Contacts of the strand formed by residues 362 - 365 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356D TRP* 3.5 8.7 - - - +
357D THR* 2.7 48.1 + - + +
358D GLY 4.5 1.0 + - - -
359D ARG* 3.1 39.0 + - - +
360D GLY 3.3 1.4 - - - +
361D MET* 1.3 76.2 - - - +
363D PHE* 1.3 64.0 + - - +
405D VAL* 3.6 24.5 - - + +
411D VAL* 3.4 25.5 - - + +
412D TYR 3.3 8.1 - - - +
413D LYS* 3.8 9.4 - - + +
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Residues in contact with PHE 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D LEU* 4.2 15.3 - - + -
345D LEU* 3.7 26.2 - - + -
354D ILE* 4.3 6.7 - - + -
355D ALA 3.3 12.6 - - - +
356D TRP* 3.9 4.0 - + + +
357D THR* 4.1 4.7 - - - -
361D MET 3.9 10.3 - - - -
362D GLU* 1.3 75.0 - - - +
364D LYS* 1.3 62.0 + - - +
365D LEU* 3.9 28.7 - - + -
393D LEU* 5.4 1.3 - - + -
402D MET* 3.5 25.6 - - - -
410D TYR 4.0 0.2 - - - +
411D VAL* 3.5 3.5 - - - +
412D TYR* 2.8 62.5 + + + +
413D LYS 4.1 1.6 - - - -
414D PHE* 3.5 32.8 - + - -
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Residues in contact with LYS 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B ARG* 4.8 6.5 - - - +
388B LYS* 4.1 12.5 - - - +
1427B EDO 2.7 29.7 + - - +
354D ILE* 3.4 4.5 - - - +
355D ALA 2.9 31.4 + - - +
357D THR* 4.0 16.1 - - + +
363D PHE* 1.3 74.6 - - - +
365D LEU* 1.3 72.1 + - - +
366D ILE* 3.2 25.5 + - + +
408D GLU* 6.1 0.2 - - - -
410D TYR* 3.5 12.3 - - + +
411D VAL* 4.0 17.0 - - + -
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Residues in contact with LEU 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D LEU* 4.8 3.6 - - + -
353D PHE 3.8 5.4 - - - -
354D ILE* 3.6 28.3 - - + -
363D PHE* 3.9 17.5 - - + -
364D LYS* 1.3 70.4 - - - +
366D ILE* 1.3 64.3 + - - +
367D GLU 3.3 1.8 - - - -
368D PRO* 3.4 23.5 - - + +
371D VAL* 4.3 11.7 - - + -
386D TYR* 3.7 28.0 - - + -
389D LEU* 4.4 13.5 - - + -
393D LEU* 4.4 4.9 - - + -
410D TYR* 2.9 29.2 + - + +
412D TYR* 3.6 29.4 - - + +
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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