Contacts of the strand formed by residues 341 - 348 (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 PRO 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285A THR* 5.5 4.9 - - - +
286A PHE 3.4 9.6 - - - +
287A GLN* 3.9 14.1 - - + +
339A LEU 3.5 9.8 - - - +
340A SER* 1.3 87.3 - - - +
342A ARG* 1.3 66.1 + - - +
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Residues in contact with ARG 342 (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* 3.4 5.2 - - - -
286A PHE 2.7 35.6 + - - +
288A HIS* 4.6 20.2 + - + +
290A SER* 5.6 3.4 + - - -
340A SER 4.8 2.9 - - - +
341A PRO* 1.3 77.5 + - - +
343A THR* 1.3 71.5 + - - +
344A ILE* 3.4 27.2 + - + +
419A LEU* 4.2 22.3 - - + +
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Residues in contact with THR 343 (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 4.3 0.2 - - - -
285A THR* 3.3 29.6 - - + +
342A ARG* 1.3 76.6 - - - +
344A ILE* 1.3 64.2 + - - +
416A PRO* 6.0 3.8 - - + -
417A GLU* 2.7 42.6 + - - +
418A VAL* 3.6 10.6 - - + -
419A LEU* 3.1 19.2 + - - +
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Residues in contact with ILE 344 (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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282A GLY 3.8 0.2 - - - +
283A MET* 4.5 0.3 - - - -
284A GLY 3.0 31.1 + - - +
286A PHE* 4.0 20.9 - - + +
288A HIS* 3.9 18.8 - - + +
299A THR* 4.4 9.6 - - + -
342A ARG* 3.5 32.8 - - + +
343A THR* 1.3 86.9 - - - +
345A HIS* 1.3 66.3 + - - +
346A LEU* 3.5 8.6 + - + +
418A VAL* 5.1 3.3 - - - +
419A LEU* 3.5 24.5 - - + +
421A VAL* 3.3 32.5 - - + -
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Residues in contact with HIS 345 (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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281A SER* 4.6 3.6 - - - -
282A GLY 3.5 2.2 - - - -
283A MET* 3.2 43.4 - - + +
344A ILE* 1.3 70.1 - - - +
346A LEU* 1.3 62.1 + - - +
347A THR* 3.1 31.9 - - + +
418A VAL* 4.7 15.4 - - + +
419A LEU 2.9 16.4 + - - +
420A GLU* 4.0 27.9 + - + -
421A VAL 3.1 22.3 + - - +
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Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A PHE* 3.7 31.4 - - + -
280A LEU 4.8 0.2 - - - +
282A GLY* 2.7 42.2 + - - +
286A PHE* 4.4 16.8 - - + -
299A THR* 4.9 14.8 - - - +
300A GLN 4.6 5.8 - - - +
301A VAL* 4.3 17.7 - - + -
311A LEU* 4.4 12.1 - - + -
344A ILE* 3.5 9.3 + - + -
345A HIS* 1.3 73.1 + - - +
347A THR* 1.3 85.0 + - - +
348A MET* 3.6 33.0 - - + -
421A VAL* 4.0 7.6 - - + +
423A LEU* 5.6 1.6 - - + -
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Residues in contact with THR 347 (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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279A MET* 3.3 26.6 - - + +
280A LEU 3.7 1.3 - - - -
281A SER* 4.3 6.7 - - - -
345A HIS* 3.1 35.0 + - + +
346A LEU* 1.3 80.0 - - - +
348A MET* 1.3 61.4 + - - +
421A VAL 2.8 22.5 + - - +
422A THR* 3.1 24.0 + - - +
423A LEU* 3.2 26.0 + - - +
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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
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255A MET* 4.4 20.2 - - + +
258A PHE* 5.5 0.9 - - + -
267A PHE* 4.8 0.2 - - - -
279A MET* 3.2 11.5 - - - +
280A LEU* 2.8 42.2 + - + +
309A LEU* 5.2 0.9 - - + -
311A LEU* 3.6 24.9 - - + -
346A LEU* 3.6 17.0 - - + -
347A THR* 1.3 74.4 - - - +
349A PRO* 1.3 92.7 - - + +
351A LEU* 3.8 11.7 - - + -
399A LEU* 3.6 28.0 - - + -
423A LEU* 3.7 15.3 - - + -
427A PHE* 5.1 3.1 - - + -
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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