Contacts of the strand formed by residues 322 - 331 (chain A) in PDB entry 2WXL
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 PRO 322 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A GLU 3.6 4.0 - - - +
321A GLN* 1.3 96.0 - - + +
323A PHE* 1.3 64.3 + - - +
324A SER* 3.6 9.0 + - - -
376A GLU* 3.6 32.3 - - - +
377A PHE 3.4 16.8 - - - +
378A ASP* 5.5 0.4 - - - -
379A ILE 3.2 12.6 - - - +
380A SER* 4.3 0.7 - - - -
381A VAL* 4.1 0.7 - - - +
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Residues in contact with PHE 323 (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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321A GLN 3.6 2.0 + - - -
322A PRO* 1.3 73.0 - - - +
324A SER* 1.3 61.4 + - - +
325A ILE* 3.7 23.3 - - + -
347A LEU* 3.7 21.5 - - + -
376A GLU* 3.5 0.9 - - - +
377A PHE* 2.6 74.7 + + + -
379A ILE* 2.7 24.4 + - + +
381A VAL* 3.8 18.6 - - + +
384A LEU* 3.7 24.0 - - + -
390A LEU* 4.3 1.8 - - + -
425A LEU* 3.5 32.5 - - + -
432A LEU* 5.6 7.2 - - + -
475A LEU* 4.4 8.5 - - + -
476A PRO* 5.5 3.4 - - + -
478A VAL* 6.3 1.3 - - + -
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Residues in contact with SER 324 (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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322A PRO 3.9 6.1 + - - -
323A PHE* 1.3 84.5 - - - +
325A ILE* 1.3 67.7 + - - +
374A ARG* 4.5 17.6 + - - -
375A LEU 3.1 15.3 - - - -
376A GLU* 3.8 19.3 + - - -
377A PHE* 4.0 2.2 - - - -
476A PRO* 3.2 33.5 - - - +
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Residues in contact with ILE 325 (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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323A PHE* 3.7 18.4 - - + -
324A SER* 1.3 79.5 - - - +
326A GLU* 1.3 63.6 + - - +
327A LEU* 4.5 3.8 - - + +
374A ARG* 3.5 10.3 - - - +
375A LEU* 2.7 56.7 + - + +
377A PHE* 4.0 8.7 - - + -
390A LEU* 3.8 7.4 - - + -
392A PHE* 3.6 35.7 - - + -
473A ILE* 4.1 14.8 - - + -
474A TYR 3.6 8.7 - - - +
475A LEU* 3.5 27.8 - - + -
476A PRO* 4.5 0.9 - - - -
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Residues in contact with GLU 326 (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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325A ILE* 1.3 76.6 - - - +
327A LEU* 1.3 65.8 + - - +
328A ILE* 3.7 15.1 + - + +
372A LYS* 3.8 25.1 - - - +
373A GLN 3.5 18.2 - - - +
374A ARG* 3.6 23.7 + - - +
473A ILE* 3.3 10.0 - - - +
474A TYR* 3.0 50.9 + - + +
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Residues in contact with LEU 327 (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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325A ILE* 4.0 4.5 + - + +
326A GLU* 1.3 70.5 - - - +
328A ILE* 1.3 61.5 + - - +
329A GLU 5.0 0.4 - - - +
343A VAL* 3.8 21.3 - - + -
360A SER* 3.0 31.2 - - - +
371A TRP* 3.4 35.7 - - + +
372A LYS* 3.3 7.3 + - - -
373A GLN* 2.9 37.8 + - + +
375A LEU* 4.7 16.6 - - + +
392A PHE* 5.4 2.0 - - + -
471A LEU* 4.0 26.0 - - + -
472A VAL 4.3 2.0 - - - +
473A ILE* 4.5 13.7 - - + -
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Residues in contact with ILE 328 (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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326A GLU* 4.2 20.9 - - - +
327A LEU* 1.3 73.7 - - - +
329A GLU* 1.3 72.0 + - + +
370A VAL* 4.2 0.3 - - - +
371A TRP* 1.9 35.6 + - - +
372A LYS* 3.7 27.7 - - + +
436A GLU* 4.4 12.3 - - + -
472A VAL* 3.1 25.5 + - + +
473A ILE 3.6 31.6 - - - +
474A TYR* 3.7 15.5 - - + +
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Residues in contact with GLU 329 (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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327A LEU* 5.0 0.4 - - - +
328A ILE* 1.3 88.8 - - + +
330A GLY* 1.3 59.5 + - - +
331A ARG* 4.1 22.5 + - - +
368A GLU* 4.7 7.5 - - - +
369A PRO 2.9 18.8 - - - +
370A VAL* 3.5 23.5 - - + +
371A TRP* 3.8 13.8 - - - -
372A LYS* 5.3 3.0 + - - -
470A ALA 3.9 0.3 - - - +
471A LEU* 3.6 5.2 - - - +
472A VAL* 3.0 44.5 + - + +
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Residues in contact with GLY 330 (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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329A GLU* 1.3 75.2 - - - +
331A ARG* 1.3 68.9 + - - +
332A LYS* 5.2 1.1 - - - -
368A GLU* 3.2 23.2 - - - +
369A PRO* 2.8 24.2 + - - +
371A TRP* 3.5 8.1 - - - -
394A LEU* 6.2 0.9 - - - -
470A ALA 3.2 10.5 - - - -
471A LEU* 4.1 4.9 - - - -
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Residues in contact with ARG 331 (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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329A GLU* 4.1 18.4 + - - +
330A GLY* 1.3 76.2 - - - +
332A LYS* 1.3 61.0 - - - +
368A GLU* 3.0 31.2 - - - +
369A PRO* 4.0 0.4 - - - +
438A CYS* 3.5 26.9 - - - -
440A TYR* 4.3 8.5 + - - -
468A ALA 4.3 1.7 - - - +
469A ALA* 3.0 24.1 - - - -
470A ALA* 3.1 24.5 + - + +
472A VAL* 3.9 20.6 - - - +
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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