Contacts of the strand formed by residues 124 - 131 (chain C) in PDB entry 2GH0
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 ARG 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120C ASP* 4.0 36.4 - - - +
122C GLY 3.1 9.4 + - - +
123C CYS* 1.3 77.4 - - - +
125C LEU* 1.3 79.2 + - - +
126C ARG* 3.5 32.3 + - - +
150C CYS* 3.5 2.1 - - - -
151C SER 3.1 28.1 + - - +
216C CYS* 3.6 11.7 - - - -
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Residues in contact with LEU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ARG* 1.3 97.0 + - - +
126C ARG* 1.3 60.9 - - - +
148C ARG* 3.9 28.9 - - + +
149C PHE 3.6 3.6 - - - +
213C ALA* 3.7 39.9 - - + +
214C THR* 3.7 23.3 - - - +
215C ALA* 5.0 2.7 - - - -
216C CYS* 3.5 19.6 - - + +
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Residues in contact with ARG 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C ASP 2.9 29.1 + - - +
121C PRO 3.9 3.4 - - - -
122C GLY 3.3 8.7 + - - -
124C ARG* 3.5 30.7 + - - +
125C LEU* 1.3 78.1 - - - +
127C SER* 1.3 60.8 + - - +
148C ARG* 3.0 8.9 - - - +
149C PHE* 2.9 60.3 + - + +
151C SER* 2.8 46.8 + - - +
177D PRO* 3.9 9.6 - - + +
178D PRO* 3.6 34.2 + - - +
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Residues in contact with SER 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C LEU* 6.2 0.2 - - - -
126C ARG* 1.3 76.8 - - - +
128C GLN* 1.3 63.5 + - - +
146C ARG* 4.1 18.0 + - - +
147C PHE 3.6 5.2 + - - -
148C ARG* 3.7 32.2 + - - +
149C PHE* 4.8 2.2 - - - -
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Residues in contact with GLN 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C SER* 1.3 77.1 + - - +
129C LEU* 1.3 75.0 + - + +
130C VAL* 3.6 3.9 + - + +
146C ARG* 4.3 3.1 - - - -
147C PHE* 2.8 39.5 + - - +
149C PHE* 4.7 4.7 - - + -
173D ALA 3.2 22.1 + - - -
174D LEU* 3.4 23.4 - - + +
175D ARG* 3.0 52.5 + - - +
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Residues in contact with LEU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A MET* 6.2 0.2 - - - -
170A THR* 3.7 30.3 - - + +
171A LEU* 3.9 27.1 - - + -
128C GLN* 1.3 85.8 + - + +
130C VAL* 1.3 64.2 + - - +
131C PRO* 4.8 0.9 - - - +
144C LEU* 3.8 32.7 - - + +
145C VAL 3.4 15.0 - - - -
146C ARG* 3.8 14.1 - - + +
173D ALA 5.0 0.3 - - - +
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Residues in contact with VAL 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C GLN* 3.9 8.3 - - + +
129C LEU* 1.3 79.2 - - - +
131C PRO* 1.3 78.2 - - + +
135C LEU* 4.2 7.9 - - + -
144C LEU* 3.2 6.4 - - - -
145C VAL* 2.8 44.0 + - + +
147C PHE* 3.8 20.0 - - + -
168D LEU* 3.9 24.2 - - + -
173D ALA 3.8 12.6 - - - +
174D LEU* 3.8 28.7 - - + -
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Residues in contact with PRO 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C LEU 4.8 0.9 - - - +
130C VAL* 1.3 92.7 - - + +
132C VAL* 1.3 64.5 + - - +
133C ARG* 4.0 12.8 - - + +
134C ALA* 3.0 29.3 + - + +
135C LEU* 3.9 2.6 + - - +
143C GLU 3.8 2.7 - - - +
144C LEU* 3.7 22.4 - - + -
173D ALA* 4.5 9.6 - - + +
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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