Contacts of the strand formed by residues 307 - 314 (chain A) in PDB entry 2WXW
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 ALA 307 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LEU* 4.1 20.2 - - + +
170A LEU* 3.8 17.9 - - + -
251A PHE* 6.5 0.2 - - + -
303A PHE* 2.7 56.8 + - + +
305A GLU 3.1 6.7 - - - +
306A SER* 1.3 77.1 - - - +
308A CYS* 1.3 60.5 + - - +
431A VAL* 6.4 1.1 - - + -
432A TYR 3.4 6.5 - - - +
433A ASP* 4.3 2.5 - - - +
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Residues in contact with CYS 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLN* 3.6 27.4 - - - +
302A PRO* 3.9 23.1 - - + -
303A PHE* 4.2 2.7 - - - +
305A GLU* 3.1 28.5 - - - -
307A ALA* 1.3 76.1 - - - +
309A LEU* 1.3 60.9 + - - +
310A LEU* 3.5 10.0 + - + +
430A ALA 3.7 0.5 - - - +
431A VAL* 3.4 2.4 - - - +
432A TYR* 2.8 47.5 + - + +
434A GLN* 4.2 14.4 - - - +
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A MET* 3.3 33.9 - - + -
300A GLN* 3.2 23.4 - - - +
301A VAL* 3.3 17.8 + - + -
303A PHE* 3.6 23.8 - - + -
308A CYS* 1.3 69.4 - - - +
310A LEU* 1.3 71.0 + - - +
311A LEU* 3.3 18.0 - - + +
348A MET* 5.2 0.2 - - - -
397A PHE* 5.0 0.4 - - + -
399A LEU* 3.9 19.3 - - + -
429A PHE* 3.8 26.5 - - + -
430A ALA 4.1 2.5 - - - -
431A VAL* 3.7 20.4 - - + +
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Residues in contact with LEU 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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289A TRP* 6.4 1.8 - - + -
298A VAL* 4.2 15.3 - - + -
299A THR 3.8 2.7 - - - +
300A GLN* 3.2 34.5 - - + +
308A CYS* 4.1 12.3 - - + +
309A LEU* 1.3 73.3 - - - +
311A LEU* 1.3 60.4 + - - +
312A ILE* 3.6 9.6 - - + +
333A LEU 5.2 9.6 - - - +
336A MET* 5.6 10.3 - - + +
429A PHE* 3.2 5.2 - - - +
430A ALA* 2.9 44.9 + - + +
432A TYR* 4.5 18.4 - - + -
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A VAL* 3.4 3.1 - - - -
299A THR* 2.8 48.2 + - - +
300A GLN* 4.1 6.3 - - - -
301A VAL* 4.4 7.6 - - + -
309A LEU* 3.3 38.8 - - + +
310A LEU* 1.3 70.8 - - - +
312A ILE* 1.3 63.6 + - - +
313A GLN* 3.3 6.1 + - - +
346A LEU* 4.4 13.2 - - + -
348A MET* 3.6 32.5 - - + -
423A LEU* 3.9 28.4 - - + +
427A PHE* 4.7 3.4 - - + -
428A LEU 3.5 6.7 - - - +
429A PHE* 4.3 5.2 - - + +
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Residues in contact with ILE 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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296A PHE* 3.4 33.0 - - + -
298A VAL* 3.8 16.8 - - + -
310A LEU* 3.6 26.9 - - + +
311A LEU* 1.3 69.4 - - - +
313A GLN* 1.3 65.6 + - - +
314A PRO* 3.8 1.7 - - + +
323A VAL* 5.0 4.3 - - + -
327A THR* 3.5 26.0 - - + -
336A MET* 4.9 6.3 - - + -
423A LEU* 6.1 0.2 - - - -
427A PHE* 3.7 4.1 - - - +
428A LEU* 2.7 46.5 + - + +
429A PHE* 3.8 17.3 - - - +
430A ALA* 4.2 6.3 - - + +
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Residues in contact with GLN 313 (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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296A PHE* 4.0 1.9 - - - -
297A SER* 2.7 60.0 + - - +
298A VAL* 5.4 0.2 - - - -
299A THR* 5.8 0.6 - - - +
311A LEU 3.3 4.2 + - - +
312A ILE* 1.3 76.2 - - - +
314A PRO* 1.3 77.4 + - + +
315A HIS* 5.1 4.9 + - - +
421A VAL* 3.1 32.5 - - - +
422A THR 3.8 11.8 + - - +
423A LEU* 3.7 24.4 - - + +
427A PHE* 4.8 1.6 - - + -
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Residues in contact with PRO 314 (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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295A ASN 5.0 0.4 - - - +
296A PHE* 5.5 0.2 - - - -
297A SER* 4.4 0.4 - - - -
312A ILE* 3.8 7.6 - - + +
313A GLN* 1.3 95.0 + - + +
315A HIS* 1.3 68.4 + - - +
316A TYR 3.3 1.6 - - - -
317A ALA* 3.1 27.8 + - + +
320A LEU* 3.4 30.3 - - + -
323A VAL* 4.1 32.1 - - + -
426A PRO 3.8 16.2 - - - +
427A PHE* 4.2 5.6 - - - -
428A LEU* 5.0 3.8 - - + +
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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