Contacts of the strand formed by residues 191 - 196 (chain A) in PDB entry 1ZQQ
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 MET 191 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ILE* 4.5 2.8 - - + +
155A MET* 3.7 33.1 - - + +
158A MET* 4.1 15.5 - - + +
159A GLN* 3.8 20.6 - - + +
162A VAL* 3.9 15.9 - - - -
177A VAL* 3.6 28.5 - - + -
190A ASP* 1.3 70.6 - - - +
192A ASP* 1.3 60.1 - - - +
193A VAL* 3.8 18.2 - - + -
223A PHE* 4.9 0.9 - - - -
239A CYS* 5.7 0.2 - - - -
254A ARG 3.2 9.1 + - - -
255A ILE* 3.0 29.2 - - + +
256A ASP 3.0 26.0 + - - +
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Residues in contact with ASP 192 (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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176A THR 3.4 1.0 - - - +
177A VAL* 2.9 12.5 - - - +
178A CYS* 2.9 43.4 + - + +
179A GLY* 6.3 0.7 - - - -
190A ASP* 2.6 31.2 + - - +
191A MET* 1.3 71.7 - - - +
193A VAL* 1.3 57.3 + - - +
194A LEU* 3.8 7.4 + - + +
256A ASP* 3.6 17.9 - - - +
258A ARG* 4.1 10.3 + - - +
272A PHE* 6.0 6.4 - - + -
340A MN 2.7 23.2 + - - -
7P G 3.9 4.0 - - - +
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Residues in contact with VAL 193 (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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162A VAL* 4.4 15.9 - - + -
166A VAL* 5.7 1.3 - - + -
175A ALA* 4.1 24.0 - - + -
176A THR 3.2 4.9 - - - +
177A VAL* 4.0 10.3 - - + -
191A MET* 3.8 31.2 - - + -
192A ASP* 1.3 70.7 - - - +
194A LEU* 1.4 60.9 - - - +
195A LEU* 4.8 0.9 - - + -
255A ILE* 4.2 11.0 - - + -
256A ASP 2.8 19.5 + - - +
257A ILE* 3.4 23.0 - - + +
258A ARG* 3.3 21.7 + - - +
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Residues in contact with LEU 194 (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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175A ALA* 3.2 2.6 - - - +
176A THR 2.4 38.9 + - - +
178A CYS* 3.5 28.5 - - + -
192A ASP* 3.8 6.0 + - + +
193A VAL* 1.4 61.7 - - - +
195A LEU* 1.3 66.8 + - - +
258A ARG* 3.7 31.2 - - + -
260A ILE* 4.7 12.6 - - + -
265A TYR* 2.8 18.6 + - + +
268A GLY* 3.8 8.1 - - - +
269A VAL* 3.7 22.9 - - + -
272A PHE* 3.3 36.3 - - + -
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Residues in contact with LEU 195 (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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166A VAL* 4.9 7.2 - - + -
173A TYR* 3.8 20.9 - - + -
174A ILE 3.4 16.6 - - - +
175A ALA* 4.2 9.6 - - + +
193A VAL* 4.8 0.2 - - + -
194A LEU* 1.3 80.7 - - - +
196A THR* 1.3 75.8 - - - +
210A LEU 5.0 1.1 - - - +
211A LEU* 4.8 6.1 - - + -
214A VAL* 4.4 25.4 - - + -
257A ILE* 4.4 21.5 - - + -
258A ARG 3.2 14.5 + - - +
259A LEU* 2.8 19.9 - - + +
260A ILE* 2.4 39.5 + - - +
265A TYR* 3.5 4.6 - - - -
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Residues in contact with THR 196 (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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173A TYR* 3.5 1.6 - - - -
174A ILE* 3.0 55.4 + - + -
195A LEU* 1.3 80.7 - - - +
197A HIS* 1.3 76.6 + - - +
259A LEU* 3.8 3.6 - - - -
260A ILE 2.6 18.8 + - - -
262A LYS* 2.8 27.6 + - + -
265A TYR* 3.2 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