Contacts of the strand formed by residues 362 - 365 (chain B) in PDB entry 4AVP
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 GLU 362 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B TRP* 3.5 10.0 - - - +
357B THR* 2.7 47.2 + - - +
358B GLY 4.5 1.0 + - - -
359B ARG* 3.1 40.5 + - - +
360B GLY 3.3 1.5 - - - +
361B MET* 1.3 77.8 - - - +
363B PHE* 1.3 62.5 + - - +
405B VAL* 3.5 24.9 - - + +
411B VAL* 3.4 25.6 - - + +
412B TYR 3.3 8.3 - - - +
413B LYS* 3.8 9.4 - - + +
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Residues in contact with PHE 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 4.2 13.9 - - + -
345B LEU* 3.7 26.0 - - + -
354B ILE* 4.4 5.6 - - + -
355B ALA 3.3 13.2 - - - +
356B TRP* 3.9 5.8 - + + -
357B THR* 4.1 4.5 - - - -
361B MET 3.9 4.7 - - - -
362B GLU* 1.3 75.4 - - - +
364B LYS* 1.3 62.3 + - - +
365B LEU* 4.0 26.9 - - + -
393B LEU* 5.1 0.9 - - + -
402B MET* 4.0 20.4 - - + -
410B TYR 4.0 0.2 - - - +
411B VAL* 3.4 3.8 - - - +
412B TYR* 2.8 67.9 + + + +
413B LYS* 4.2 4.0 - - - -
414B PHE* 3.5 38.8 - + - -
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Residues in contact with LYS 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ILE* 3.4 5.2 - - - +
355B ALA 2.9 31.8 + - - +
357B THR* 4.0 14.6 - - + +
363B PHE* 1.3 75.0 - - - +
365B LEU* 1.3 68.1 + - - +
366B ILE* 3.2 34.5 + - + +
408B GLU* 3.9 11.1 + - - -
410B TYR* 3.4 16.5 - - - +
411B VAL* 3.7 28.6 - - + +
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Residues in contact with LEU 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B LEU* 4.8 3.6 - - + -
353B PHE 3.8 5.4 - - - -
354B ILE* 3.6 28.3 - - + -
363B PHE* 4.0 16.8 - - + -
364B LYS* 1.3 71.2 - - - +
366B ILE* 1.3 63.8 + - - +
367B GLU 3.3 2.2 - - - -
368B PRO* 3.4 19.5 - - + +
371B VAL* 4.3 10.8 - - + -
386B TYR* 3.7 31.2 - - + -
389B LEU* 4.4 8.7 - - + -
393B LEU* 3.8 12.3 - - + -
410B TYR* 2.9 31.8 + - + +
412B TYR* 3.7 25.4 - - + -
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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