Contacts of the strand formed by residues 345 - 352 (chain A) in PDB entry 2W8B
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 PHE 345 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A VAL* 3.6 1.7 - - - +
340A SER* 2.7 58.4 + - - -
342A ASP* 4.5 7.4 - - - -
343A GLY 3.4 0.8 - - - -
344A LYS* 1.3 85.5 - - + +
346A MET* 1.3 61.8 + - - +
347A VAL* 4.2 2.9 - - + -
360A LYS* 3.7 28.0 - - + -
361A GLN 3.2 18.8 - - - +
362A ASP* 4.1 4.0 - - + -
363A LEU* 3.7 10.4 - - - +
382A LEU* 3.8 22.4 - - + -
386A GLY* 3.3 32.5 - - - -
406A THR* 4.0 12.1 - - + -
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Residues in contact with MET 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ALA* 4.7 5.4 - - - -
314A VAL* 4.0 5.8 - - + -
327A ILE* 3.3 34.8 - - + -
328A THR* 3.7 27.4 - - + -
337A ALA* 3.9 20.4 - - - -
338A ASP 3.3 15.9 - - - +
339A VAL* 3.9 12.6 - - + -
345A PHE* 1.3 79.2 - - - +
347A VAL* 1.3 71.2 + - - +
348A MET* 4.1 7.4 - - - +
360A LYS* 3.3 3.8 - - - -
361A GLN* 2.9 47.6 + - + +
363A LEU* 3.9 15.7 - - + +
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Residues in contact with VAL 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ASP 4.3 0.2 - - - +
337A ALA* 3.3 4.0 - - - +
338A ASP* 2.9 43.0 + - + +
345A PHE* 4.2 9.2 - - + -
346A MET* 1.3 78.3 - - - +
348A MET* 1.3 63.5 + - - +
358A ILE* 4.1 7.9 - - + -
359A ALA 3.0 11.9 - - - +
360A LYS* 4.3 3.6 - - + -
371A LEU* 4.2 11.2 - - + -
380A PRO* 3.9 22.8 - - + +
382A LEU* 3.8 37.4 - - + +
389A VAL* 4.0 15.5 - - + -
406A THR* 4.8 0.9 - - + -
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Residues in contact with MET 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A VAL* 4.6 1.3 - - + -
328A THR* 3.7 21.8 - - + -
330A GLU* 4.4 10.8 - - + -
334A ASN* 3.4 25.4 - - - +
335A GLN 3.7 11.4 - - - +
336A ASP 3.9 8.5 - - - -
337A ALA* 4.1 10.1 - - + -
346A MET* 4.1 13.2 - - + +
347A VAL* 1.3 77.1 - - - +
349A VAL* 1.3 69.2 + - - +
358A ILE* 3.3 7.8 - - - +
359A ALA* 2.7 52.9 + - + +
361A GLN* 3.6 29.8 - - + +
368A VAL* 4.4 3.6 - - + -
380A PRO* 4.2 4.2 - - - +
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Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A GLN 4.0 0.5 - - - +
334A ASN* 3.4 3.6 - - - -
335A GLN* 3.0 40.7 + - + +
336A ASP* 3.7 11.7 - - + +
348A MET* 1.3 74.5 - - - +
350A SER* 1.3 62.0 + - - +
351A SER* 4.2 4.2 + - - +
356A GLN* 3.9 24.5 - - + +
357A HIS 3.4 5.6 - - - +
358A ILE* 3.9 4.7 - - + -
377A ASP 3.5 17.7 - - - +
378A GLU* 3.7 19.1 - - - -
380A PRO* 3.7 26.5 - - + -
114H THR* 3.9 13.2 - - + -
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Residues in contact with SER 350 (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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330A GLU* 3.4 20.0 + - - +
331A GLY* 5.2 1.0 - - - -
333A GLN 3.5 5.1 + - - -
334A ASN* 2.7 20.9 + - - -
348A MET* 4.8 0.9 - - - -
349A VAL* 1.3 73.9 - - - +
351A SER* 1.3 62.5 + - - +
352A ASN* 4.2 0.7 + - - +
355A GLN 4.0 0.3 - - - +
356A GLN* 3.3 2.0 - - - -
357A HIS* 2.9 32.1 + - - +
359A ALA* 3.9 25.1 - - - -
370A VAL* 5.8 3.6 - - - -
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Residues in contact with SER 351 (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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311A ARG* 4.9 5.8 + - - -
331A GLY* 4.5 0.3 - - - -
332A SER* 3.3 22.9 + - - -
333A GLN* 2.9 42.4 + - - -
335A GLN* 4.3 6.1 + - - -
349A VAL* 4.5 4.3 + - - +
350A SER* 1.3 73.8 + - - +
352A ASN* 1.3 65.5 + - - +
355A GLN 3.2 10.1 - - - -
356A GLN* 3.5 18.7 + - - +
113H GLY* 5.9 1.6 - - - -
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Residues in contact with ASN 352 (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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311A ARG* 5.9 1.6 - - - +
331A GLY* 3.8 18.2 - - - -
332A SER* 3.1 23.8 + - - -
350A SER* 4.2 1.5 + - - +
351A SER* 1.3 75.6 - - - +
353A GLY* 1.3 72.5 + - - +
354A GLY 3.2 2.2 - - - -
355A GLN* 2.8 25.7 + - - +
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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