Contacts of the strand formed by residues 231 - 234 (chain A) in PDB entry 1QAP
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 ILE 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ARG* 6.4 0.2 - - - +
174A HIS* 5.7 5.2 - - + -
210A PRO* 4.6 14.6 - - + -
211A VAL 3.2 4.7 + - - +
212A GLU* 3.0 57.4 - - + +
213A VAL 3.1 4.9 + - - -
229A ALA* 3.3 2.0 - - - +
230A ASP* 1.3 95.6 - - + +
232A ILE* 1.3 70.0 + - - +
254A ARG* 3.2 28.5 - - + +
255A LEU 5.0 0.4 - - - -
256A GLU* 4.5 11.2 - - + +
276A PHE* 5.2 10.1 - - + -
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Residues in contact with ILE 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLU* 4.3 0.9 - - - -
213A VAL 3.5 4.9 - - - +
215A VAL* 3.5 27.4 - - + -
221A LEU* 3.7 26.0 - - + -
224A ALA* 3.7 27.8 - - + +
225A LEU* 3.9 22.4 - - + +
229A ALA* 4.4 14.4 - - + +
231A ILE* 1.3 81.1 - - - +
233A MET* 1.3 62.1 + - - +
234A LEU* 3.7 10.8 - - + +
249A VAL* 5.4 2.5 - - + -
252A GLN* 6.1 1.8 - - + +
254A ARG 2.6 12.3 + - - +
255A LEU* 3.2 17.1 - - + +
256A GLU 3.1 17.9 + - - -
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Residues in contact with MET 233 (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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183A LEU* 3.7 34.3 - - + -
185A LYS* 5.6 0.2 - - - -
212A GLU* 3.2 22.4 + - + +
213A VAL 3.3 6.0 + - - +
214A GLU* 3.6 29.2 - - + +
215A VAL* 2.9 28.4 + - - +
232A ILE* 1.3 73.5 - - - +
234A LEU* 1.3 72.0 + - - +
235A ASP* 5.4 1.3 - - - -
256A GLU* 2.9 35.7 - - + +
258A SER* 4.3 21.5 - - - +
300A NTM 4.9 7.4 - - + -
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Residues in contact with LEU 234 (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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215A VAL* 3.6 5.4 - - + -
221A LEU* 4.7 5.4 - - + -
232A ILE* 3.7 26.5 - - + +
233A MET* 1.3 85.5 - - - +
235A ASP* 1.3 60.3 + - - +
236A ASN 3.8 2.3 + - - -
237A PHE* 3.6 48.0 - - + -
242A MET* 4.4 11.7 - - + -
245A ALA* 4.2 15.5 - - + -
255A LEU* 4.0 19.1 - - + -
256A GLU 3.1 9.1 + - - +
257A VAL* 4.4 21.1 - - + +
258A SER* 4.1 15.4 + - - -
274A VAL* 5.1 1.6 - - + -
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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