Contacts of the strand formed by residues 335 - 345 (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 ALA 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A LEU* 3.8 7.0 - - - +
320A GLU* 3.3 11.2 - - - +
322A LYS* 4.0 19.1 - - + -
327A LEU* 4.7 6.3 - - + -
332A ASN* 3.2 24.6 + - + +
333A SER 3.3 2.0 - - - +
334A GLY* 1.3 79.2 - - - +
336A VAL* 1.3 59.1 + - - +
388A GLU* 2.8 31.2 + - - -
389A PRO* 4.3 3.6 - - + -
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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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301A LEU* 3.9 28.3 - - + -
304A CYS* 4.2 16.8 - - + +
319A LEU* 3.9 22.2 - - + +
320A GLU 3.0 3.7 + - - +
321A LEU* 3.3 23.7 - - + +
322A LYS* 3.0 25.1 + - - +
335A ALA* 1.3 75.4 - - - +
337A ILE* 1.3 77.4 + - - +
385A ALA* 4.3 0.7 - - + -
386A ILE 3.4 23.6 - - - +
387A PRO* 3.9 4.9 - - + -
389A PRO* 4.5 0.4 - - - -
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Residues in contact with ILE 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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321A LEU* 3.9 2.2 - - - -
322A LYS* 3.4 20.9 - - + +
324A LEU* 4.0 26.7 - - + +
327A LEU* 3.7 37.2 - - + -
335A ALA* 5.7 0.2 - - + -
336A VAL* 1.3 79.9 - - - +
338A LEU* 1.3 64.0 + - - +
339A GLY 4.5 1.3 - - - +
357A LEU* 3.8 21.8 - - + -
359A ASP* 5.0 0.4 - - - +
384A VAL 4.2 2.7 - - - +
385A ALA* 3.2 6.8 - - - +
386A ILE* 3.1 53.7 + - + +
389A PRO* 4.0 8.7 - - + -
408A VAL* 5.8 0.4 - - + -
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Residues in contact with LEU 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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296A LEU* 3.7 22.8 - - + +
297A ARG 3.3 30.3 - - - +
298A PRO* 4.8 1.3 - - + -
300A HIS* 3.8 22.2 - - + +
301A LEU* 4.2 16.4 - - + +
321A LEU* 3.6 26.1 - - + +
322A LYS 4.8 0.8 + - - -
337A ILE* 1.3 77.2 - - - +
339A GLY* 1.3 59.8 + - - +
359A ASP* 3.1 22.5 + - - +
383A SER* 4.1 11.2 - - - -
384A VAL 3.4 21.3 - - - +
385A ALA* 4.0 10.1 - - + +
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Residues in contact with GLY 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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296A LEU* 3.9 10.3 - - - +
324A LEU* 5.3 0.7 - - - -
337A ILE* 4.3 2.8 - - - +
338A LEU* 1.3 74.7 - - - +
340A LYS* 1.3 60.5 + - - -
357A LEU* 3.9 15.4 - - - +
358A VAL 3.3 13.0 - - - -
359A ASP* 4.1 3.1 - - - -
382A ASP 3.7 0.3 - - - +
383A SER* 3.3 5.2 - - - -
384A VAL 2.8 35.1 + - - -
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Residues in contact with LYS 340 (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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292A MET* 3.2 39.0 - - + +
293A LEU* 4.3 2.7 - - + +
295A SER* 3.0 30.8 + - - -
296A LEU* 3.8 17.5 - - + +
300A HIS* 4.9 2.4 - - - -
339A GLY* 1.3 72.5 - - - -
341A VAL* 1.3 62.8 + - - +
342A VAL 3.5 0.9 + - - -
357A LEU* 3.3 6.2 - - - -
358A VAL* 2.8 45.8 + - + +
381A GLY 2.7 24.8 + - - +
382A ASP 3.3 5.8 - - - +
383A SER* 2.9 32.0 + - - +
419A ASN* 4.5 2.8 + - - -
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Residues in contact with VAL 341 (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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292A MET* 4.0 2.4 - - - +
340A LYS* 1.3 72.0 - - - +
342A VAL* 1.3 63.4 + - - +
343A PHE 3.7 22.4 - - - +
344A SER* 5.2 1.1 - - - -
355A PHE* 4.0 14.6 - - + -
356A GLY 3.2 6.5 - - - +
357A LEU* 3.8 7.4 - - + -
378A VAL* 4.1 11.4 - - + +
379A LEU 3.4 26.2 - - - +
380A ILE* 3.6 10.4 - - - +
381A GLY* 2.9 23.7 + - - -
382A ASP* 2.9 22.3 + - + +
384A VAL* 3.6 25.4 - - + -
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Residues in contact with VAL 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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281A LYS 3.7 15.9 - - - +
282A GLY* 3.7 11.6 - - - +
284A VAL* 3.7 15.8 - - + +
289A LEU* 3.7 29.8 - - + -
292A MET* 4.0 11.7 - - - -
340A LYS 4.5 0.2 - - - +
341A VAL* 1.3 77.1 - - - +
343A PHE* 1.3 71.4 + - + +
356A GLY 2.8 20.5 + - - +
358A VAL* 3.8 21.5 - - + -
364A CYS* 3.6 26.5 - - - -
380A ILE* 3.7 13.7 - - - +
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Residues in contact with PHE 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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274A LEU* 3.8 12.8 - - + -
277A LEU* 3.6 48.9 - - + -
278A LEU* 3.8 17.9 - - + -
282A GLY* 3.8 21.8 - - - +
341A VAL* 3.7 6.1 - - - +
342A VAL* 1.3 81.9 - - + +
344A SER* 1.3 63.2 + - - +
345A LEU* 3.6 29.8 - - + -
355A PHE* 3.1 9.3 - - - +
356A GLY* 3.0 52.1 + - - -
364A CYS* 3.9 10.5 - - - -
380A ILE* 3.9 14.0 - - + +
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Residues in contact with SER 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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273A ARG* 5.0 3.3 + - - -
277A LEU* 5.1 2.3 - - - +
341A VAL* 5.2 1.3 - - - -
343A PHE* 1.3 78.6 - - - +
345A LEU* 1.3 67.2 + - - +
353A PHE* 4.0 16.5 - - - -
354A THR 3.1 13.9 - - - -
355A PHE* 4.1 5.6 - - - -
378A VAL* 4.5 10.7 + - - -
380A ILE* 4.9 5.2 - - - +
1427A CL 3.3 17.8 - - - +
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Residues in contact with LEU 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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270A PHE* 3.7 25.8 - - + -
273A ARG* 3.9 51.8 - - + +
274A LEU* 4.0 13.0 - - + +
277A LEU* 4.1 6.5 - - + -
343A PHE* 3.6 32.1 - - + -
344A SER* 1.3 74.9 - - - +
346A THR* 1.3 62.7 + - - +
353A PHE* 4.3 1.1 - - - -
354A THR* 2.9 53.0 + - + +
1427A CL 3.9 10.5 - - - +
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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