Contacts of the strand formed by residues 264 - 269 (chain A) in PDB entry 4H3I
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 264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A VAL* 5.0 0.7 - - + -
263A ILE* 1.3 74.6 - - - +
265A VAL* 1.3 62.7 + - - +
266A ARG 3.7 17.0 - - - +
267A VAL* 3.9 16.8 - - + -
278A CYS 4.0 4.0 - - - +
281A TYR* 4.1 12.0 - - + +
282A ASN* 2.8 33.8 + - - +
286A SER* 4.0 13.2 - - - +
297A LEU* 5.9 1.3 - - + -
346A LEU* 4.3 23.6 - - + -
347A TYR 3.3 13.9 - - - +
348A LEU* 3.6 17.7 - - + -
392A THR* 3.8 31.4 - - + +
394A MET* 4.6 5.6 - - - -
443A CYS* 3.9 2.8 - - - +
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Residues in contact with VAL 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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263A ILE* 4.0 15.9 - - + +
264A ILE* 1.3 78.0 - - - +
266A ARG* 1.3 61.5 + - + +
278A CYS* 3.7 17.8 - - - +
281A TYR* 4.4 1.1 - - - -
347A TYR* 2.8 33.4 + - + +
348A LEU 4.3 1.3 - - - -
349A MET* 4.2 4.0 - - - +
356A SER* 4.0 19.7 - - - +
437A THR* 4.1 18.4 - - + +
440A MET* 3.8 31.2 - - + -
443A CYS* 3.9 16.7 - - - -
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Residues in contact with ARG 266 (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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264A ILE* 3.7 3.7 - - - +
265A VAL* 1.3 83.8 - - + +
267A VAL* 1.3 72.4 + - - +
268A GLU* 2.8 36.0 + - - +
271A GLY 4.4 5.3 + - - -
273A ASP* 3.5 42.1 + - - +
281A TYR* 3.9 7.6 - - - -
347A TYR* 2.8 59.6 + - + -
437A THR* 6.2 1.1 - - + -
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Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ILE* 3.9 9.4 - - + -
266A ARG* 1.3 82.1 - - - +
268A GLU* 1.3 72.3 + - - +
269A ILE* 4.6 7.4 - - + -
273A ASP* 3.5 7.1 + - - +
274A LEU* 2.9 46.9 + - + +
281A TYR* 3.7 39.2 + - + +
297A LEU* 6.4 1.3 - - + -
301A VAL* 5.5 3.4 - - + -
305A ALA* 6.1 1.1 - - + -
344A ILE* 4.9 3.1 - - + -
345A SER 3.4 8.5 - - - +
346A LEU* 3.9 23.1 - - + -
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Residues in contact with GLU 268 (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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266A ARG* 2.8 40.1 + - - +
267A VAL* 1.3 76.8 - - - +
269A ILE* 1.3 69.9 + - - +
270A ASN 4.0 0.4 - - - -
271A GLY* 3.4 32.3 + - - +
272A GLN 3.2 10.8 - - - +
273A ASP 4.3 0.2 - - - +
344A ILE* 3.5 1.7 - - - +
345A SER* 3.0 44.6 + - - +
347A TYR* 2.5 35.5 + - + -
358A ARG* 4.4 6.8 + - - -
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Residues in contact with ILE 269 (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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267A VAL* 4.6 8.3 - - + -
268A GLU* 1.3 80.4 - - - +
270A ASN* 1.3 71.0 + - + +
272A GLN* 2.9 22.9 + - - +
274A LEU* 4.2 13.5 - - + -
305A ALA* 4.8 10.1 - - + +
308A SER* 3.3 38.8 + - - +
309A ILE* 4.1 16.6 - - + -
312A ALA* 4.8 1.8 - - + -
342A PRO* 3.6 32.3 - - + -
343A VAL 3.6 3.1 - - - +
344A ILE* 3.9 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