Contacts of the strand formed by residues 156 - 163 (chain A) in PDB entry 1GZH
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 156 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A GLY 3.7 10.8 - - - +
155A THR* 1.3 82.3 - - - +
157A VAL* 1.3 65.3 + - - +
158A ARG* 3.7 19.6 - - - +
204A GLU* 2.8 36.0 + - - -
217A VAL* 3.4 34.0 + - + +
218A VAL 3.5 10.8 - - - +
219A PRO* 4.8 6.5 - - + -
220A TYR 4.0 0.2 - - - +
256A THR 3.6 0.5 - - - +
257A LEU* 3.5 4.9 - - - -
258A GLU* 2.7 50.7 + - + +
259A ASP 4.6 6.3 + - - +
260A SER* 4.8 12.6 + - - +
261A SER 6.3 0.4 - - - -
262A GLY* 6.0 2.4 - - - +
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Residues in contact with VAL 157 (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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145A LEU* 3.5 26.2 - - + -
156A ARG* 1.3 76.4 - - - +
158A ARG* 1.3 60.4 + - - +
216A VAL 3.7 1.4 - - - +
217A VAL* 3.2 5.1 - - - -
218A VAL* 3.0 33.9 + - + +
219A PRO 5.1 0.2 - - - +
220A TYR* 3.9 23.3 - - + -
232A ILE* 3.5 26.7 - - + -
234A TYR* 3.9 6.8 + - - +
255A ILE* 3.8 26.7 - - + -
256A THR 3.4 4.7 - - - +
257A LEU* 3.9 10.3 - - + -
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Residues in contact with ARG 158 (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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156A ARG* 3.7 21.2 + - - +
157A VAL* 1.3 75.8 - - - +
159A ALA* 1.3 65.5 + - - +
160A MET* 5.0 9.6 - - + +
206A LEU* 3.7 23.6 - - - +
215A SER* 2.6 46.2 + - - -
216A VAL 3.5 5.2 - - - +
217A VAL* 3.9 23.0 - - + +
254A ILE 3.6 1.0 - - - +
255A ILE* 3.3 7.8 - - - +
256A THR* 2.9 47.1 + - - +
258A GLU* 2.8 40.6 + - - +
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Residues in contact with ALA 159 (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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158A ARG* 1.3 76.0 - - - +
160A MET* 1.3 60.8 + - - +
195A ILE* 4.6 5.8 - - + +
215A SER* 3.3 5.9 - - - -
216A VAL* 2.9 39.8 + - + +
234A TYR* 3.6 38.4 - - + +
253A THR* 4.6 6.1 - - + -
254A ILE 3.5 4.5 - - - -
255A ILE* 3.8 8.7 - - + -
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Residues in contact with MET 160 (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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98A PRO* 3.9 31.2 - - - -
158A ARG* 5.0 9.9 - - + -
159A ALA* 1.3 75.9 - - - +
161A ALA* 1.3 71.9 + - - +
162A ILE* 4.6 2.7 - - + -
195A ILE* 4.3 6.4 - - - +
208A ASP* 5.9 2.2 - - + -
213A ARG* 3.5 27.4 - - + +
214A HIS 3.3 25.1 - - - +
215A SER* 3.5 17.5 - - - +
253A THR* 3.5 0.7 - - - +
254A ILE* 2.7 51.4 + - + +
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Residues in contact with ALA 161 (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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160A MET* 1.3 79.0 - - - +
162A ILE* 1.3 69.8 + - - +
173A VAL* 3.7 34.0 + - + +
194A LEU* 4.5 3.6 - - + -
195A ILE* 3.9 20.1 - - + +
213A ARG* 4.1 6.1 + - - -
214A HIS 4.7 2.9 + - - +
251A ILE* 4.2 15.5 - - + -
252A LEU 3.1 10.3 - - - +
253A THR* 4.5 0.4 - - - +
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Residues in contact with ILE 162 (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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97A VAL* 5.1 8.1 - - + -
98A PRO* 4.1 33.9 - - + +
100A GLN* 4.1 17.9 - - + +
160A MET* 4.6 4.7 - - + -
161A ALA* 1.3 81.4 - - - +
163A TYR* 1.3 66.4 + - - +
169A MET* 5.2 4.3 - - - +
173A VAL* 3.6 9.4 - - - -
213A ARG* 3.9 17.7 - - - +
251A ILE* 3.2 3.6 - - - +
252A LEU* 2.8 49.4 + - + -
254A ILE* 3.2 31.2 - - + -
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Residues in contact with TYR 163 (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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100A GLN* 5.7 0.2 - - - +
162A ILE* 1.3 82.3 - - - +
164A LYS* 1.3 63.7 + - - +
165A GLN* 4.5 0.9 - - + +
168A HIS* 3.7 37.7 - - + +
169A MET* 3.3 22.1 - - - +
171A GLU* 3.7 20.9 + - + -
172A VAL 4.1 5.0 + - - -
173A VAL* 3.3 36.8 - - + +
174A ARG 4.4 2.1 + - - -
245A GLY 3.8 1.4 + - - -
246A MET* 3.0 31.2 + - - +
249A ARG* 3.3 55.1 + - + -
250A PRO 3.5 9.0 - - - +
251A ILE* 3.5 18.6 - - + -
1845B ASN* 4.8 0.5 + - - -
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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