Contacts of the strand formed by residues 316 - 320 (chain B) in PDB entry 4U7D
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 SER 316 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B GLY 4.1 0.7 + - - -
315B GLN* 1.3 75.3 - - - +
317B GLY* 1.3 54.9 + - - +
360B TRP* 4.2 7.5 + - - -
363B ASN* 2.9 26.8 + - - +
365B ILE 4.4 4.3 + - - -
366B GLN* 3.4 10.6 + - - -
380B LYS* 3.5 19.8 - - - -
382B ASP* 3.6 20.7 + - - -
383B VAL* 4.3 1.8 - - - -
384B ARG* 2.8 29.8 + - - +
385B PHE* 3.6 6.8 + - - -
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Residues in contact with GLY 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B SER* 1.3 76.2 - - - +
318B ILE* 1.3 63.2 + - - +
360B TRP* 3.4 9.2 + - - +
366B GLN 3.1 7.9 + - - -
367B VAL* 3.4 21.0 - - - -
368B VAL 3.4 4.3 + - - -
383B VAL* 3.8 7.2 - - - -
385B PHE* 3.0 31.4 - - - -
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Residues in contact with ILE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B GLY* 1.3 78.8 - - - +
319B ILE* 1.3 71.9 + - - +
320B TYR* 4.0 28.7 - - + +
360B TRP* 3.8 28.5 - - + -
367B VAL* 4.3 0.2 - - - -
368B VAL* 3.6 15.9 - - + +
370B ALA* 5.2 1.8 - - + -
374B PHE* 4.2 21.1 - - + -
378B ILE* 5.1 0.7 - - + -
383B VAL* 4.2 11.7 - - + -
385B PHE* 2.7 12.5 + - - +
386B VAL* 3.2 15.3 - - + +
387B ILE* 2.6 33.3 + - - +
404B ARG* 4.4 17.9 - - + -
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Residues in contact with ILE 319 (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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304B ILE* 4.5 21.1 - - + -
308B ILE* 4.7 5.2 - - + -
318B ILE* 1.3 80.2 - - - +
320B TYR* 1.3 61.2 + - - +
321B CYS* 3.9 9.1 + - - -
330B VAL* 5.0 5.2 - - + -
334B LEU* 4.0 25.1 - - + -
367B VAL* 3.8 20.1 - - + +
368B VAL 3.0 8.7 + - - +
369B VAL* 3.4 12.5 - - + +
370B ALA 2.9 26.3 + - - -
385B PHE* 4.9 0.9 - - + -
387B ILE* 3.2 24.9 - - + +
389B HIS* 3.9 28.5 - - + +
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Residues in contact with TYR 320 (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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318B ILE* 4.0 21.6 - - + +
319B ILE* 1.3 71.4 - - - +
321B CYS* 1.3 60.6 + - - +
370B ALA* 3.4 15.9 - - + -
371B THR 3.7 16.8 - - - -
372B VAL* 4.2 7.6 - - + -
374B PHE* 2.7 26.7 + + + -
386B VAL* 4.0 9.2 - - + -
387B ILE 2.7 10.2 + - - +
388B HIS* 3.7 37.9 - + + +
389B HIS* 2.9 30.0 + - - +
390B SER 3.6 5.4 + - - +
401B GLU* 3.4 35.0 - - + +
404B ARG* 2.6 34.6 + - - -
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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
------------------------------------------------------------
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