Contacts of the strand formed by residues 308 - 312 (chain A) in PDB entry 4WPN
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 ARG 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A LYS* 3.1 40.4 + - + +
274A SER 3.3 4.5 + - - +
275A PRO* 3.1 17.9 - - + +
276A CYS 2.9 26.3 + - - +
306A ALA 3.3 0.4 - - - -
307A SER* 1.3 83.9 - - - +
309A ILE* 1.3 62.3 + - - +
310A PHE* 3.9 22.6 + - + -
392A ASP* 5.7 2.0 + - - -
397A ALA* 3.4 24.1 + - - +
407A GLN* 4.0 3.1 - - + -
409A MET* 4.1 23.7 - - + +
420A ARG 3.1 24.5 + - - -
421A ALA 2.8 23.6 + - - -
423A ASN 4.7 6.1 + - - -
424A THR* 3.6 16.6 - - - +
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Residues in contact with ILE 309 (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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276A CYS* 3.8 16.4 - - + -
278A VAL* 4.3 9.9 - - + -
291A ALA* 3.7 21.1 - - + +
306A ALA 3.6 20.2 - - - +
308A ARG* 1.3 76.3 - - - +
310A PHE* 1.3 57.9 + - - +
311A VAL* 3.8 19.5 - - + -
319A PHE* 3.9 19.7 - - + -
406A GLN* 3.3 37.2 - - + +
407A GLN 3.1 12.8 + - - +
408A ILE* 3.5 6.2 - - + +
409A MET* 2.8 35.0 + - - +
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Residues in contact with PHE 310 (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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275A PRO* 3.9 22.7 - - + -
276A CYS 2.9 20.7 + - - +
277A ILE* 3.5 6.4 - - + -
278A VAL* 2.8 27.5 + - - +
308A ARG* 3.9 30.7 - - + -
309A ILE* 1.3 72.7 - - - +
311A VAL* 1.3 61.4 + - - +
392A ASP* 4.5 1.1 - - - -
409A MET* 3.4 32.5 - - + -
410A LYS 4.8 1.1 - - - -
411A PHE* 3.6 6.7 - - + -
417A VAL* 3.4 30.7 - - + -
420A ARG* 3.6 50.0 - - + -
421A ALA* 4.3 6.3 - - + -
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Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A VAL* 3.7 8.3 - - + -
309A ILE* 3.8 16.4 - - + -
310A PHE* 1.3 78.8 - - - +
312A GLU* 1.3 74.2 + - - +
313A GLU* 3.3 0.5 + - - -
315A ILE* 3.7 19.1 - - + -
316A TYR* 3.7 28.1 - - + +
319A PHE* 3.8 39.3 - - + -
408A ILE* 4.2 9.2 - - + -
409A MET 2.9 9.7 + - - +
410A LYS* 3.4 7.6 - - - +
411A PHE* 3.2 18.4 + - - -
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Residues in contact with GLU 312 (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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278A VAL 3.1 11.8 + - - +
279A LEU* 5.3 0.2 - - - -
280A ALA* 3.8 35.6 - - + +
311A VAL* 1.3 74.0 - - - +
313A GLU* 1.3 82.0 + - - +
314A SER* 2.5 46.2 + - - -
315A ILE* 3.1 15.1 + - + +
316A TYR 3.1 6.4 + - - -
411A PHE* 3.3 31.6 - - + +
412A LYS* 4.7 12.2 - - - +
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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