Contacts of the strand formed by residues 304 - 308 (chain A) 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 SER 304 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A GLY 4.0 1.0 + - - -
303A ALA* 1.3 76.9 - - - +
305A LEU* 1.3 63.9 + - - +
306A THR* 5.9 0.4 - - - -
315A ARG* 3.4 29.5 + - - -
316A MET 3.7 13.7 - - - -
317A PRO* 4.3 2.9 - - - -
318A LEU* 4.3 2.3 - - - +
339A VAL* 3.4 9.5 - - - +
340A THR* 2.9 46.3 + - - +
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Residues in contact with LEU 305 (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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285A ILE* 4.1 9.9 - - + -
304A SER* 1.3 76.6 - - - +
306A THR* 1.3 68.5 + - - +
307A LEU* 4.4 10.4 + - + -
315A ARG* 3.4 17.0 - - - +
316A MET* 3.0 28.1 + - - +
318A LEU* 3.9 22.8 - - + +
321A PHE* 3.6 44.6 - - + -
336A VAL* 3.9 21.1 - - + -
338A SER 3.3 18.6 - - - +
339A VAL* 3.5 16.6 - - + +
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Residues in contact with THR 306 (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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304A SER* 5.7 0.3 + - - -
305A LEU* 1.3 74.3 - - - +
307A LEU* 1.3 80.4 + - - +
313A ARG* 4.3 17.5 - - - +
314A ARG 3.7 7.9 - - - +
315A ARG* 3.4 24.0 - - + +
336A VAL* 3.9 0.9 - - - -
337A GLU* 3.0 43.4 + - + +
338A SER* 2.7 33.7 + - - +
340A THR* 4.7 7.6 + - - -
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Residues in contact with LEU 307 (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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305A LEU* 4.3 11.6 - - + +
306A THR* 1.3 88.3 - - - +
308A ARG* 1.3 62.8 + - - +
313A ARG* 3.3 24.1 - - - +
314A ARG* 3.1 26.8 + - + +
316A MET* 5.1 5.8 - - - -
321A PHE* 4.0 16.6 - - + -
329A ASP 3.3 20.4 - - - +
330A ARG* 4.8 3.6 - - + -
334A GLU* 3.2 35.9 - - + +
335A PHE 3.7 4.3 - - - +
336A VAL* 3.7 33.4 - - + +
337A GLU* 4.4 0.2 - - - -
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Residues in contact with ARG 308 (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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186A SER* 3.8 20.2 - - - -
187A ASP* 3.1 44.9 + - - +
190A ALA* 3.6 11.8 - - - +
191A ASP* 5.2 0.4 + - - -
307A LEU* 1.3 77.2 - - - +
309A ARG* 1.3 62.7 + - - +
310A GLY 2.6 25.3 + - - +
311A GLN* 4.9 7.8 + - - +
312A GLU* 3.2 14.6 - - - +
313A ARG* 4.6 10.3 - - - +
334A GLU* 3.0 3.0 - - - -
335A PHE* 2.7 59.0 + - + +
337A GLU* 3.1 39.6 + - + +
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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