Contacts of the strand formed by residues 124 - 131 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121D PRO* 4.0 18.9 - - - +
122D GLY* 3.7 35.3 + - - +
123D CYS* 1.3 77.8 + - - +
125D LEU* 1.3 70.3 + - - +
126D ARG* 3.6 18.8 + - - +
150D CYS* 3.6 1.4 - - - -
151D SER 3.2 29.8 + - - +
216D CYS* 3.7 9.9 - - - -
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Residues in contact with LEU 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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124D ARG* 1.3 80.8 - - - +
126D ARG* 1.3 68.4 + - - +
148D ARG* 3.9 24.0 - - + -
149D PHE 3.6 6.3 - - - +
213D ALA* 3.7 35.4 - - + +
214D THR* 3.9 18.8 - - - +
215D ALA* 4.0 5.8 - - - +
216D CYS* 3.5 27.8 - - - +
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Residues in contact with ARG 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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177C PRO* 3.9 10.3 - - + +
178C PRO* 3.5 34.1 + - - +
121D PRO* 3.2 26.5 - - - +
122D GLY 3.0 18.5 + - - -
124D ARG* 3.7 20.5 + - - +
125D LEU* 1.3 78.5 - - - +
127D SER* 1.3 61.8 + - - +
128D GLN* 5.7 0.7 - - - +
148D ARG* 3.1 8.7 - - - +
149D PHE* 2.7 63.4 + - + +
151D SER* 3.0 44.9 + - - +
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Residues in contact with SER 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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126D ARG* 1.3 78.9 - - - +
128D GLN* 1.3 71.7 + - - +
146D ARG* 4.2 16.8 - - - -
147D PHE 3.6 6.1 + - - -
148D ARG* 3.8 27.7 + - - +
149D PHE* 4.9 0.4 - - - -
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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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173C ALA 4.3 2.3 - - - +
174C LEU* 3.5 25.9 - - + +
175C ARG* 2.8 57.2 + - - +
177C PRO* 4.9 4.4 - - - +
126D ARG* 5.7 1.2 - - + +
127D SER* 1.3 86.2 + - - +
129D LEU* 1.3 68.4 + - - +
130D VAL* 3.6 1.0 + - - +
146D ARG* 4.5 4.0 - - - -
147D PHE* 2.8 35.6 + - - +
149D PHE* 3.7 20.8 - - + -
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Residues in contact with LEU 129 (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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170B THR* 3.7 20.9 - - + +
171B LEU* 3.4 38.4 - - + -
173C ALA 4.9 3.8 - - - +
128D GLN* 1.3 74.1 - - - +
130D VAL* 1.3 63.8 + - - +
131D PRO* 4.8 0.9 - - - +
144D LEU* 4.6 24.8 - - + +
145D VAL* 3.4 4.3 - - - +
146D ARG* 3.6 43.5 - - + +
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Residues in contact with VAL 130 (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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168C LEU* 3.9 26.9 - - + -
173C ALA 4.2 10.1 - - - +
174C LEU* 3.7 30.3 - - + -
128D GLN* 4.1 5.6 - - + +
129D LEU* 1.3 81.8 - - - +
131D PRO* 1.3 73.8 - - + +
132D VAL 3.3 0.2 + - - -
135D LEU* 4.3 4.5 - - + -
144D LEU* 3.3 6.5 - - - -
145D VAL* 2.9 43.7 + - + +
147D PHE* 3.7 20.4 - - + -
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Residues in contact with PRO 131 (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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173C ALA* 4.3 18.4 - - + +
129D LEU 4.8 0.4 - - - +
130D VAL* 1.3 87.8 - - + +
132D VAL* 1.3 66.2 + - - +
133D ARG* 4.1 11.7 - - + +
134D ALA* 2.9 26.1 + - + +
135D LEU* 3.8 6.4 + - - +
143D GLU 3.8 7.2 - - - +
144D LEU* 3.9 14.3 - - + -
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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