Contacts of the strand formed by residues 280 - 289 (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 LEU 280 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A MET* 5.3 5.6 - - + -
258A PHE* 4.2 15.1 - - + -
259A SER 3.5 16.8 - - - +
260A LEU* 3.7 20.4 - - + +
279A MET* 1.3 88.1 - - - +
281A SER* 1.3 64.0 + - - +
282A GLY 3.7 0.3 + - - -
346A LEU 3.8 0.5 - - - +
347A THR* 3.7 3.5 - - - -
348A MET* 2.8 47.1 + - + +
349A PRO 4.3 4.7 - - - +
350A GLN* 3.9 29.2 - - + -
351A LEU 4.8 1.1 - - - +
399A LEU* 4.7 18.6 - - + +
400A GLU* 5.2 5.6 - - - +
401A ALA* 4.7 12.3 - - + +
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Residues in contact with SER 281 (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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257A GLY 3.9 0.2 - - - +
258A PHE* 3.4 25.3 - - - -
259A SER* 3.5 14.2 + - - -
261A LEU* 3.6 28.1 - - - +
279A MET* 4.2 1.4 - - - +
280A LEU* 1.3 71.8 - - - +
282A GLY* 1.3 58.8 + - - +
283A MET* 3.8 23.7 - - - +
345A HIS* 4.6 6.1 - - - -
346A LEU 3.6 5.4 - - - -
347A THR* 4.3 7.6 - - - -
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Residues in contact with GLY 282 (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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257A GLY 3.7 2.5 - - - -
258A PHE* 3.4 27.1 - - - -
280A LEU 3.7 0.2 + - - -
281A SER* 1.3 74.2 - - - +
283A MET* 1.3 70.4 + - - +
286A PHE* 5.0 0.9 - - - -
344A ILE 3.8 0.7 - - - +
345A HIS* 3.5 3.3 - - - -
346A LEU* 2.7 41.9 + - - +
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Residues in contact with MET 283 (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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257A GLY* 3.6 19.1 + - - +
281A SER* 3.8 24.9 - - - +
282A GLY* 1.3 74.4 - - - +
284A GLY* 1.3 57.4 + - - +
286A PHE* 4.4 5.1 - - - -
344A ILE 4.5 1.8 - - - -
345A HIS* 3.2 41.5 - - + +
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Residues in contact with GLY 284 (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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283A MET* 1.3 74.8 - - - +
285A THR* 1.3 63.7 + - - -
286A PHE* 3.3 23.1 - - - -
343A THR* 5.0 0.2 - - - -
344A ILE 3.0 30.6 + - - +
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Residues in contact with THR 285 (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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284A GLY* 1.3 71.0 - - - -
286A PHE* 1.3 65.9 + - - +
287A GLN* 4.9 2.3 - - - +
341A PRO* 5.5 4.9 - - - +
342A ARG 3.4 11.0 - - - -
343A THR* 3.3 32.3 - - + +
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Residues in contact with PHE 286 (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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256A LYS 5.8 1.8 - - - -
258A PHE* 4.1 21.3 - + - -
282A GLY 4.9 0.2 - - - -
283A MET 4.4 4.5 - - - -
284A GLY* 3.3 43.3 - - - -
285A THR* 1.3 74.9 - - - +
287A GLN* 1.3 69.9 + - - +
299A THR* 5.7 3.4 - - - -
300A GLN* 3.3 27.8 - - + +
301A VAL* 4.3 16.6 - - + -
302A PRO* 4.5 7.9 - - + -
341A PRO* 3.4 2.1 - - - +
342A ARG* 2.7 38.5 + - - +
344A ILE* 4.0 23.9 - - + +
346A LEU* 4.4 20.9 - - + -
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Residues in contact with GLN 287 (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 THR 4.9 1.9 - - - +
286A PHE* 1.3 81.9 - - - +
288A HIS* 1.3 65.3 + - - +
289A TRP* 3.9 15.6 - - + -
298A VAL 4.1 0.7 - - - +
299A THR* 3.9 0.7 - - - -
300A GLN* 3.2 52.3 + - - +
302A PRO* 4.6 8.4 - - - +
339A LEU* 3.8 27.2 - - + +
340A SER 3.3 8.3 - - - +
341A PRO* 3.9 20.4 - - + +
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Residues in contact with HIS 288 (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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286A PHE 4.1 1.3 + - - +
287A GLN* 1.3 76.1 - - - +
289A TRP* 1.3 82.6 + - - +
290A SER* 4.3 11.8 - - - -
297A SER* 4.0 19.2 - - - -
298A VAL 3.2 27.8 - - - +
299A THR* 3.4 27.2 - - + +
340A SER* 2.8 23.0 + - - +
342A ARG* 4.6 22.3 + - + +
344A ILE* 3.9 17.7 - - + +
419A LEU* 3.5 32.8 - - + +
421A VAL* 4.9 2.9 - - + +
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Residues in contact with TRP 289 (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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287A GLN* 3.9 11.9 - - + -
288A HIS* 1.3 102.5 - - - +
290A SER* 1.3 63.8 + - - +
291A ASP* 3.9 3.8 + - + -
296A PHE* 5.9 0.9 - - - -
297A SER* 4.3 0.5 + - - -
298A VAL* 3.8 24.0 + - + +
300A GLN* 5.5 6.5 - - + -
310A LEU* 6.4 1.8 - - + -
336A MET* 3.6 19.0 - - + +
337A LYS* 3.4 19.9 - - + +
338A LYS* 3.3 46.8 - - + +
339A LEU* 3.5 27.8 - - + -
340A SER* 3.6 22.0 - - - -
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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