Contacts of the strand formed by residues 265 - 269 (chain P) in PDB entry 1HI0
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 265 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88P ARG 3.0 4.6 + - - -
89P HIS* 3.2 11.9 - - - +
90P MET* 2.8 28.8 + - - +
211P ILE* 3.3 38.4 - - + -
220P PHE* 3.7 27.1 - - + -
222P SER* 3.4 37.7 - - - -
247P LYS* 3.2 20.0 - - + +
248P ASP* 5.0 3.8 - - - -
249P ALA* 4.0 8.1 - - - -
263P GLY* 3.3 26.5 - - - -
264P PHE* 1.3 80.2 - - - +
266P CYS* 1.3 66.8 + - - +
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Residues in contact with CYS 266 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89P HIS* 3.4 9.9 + - - -
90P MET* 4.8 1.3 - - - +
93P PHE* 3.3 20.4 - - - +
94P PRO 3.4 21.8 - - - +
95P MET* 3.9 7.4 - - - +
246P SER 5.3 0.4 - - - -
247P LYS* 2.7 30.9 + - - +
248P ASP 3.6 21.5 - - - -
249P ALA* 3.9 13.5 - - - -
251P ARG* 3.8 17.7 - - - -
252P LEU* 4.9 2.2 - - - -
265P PHE* 1.3 76.2 - - - +
267P GLU* 1.3 64.4 + - - +
268P ARG 3.9 0.2 + - - -
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Residues in contact with GLU 267 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P ILE* 5.5 0.5 - - - +
89P HIS* 4.3 12.8 - - + -
90P MET 4.8 0.4 + - - -
91P ASN* 3.2 39.6 - - - +
92P GLY* 2.9 21.4 + - - -
93P PHE 2.7 16.1 + - - +
94P PRO* 3.4 3.8 - - + +
95P MET* 2.7 32.5 + - - +
205P ALA* 3.8 22.7 - - + +
206P GLN 4.7 0.9 - - - +
207P SER* 3.4 31.8 - - - -
265P PHE 3.9 0.6 + - - -
266P CYS* 1.3 72.7 - - - +
268P ARG* 1.3 68.5 + - - +
269P ARG* 5.6 0.7 - - + -
528P PRO 4.4 2.6 - - - +
529P GLU* 5.3 0.9 - - - +
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Residues in contact with ARG 268 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89P HIS* 5.3 1.4 + - - -
95P MET* 3.7 11.7 - - + -
205P ALA* 3.8 1.4 - - - -
206P GLN* 3.0 76.4 + - + +
209P ASP* 3.5 23.4 + - + +
225P ARG* 2.4 49.5 - - - +
247P LYS* 4.3 10.6 - - - +
266P CYS 3.9 1.2 + - - -
267P GLU* 1.3 74.9 - - - +
269P ARG* 1.3 72.7 + - - +
270P ARG* 4.2 21.4 - - - +
667P GTP 2.9 28.3 + - - -
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Residues in contact with ARG 269 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32P PHE* 3.4 29.9 - - - -
33P LYS 4.5 9.5 + - - -
94P PRO* 3.5 40.2 - - + +
95P MET* 3.6 30.0 + - + +
98P ALA* 4.4 13.5 - - + +
99P THR* 5.3 1.9 + - - +
203P TYR* 3.5 55.7 + - + +
204P ARG 3.8 3.8 - - - +
205P ALA* 4.8 7.0 - - + +
267P GLU* 5.1 0.7 - - + -
268P ARG* 1.3 82.3 + - - +
270P ARG* 1.3 63.0 + - - +
271P THR* 4.0 6.1 + - - +
369P ALA 4.1 2.2 + - - -
370P PRO 4.0 11.7 + - - -
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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