Contacts of the strand formed by residues 193 - 197 (chain A) in PDB entry 1QX3
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 PHE 193 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A THR* 3.7 17.7 - - - -
143A PHE* 3.4 29.8 - - + -
144A ARG* 3.9 4.3 - - + -
156A LYS* 3.4 28.3 - - + -
158A PHE* 3.6 33.0 - + - -
189A VAL 3.8 17.7 - - - -
190A ASP* 3.5 24.2 - - - +
191A ALA 3.3 6.0 - - - -
192A ASP* 1.3 79.6 - - - +
194A LEU* 1.3 61.0 + - - +
195A TYR* 3.2 39.7 - + + +
266A VAL 4.3 0.2 - - - +
268A MET* 2.8 29.3 + - + +
269A LEU* 3.4 4.7 + - - -
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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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156A LYS 2.8 11.6 + - - +
157A LEU* 4.3 12.1 - - + -
158A PHE* 2.8 29.4 + - - +
159A ILE* 6.0 0.7 - - + -
193A PHE* 1.3 76.6 - - - +
195A TYR* 1.3 66.1 + - - +
196A ALA* 3.8 22.4 - - + +
232A PHE* 3.5 37.7 - - + -
233A MET* 4.1 19.1 - - - -
236A LEU* 4.2 5.6 - - + -
265A ILE* 5.2 2.0 - - + -
266A VAL 3.6 8.3 - - - +
267A SER* 4.6 2.9 - - - +
269A LEU* 3.3 36.1 - - + -
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Residues in contact with TYR 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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137A LYS* 5.9 3.9 - - + +
140A THR* 3.7 31.2 + - + -
158A PHE* 3.4 18.6 - + + +
160A ILE* 4.7 4.3 - - + -
190A ASP* 3.9 13.9 + - - -
193A PHE* 3.2 44.1 - + + +
194A LEU* 1.3 76.1 - - - +
196A ALA* 1.3 60.6 + - - +
197A TYR* 3.6 31.3 + + + -
264A CYS 3.5 3.5 - - - +
266A VAL* 2.7 61.6 + - + +
268A MET* 3.7 23.2 - - + +
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Residues in contact with ALA 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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158A PHE 2.8 12.5 + - - +
159A ILE* 3.4 13.7 - - + -
160A ILE* 2.9 25.7 + - - -
194A LEU* 3.8 16.4 - - + +
195A TYR* 1.3 72.2 - - - +
197A TYR* 1.3 62.4 + - - +
215A PHE* 3.8 18.7 - - + -
219A LEU* 5.9 0.4 - - + -
232A PHE* 5.3 0.7 - - + -
236A LEU* 4.3 20.4 - - + -
264A CYS 4.0 2.7 - - - -
265A ILE* 4.8 5.8 - - + +
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Residues in contact with TYR 197 (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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125A GLY* 6.0 2.0 - - - -
136A LEU* 4.2 25.1 - - + +
160A ILE* 3.8 30.0 - - + +
162A ALA 5.9 0.2 - - - -
164A ARG* 3.4 46.6 + - + +
195A TYR* 3.6 33.7 - - + +
196A ALA* 1.3 74.1 - - - +
198A SER* 1.3 60.8 + - - +
199A THR 3.5 15.9 - - - +
215A PHE* 3.8 3.6 - - - -
263A PRO* 3.4 6.9 - - - +
264A CYS 2.9 34.8 + - - +
265A ILE* 5.7 0.2 - - - +
266A VAL* 3.6 25.8 - - + -
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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