Contacts of the strand formed by residues 349 - 353 (chain E) 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 ARG 349 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E ALA* 4.3 4.9 - - - +
346E PRO 4.8 0.6 - - - -
347E GLY* 3.1 22.0 + - - +
348E LEU* 1.3 98.9 + - - +
350E CYS* 1.3 65.1 + - - +
351E TYR* 3.6 24.7 - - + +
366E GLY 3.7 1.7 - - - +
367E CYS* 3.3 4.7 - - - +
368E LEU* 2.8 31.1 + - - +
446E TYR* 3.4 28.5 - - + -
449E GLU* 3.4 27.6 + - - +
450E LEU* 3.4 28.8 - - + +
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Residues in contact with CYS 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E ALA* 3.8 22.1 - - - +
263E LEU 4.5 0.4 - - - -
266E LEU* 3.6 30.2 - - + +
297E ALA* 4.4 10.8 - - - -
348E LEU* 3.8 23.6 - - - -
349E ARG* 1.3 79.9 - - - +
351E TYR* 1.3 70.4 + - - +
352E LYS 4.0 1.9 + - - -
366E GLY 3.7 2.2 - - - -
367E CYS* 3.8 22.0 - - - -
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Residues in contact with TYR 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E LEU* 5.2 0.4 - - - -
349E ARG* 3.6 28.6 - - + +
350E CYS* 1.3 83.0 - - - +
352E LYS* 1.3 60.3 + - - +
365E CYS* 3.1 10.8 - - - -
366E GLY 2.7 45.9 + - - +
367E CYS* 4.8 1.2 - - - -
368E LEU* 4.3 9.2 - - + -
442E MET* 3.6 55.2 - - + +
445E ARG* 3.5 40.8 - - + +
446E TYR* 3.7 14.9 - - + -
449E GLU* 2.7 30.0 + - - +
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Residues in contact with LYS 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E LEU* 4.2 15.8 - - + +
269E ARG* 2.7 82.8 + - + +
270E PHE* 4.2 0.2 - - - +
293E ASP* 3.1 26.3 + - - +
350E CYS 4.0 2.4 + - - -
351E TYR* 1.3 73.4 - - - +
353E LEU* 1.3 61.4 + - - +
354E SER* 4.2 6.1 - - - +
357E PHE 5.6 1.1 - - - -
360E ASP* 2.9 27.5 + - - -
361E ILE* 4.2 0.9 - - - +
362E SER* 3.1 32.5 - - - +
364E VAL 4.0 1.8 - - - -
365E CYS* 4.6 2.2 - - - +
445E ARG* 5.5 2.4 + - - -
1465E FAD 3.1 7.3 + - - -
639F GLU* 3.7 9.0 - - - +
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Residues in contact with LEU 353 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352E LYS* 1.3 74.8 - - - +
354E SER* 1.3 61.5 - - - +
362E SER* 3.5 1.8 - - - -
363E ALA* 2.8 32.8 + - + +
364E VAL* 3.0 22.6 + - + +
434E TYR* 3.3 33.9 - - + +
438E ALA* 3.5 31.6 - - + -
442E MET* 3.9 13.0 - - + -
637F THR* 3.9 14.6 - - + -
639F GLU* 3.4 38.4 - - + +
763F PRO* 4.8 0.2 - - + -
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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