Contacts of the strand formed by residues 264 - 267 (chain A) in PDB entry 2IHU
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 ASN 264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A VAL 4.0 3.7 - - - +
249A THR* 5.8 3.3 - - - +
255A GLY 5.6 2.0 - - - +
257A LEU* 3.5 26.1 + - + +
258A PRO 3.1 25.4 + - - +
259A VAL* 4.2 7.1 - - - +
260A GLY 4.6 3.1 - - - +
261A HIS* 3.0 21.2 + - + +
263A LEU* 1.3 73.9 - - - +
265A TYR* 1.3 57.9 + - - +
266A GLY* 3.2 17.7 + - - -
365A ARG* 3.0 19.6 + - - -
423A ALA 5.3 2.0 + - - -
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Residues in contact with TYR 265 (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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246A PRO* 3.6 27.8 - - + -
247A VAL 3.0 16.5 + - - +
248A ILE* 3.8 13.9 - - + -
262A GLU 3.4 18.4 - - - -
263A LEU* 3.0 13.2 + - - +
264A ASN* 1.3 72.9 - - - +
266A GLY* 1.3 59.3 + - - +
284A MET* 3.1 26.6 - - - +
358A ARG* 3.2 30.0 + - - +
359A HIS* 2.6 41.3 + + - -
361A ILE* 3.6 46.9 + - + +
362A GLU* 5.7 0.8 + - - -
364A LEU* 5.2 0.5 - - - +
365A ARG* 3.5 16.6 - - - -
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Residues in contact with GLY 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A VAL 4.0 0.8 + - - +
248A ILE* 3.3 10.7 - - - +
249A THR* 3.0 25.8 + - - +
254A LYS* 5.7 0.7 - - - -
264A ASN* 3.2 17.1 + - - -
265A TYR* 1.3 80.0 - - - +
267A ALA* 1.3 60.5 + - - -
284A MET* 4.7 1.3 - - - -
368A ILE* 6.5 1.3 - - - -
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Residues in contact with ALA 267 (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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249A THR* 3.3 23.3 - - - +
250A THR 4.0 3.6 - - - +
254A LYS* 3.7 21.3 - - + +
266A GLY* 1.3 75.3 - - - -
268A VAL* 1.3 63.4 + - - +
269A THR 4.1 0.5 + - - -
272A MET* 4.0 15.9 - - - +
284A MET* 4.4 3.4 - - - +
418A VAL* 3.8 29.8 + - + +
419A LEU* 4.2 9.4 - - - +
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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