Contacts of the strand formed by residues 312 - 317 (chain G) in PDB entry 2W3S
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 312 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308G ARG* 3.1 24.6 - - - +
309G ARG* 3.0 47.1 + - + +
311G GLN* 1.3 98.3 + - - +
313G ARG* 1.3 65.1 + - - +
314G ARG* 5.6 2.5 - - + -
334G GLU* 4.8 4.0 - - - +
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Residues in contact with ARG 313 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306G THR* 4.0 14.6 + - + +
307G LEU 3.4 15.5 - - - +
308G ARG* 4.5 11.4 - - + +
311G GLN* 4.6 3.6 - - - +
312G GLU* 1.3 81.6 - - - +
314G ARG* 1.3 73.0 + - - +
334G GLU* 5.3 0.2 - - - -
337G GLU* 2.8 37.8 + - - +
338G SER* 4.1 5.9 + - - -
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Residues in contact with ARG 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305G LEU 3.4 1.2 - - - +
306G THR* 3.3 8.5 - - - +
307G LEU* 3.0 45.7 + - + +
312G GLU* 5.6 2.9 - - + -
313G ARG* 1.3 86.0 - - - +
315G ARG* 1.3 65.7 + - - +
316G MET* 4.3 7.4 - - - +
329G ASP* 2.8 45.5 + - - +
331G ARG* 3.1 41.8 - - - +
334G GLU* 2.4 46.1 + - - +
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Residues in contact with ARG 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239G ASP* 4.6 14.5 + - - -
304G SER* 3.4 34.1 + - - -
305G LEU 3.3 7.2 - - - +
306G THR* 4.8 8.0 + - - +
314G ARG* 1.3 80.8 + - - +
316G MET* 1.3 76.4 + - - +
317G PRO* 4.9 1.1 - - + -
340G THR* 4.5 9.5 + - - +
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Residues in contact with MET 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304G SER* 3.4 2.6 - - - -
305G LEU* 2.8 39.4 + - + +
307G LEU* 4.9 7.2 - - - -
314G ARG* 4.3 9.2 - - - +
315G ARG* 1.3 84.6 - - - +
317G PRO* 1.3 85.0 - - + +
318G LEU 4.6 1.6 - - - +
320G ASP* 3.1 24.9 - - + +
321G PHE* 3.7 30.1 - - - +
329G ASP* 3.1 29.6 - - - +
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Residues in contact with PRO 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303G ALA 4.0 7.2 - - - +
304G SER* 4.5 2.9 - - - -
315G ARG* 5.5 1.1 - - + -
316G MET* 1.3 90.2 - - + +
318G LEU* 1.3 65.8 + - - +
319G GLU* 2.8 20.2 - - - +
320G ASP* 2.7 41.3 + - - +
381G ARG* 4.8 7.6 - - - +
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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
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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