 - - + +
112A CYS 3.3 2.4 + - - -
138A LYS* 4.2 18.2 - - + -
139A ILE* 1.3 77.9 - - - +
141A CYS* 1.3 65.3 + - - +
142A PHE* 3.4 27.4 - - + -
286A ILE* 4.1 7.6 - - + -
287A THR 3.5 4.0 - - - +
288A PHE* 3.4 20.9 - - + -
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Residues in contact with CYS 141 (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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112A CYS* 3.8 16.2 - - - -
116A LEU* 3.8 25.1 - - + -
126A LEU* 3.8 17.9 - - - -
129A MSE 4.6 0.9 - - - -
139A ILE* 4.1 13.7 - - - -
140A ILE* 1.3 79.6 - - - +
142A PHE* 1.3 62.3 + - - +
143A GLU* 3.7 5.6 + - + -
190A ILE* 4.0 21.2 - - + +
194A LEU* 5.2 1.6 - - - -
285A LYS 3.4 4.5 - - - +
286A ILE* 3.5 2.4 - - - +
287A THR* 2.7 39.4 + - - +
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Residues in contact with PHE 142 (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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22A TYR* 3.4 34.3 - + - +
27A VAL* 5.7 4.9 - - + -
30A LEU* 5.0 2.7 - - + -
35A TRP* 4.1 14.8 - + - -
53A LEU* 4.1 24.7 - - + -
56A VAL* 5.9 2.2 - - + -
57A LEU* 4.7 15.9 - - + -
111A ILE* 5.3 0.2 - - + -
112A CYS 2.8 16.8 + - - +
113A HIS* 3.2 22.3 - + + -
114A ALA 2.7 33.1 + - - -
140A ILE* 3.4 26.7 - - + -
141A CYS* 1.3 76.3 - - - +
143A GLU* 1.3 55.2 + - - +
284A MSE 4.0 6.6 - - + +
285A LYS 3.7 4.7 - - - -
286A ILE* 3.7 32.5 - - + -
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Residues in contact with GLU 143 (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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112A CYS* 3.6 10.9 - - - -
114A ALA* 3.2 6.1 + - - -
115A PHE* 2.6 27.8 + - - -
116A LEU* 2.9 28.8 + - + -
117A LEU* 3.1 30.0 + - - +
141A CYS* 3.7 5.6 - - + -
142A PHE* 1.3 75.8 - - - +
144A PRO* 1.3 68.7 - - + +
186A ILE* 3.7 5.4 - - + +
187A GLY* 3.8 17.7 - - - -
190A ILE* 4.1 17.3 - - + -
284A MSE 3.8 3.6 - - - -
285A LYS* 3.0 36.3 + - - +
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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