Contacts of the strand formed by residues 334 - 339 (chain A) in PDB entry 2W2Q
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 ILE 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A VAL* 3.9 27.6 - - + -
311A LEU 2.8 16.0 + - - +
312A VAL* 3.4 11.8 - - + +
313A THR 2.8 31.1 + - - +
332A GLU 5.4 0.4 - - - +
333A VAL* 1.3 68.2 - - - +
335A THR* 1.3 57.3 + - - +
336A VAL* 4.4 0.9 - - + -
360A ASP* 3.5 7.9 - - + -
361A LEU* 3.7 27.8 - - + -
392A VAL* 4.1 14.6 - - + -
396A ALA* 5.8 0.7 - - + -
408A LEU* 4.8 7.0 - - + -
411A LEU* 4.5 4.5 - - + -
412A ARG* 3.8 28.9 - - + +
415A LEU* 3.9 25.1 - - + -
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Residues in contact with THR 335 (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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313A THR* 3.7 10.7 - - + +
315A ALA* 3.7 30.3 - - + +
322A ALA* 4.8 0.9 - - + -
328A ALA* 2.7 37.5 + - + +
330A ALA 4.2 0.7 + - - -
333A VAL 3.6 2.6 + - - -
334A ILE* 1.3 70.3 - - - +
336A VAL* 1.3 62.8 + - - +
337A GLY 4.2 0.2 - - - -
358A CYS 3.2 20.9 - - - +
359A VAL* 3.8 5.5 - - + +
360A ASP* 2.7 36.6 + - - +
361A LEU 3.4 8.1 + - - +
1448A CA 2.8 10.2 - - - -
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Residues in contact with VAL 336 (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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312A VAL* 3.6 24.5 - - + -
313A THR 3.0 16.8 + - - +
314A ALA* 3.9 1.2 - - - -
315A ALA* 2.9 24.7 + - - -
334A ILE 3.8 2.2 - - - +
335A THR* 1.3 78.9 - - - +
337A GLY* 1.3 72.8 + - - +
361A LEU* 3.3 13.9 - - + +
362A PHE 4.1 0.7 - - - -
363A ALA* 3.9 8.1 - - + +
385A THR* 3.7 9.9 - - - +
388A ALA 3.6 21.8 - - - +
389A ALA* 3.9 7.9 - - - -
392A VAL* 3.7 26.0 - - + -
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Residues in contact with GLY 337 (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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315A ALA* 3.9 9.2 - - - -
336A VAL* 1.3 75.0 - - - +
338A ALA* 1.3 59.5 + - - -
353A THR* 3.5 11.7 - - - -
354A ASN 4.6 0.2 - - - -
359A VAL* 3.8 6.1 - - - +
361A LEU 2.9 11.1 + - - -
362A PHE* 3.2 19.8 - - - -
363A ALA 3.0 24.4 + - - -
385A THR* 4.0 0.7 - - - -
388A ALA* 3.5 5.7 - - - +
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Residues in contact with ALA 338 (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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337A GLY* 1.3 71.5 - - - -
339A THR* 1.3 63.3 + - - +
345A PRO* 3.5 2.8 - - - +
346A VAL* 2.9 40.5 + - + -
348A LEU* 6.3 1.1 - - + -
353A THR* 3.0 19.0 + - - +
362A PHE* 3.6 1.5 - - - -
363A ALA 3.5 4.3 - - - -
365A GLY* 3.9 15.0 - - - -
384A GLY 4.0 10.8 - - - +
385A THR* 3.7 17.8 - - + +
388A ALA* 3.9 1.8 - - + -
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Residues in contact with THR 339 (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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156A TRP* 3.8 0.3 - - - -
338A ALA* 1.3 76.1 - - - +
340A ASN* 1.3 62.3 + - - +
343A ASP* 3.8 23.7 + - - +
344A GLN 3.1 15.9 - - - +
345A PRO* 4.2 1.8 - - + -
346A VAL* 3.5 5.4 - - - +
362A PHE* 3.6 26.7 - - + -
363A ALA 3.0 20.4 + - - -
364A PRO* 3.5 6.6 - - - +
365A GLY 2.9 23.4 + - - -
366A GLU 3.8 0.3 + - - -
424A ILE* 4.0 10.5 - - + -
441A VAL* 4.0 16.4 - - + +
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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