Contacts of the strand formed by residues 265 - 269 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88R ARG 3.0 4.2 + - - -
89R HIS* 3.2 11.9 - - + +
90R MET* 2.8 28.6 + - - +
211R ILE* 3.3 37.5 - - + -
220R PHE* 3.7 27.8 - - + -
221R VAL* 4.8 0.2 - - - -
222R SER* 3.4 37.9 - - - -
247R LYS* 3.2 21.1 - - + +
248R ASP* 5.0 4.5 - - - -
249R ALA* 4.0 8.3 - - - -
263R GLY* 3.3 26.2 - - - -
264R PHE* 1.3 79.0 - - - +
266R CYS* 1.3 66.6 + - - +
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Residues in contact with CYS 266 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89R HIS* 3.4 9.8 + - - -
90R MET* 4.8 1.6 - - - +
93R PHE* 3.3 20.9 - - - +
94R PRO 3.4 22.2 - - - +
95R MET* 3.9 7.2 - - - +
246R SER 5.3 0.2 - - - -
247R LYS* 2.7 31.1 + - - +
248R ASP 3.6 21.8 - - - -
249R ALA* 3.9 13.0 - - - -
251R ARG* 3.8 17.5 - - - -
252R LEU* 4.9 2.0 - - - -
265R PHE* 1.3 75.6 - - - +
267R GLU* 1.3 62.7 + - - +
268R ARG 3.9 0.2 + - - -
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Residues in contact with GLU 267 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R ILE* 5.5 0.3 - - - +
89R HIS* 4.3 12.3 - - + -
90R MET 4.8 0.4 + - - -
91R ASN* 3.2 39.5 - - - +
92R GLY* 2.9 20.5 + - - -
93R PHE 2.7 17.3 + - - +
94R PRO* 3.4 4.4 - - + +
95R MET* 2.7 32.3 + - - +
205R ALA* 3.8 23.1 - - + +
206R GLN 4.7 1.1 - - - +
207R SER* 3.4 31.2 - - - -
265R PHE 3.9 0.6 + - - -
266R CYS* 1.3 71.8 - - - +
268R ARG* 1.3 67.5 + - - +
269R ARG* 5.6 0.8 - - + +
528R PRO 4.4 2.6 - - - +
529R GLU* 5.3 0.9 - - - +
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Residues in contact with ARG 268 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89R HIS* 5.3 1.6 + - - -
95R MET* 3.7 11.0 - - + -
205R ALA* 3.8 1.2 - - - -
206R GLN* 3.0 75.7 + - + +
209R ASP* 3.5 23.3 + - + +
225R ARG* 2.4 49.5 - - - +
247R LYS* 4.3 10.0 - - - +
266R CYS 3.9 1.4 + - - -
267R GLU* 1.3 75.2 - - - +
269R ARG* 1.3 72.6 + - - +
270R ARG* 4.2 21.6 - - - +
667R GTP 2.9 27.1 + - - -
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Residues in contact with ARG 269 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32R PHE* 3.4 29.7 - - - -
33R LYS 4.5 9.5 + - - -
94R PRO* 3.5 40.4 - - + +
95R MET* 3.6 30.2 + - + +
98R ALA* 4.4 13.3 - - + +
99R THR* 5.3 2.3 + - - +
203R TYR* 3.5 55.5 + - + +
204R ARG 3.8 4.0 - - - +
205R ALA* 4.8 6.3 - - + +
267R GLU* 3.7 1.3 + - + +
268R ARG* 1.3 82.8 + - - +
270R ARG* 1.3 60.9 + - - +
271R THR* 4.0 5.9 + - - +
369R ALA 4.1 2.0 + - - -
370R 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