Contacts of the strand formed by residues 353 - 358 (chain A) in PDB entry 2XVS
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 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A SER* 4.0 22.9 - - - -
345A LEU 4.3 2.5 - - - -
346A THR* 4.4 6.7 - - + -
350A LYS 4.8 3.2 + - - +
351A VAL* 4.5 0.4 - - - +
352A PRO* 1.3 70.0 - - - +
354A THR* 1.3 59.7 + - - +
355A PHE* 3.9 10.3 - + - -
367A VAL 3.6 1.6 - - - +
368A MET* 3.6 1.2 - - - -
369A VAL* 2.8 36.2 + - + +
372A ILE* 3.3 31.5 - - + +
376A TRP* 3.9 23.3 - + - -
377A GLY* 3.9 10.5 - - - -
378A VAL* 3.7 41.5 - - + -
1427A CL 4.0 18.6 - - + -
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Residues in contact with THR 354 (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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270A PHE* 3.4 14.2 - - + -
274A LEU* 3.8 31.2 - - + -
344A SER* 3.1 6.1 - - - -
345A LEU* 2.9 49.3 + - + -
352A PRO* 3.4 28.8 + - - +
353A PHE* 1.3 74.0 - - - +
355A PHE* 1.3 64.2 + - - +
366A ALA* 4.5 4.7 - - + -
367A VAL 3.2 12.1 - - - +
368A MET* 3.8 11.4 - - + +
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Residues in contact with PHE 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A VAL* 4.0 14.1 - - + -
343A PHE* 3.1 20.9 - - - +
344A SER* 4.1 8.3 - - - +
353A PHE* 3.9 11.7 - + - -
354A THR* 1.3 73.6 - - - +
356A GLY* 1.3 58.8 + - - +
357A LEU* 3.7 36.1 - - + -
366A ALA* 3.5 2.1 - - - -
367A VAL* 2.7 62.2 + - + +
369A VAL* 3.6 26.9 - - + -
376A TRP* 4.1 10.8 - + - -
378A VAL* 3.8 13.5 - - + -
384A VAL* 4.1 28.5 - - + -
416A LEU* 4.5 5.2 - - + -
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Residues in contact with GLY 356 (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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341A VAL* 3.2 8.1 - - - +
342A VAL* 2.8 29.0 + - - -
343A PHE* 3.0 38.1 + - - -
355A PHE* 1.3 74.0 - - - +
357A LEU* 1.3 59.6 + - - +
364A CYS* 3.7 6.5 - - - -
365A TYR 3.4 7.9 - - - -
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Residues in contact with LEU 357 (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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324A LEU* 3.8 19.7 - - + +
337A ILE* 3.8 28.5 - - + -
339A GLY* 3.9 14.8 - - - +
340A LYS 3.3 21.8 - - - -
341A VAL* 3.7 12.3 - - + +
355A PHE* 3.7 28.7 - - + -
356A GLY* 1.3 73.8 - - - +
358A VAL* 1.3 62.4 + - - +
364A CYS* 3.3 5.1 - - - -
365A TYR 2.9 33.6 + - - +
367A VAL* 3.8 20.0 - - + -
384A VAL* 4.0 14.1 - - + +
386A ILE* 4.4 2.9 - - + -
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Residues in contact with VAL 358 (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 LYS* 4.2 22.7 - - + -
289A LEU* 4.2 10.8 - - + +
292A MET* 5.5 0.9 - - - -
293A LEU* 3.6 19.4 - - + +
324A LEU* 4.5 1.6 - - - -
339A GLY* 3.3 1.6 - - - -
340A LYS* 2.8 41.1 + - + +
342A VAL* 3.8 22.0 - - + -
357A LEU* 1.3 79.0 - - - +
359A ASP* 1.3 60.2 + - - +
360A SER 4.1 11.9 - - - +
362A GLY 4.8 0.4 - - - +
363A PRO 4.8 4.0 - - - +
364A CYS* 3.9 24.7 - - + +
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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