Contacts of the strand formed by residues 508 - 516 (chain A) in PDB entry 6VSB
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 TYR 508 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A SER* 4.5 12.1 - - - -
376A THR* 5.7 2.9 - - - -
401A VAL* 3.3 7.7 - - - -
402A ILE* 2.9 32.0 + - + +
403A ARG 4.7 4.7 - - - +
404A GLY* 3.5 17.7 - - - -
407A VAL* 5.7 6.5 - - + -
435A ALA* 4.9 7.4 - - + -
436A TRP* 3.3 26.5 - - - +
437A ASN* 3.1 38.9 + - + +
438A SER* 3.4 2.5 - - - -
503A VAL* 3.4 41.5 - - - +
506A GLN* 3.2 12.8 - - + -
507A PRO* 1.3 76.4 - - - +
509A ARG* 1.3 63.7 + - - +
510A VAL* 3.8 11.0 + - + +
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Residues in contact with ARG 509 (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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342A PHE 5.1 1.6 + - - -
343A ASN 5.1 0.2 - - - -
344A ALA 2.4 29.1 + - - +
345A THR* 2.6 26.6 + - - +
346A ARG* 3.9 4.0 - - - +
347A PHE* 3.5 29.2 - - + +
400A PHE 3.8 3.6 - - - -
401A VAL* 3.8 17.5 - - + -
435A ALA* 3.4 1.2 - - - -
436A TRP* 3.2 66.9 + - + +
438A SER* 2.7 20.9 + - - +
441A LEU* 5.2 7.6 + - - +
442A ASP* 3.0 34.7 + - - -
508A TYR* 1.3 72.1 - - - +
510A VAL* 1.3 60.3 + - - +
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Residues in contact with VAL 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A PHE* 3.9 1.0 - - - -
398A ASP 3.5 1.0 - - - +
399A SER* 3.4 6.2 - - - -
400A PHE* 3.0 47.6 + - + +
402A ILE* 3.9 34.3 - - + -
407A VAL* 5.4 1.6 - - + -
410A ILE* 4.5 12.8 - - + -
433A VAL* 4.7 5.2 - - + -
434A ILE 3.6 9.6 - - - +
435A ALA* 3.9 15.7 - - + -
508A TYR* 4.2 5.8 - - + +
509A ARG* 1.3 76.2 - - - +
511A VAL* 1.3 66.1 + - - +
512A VAL* 4.0 21.8 - - + -
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Residues in contact with VAL 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A VAL* 3.7 32.5 - - + +
342A PHE* 3.6 26.5 - - + -
347A PHE* 3.8 13.2 - - + -
397A ALA* 4.1 3.8 - - + -
398A ASP 3.2 9.0 - - - +
399A SER* 4.8 0.9 - - - -
434A ILE* 2.9 31.5 + - - +
436A TRP* 3.6 26.0 - - + -
509A ARG 4.2 0.2 + - - -
510A VAL* 1.3 79.2 - - - +
512A VAL* 1.3 64.8 + - - +
513A LEU* 3.9 17.3 - - + +
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Residues in contact with VAL 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ARG* 5.9 0.3 + - - -
396A TYR 3.6 0.9 - - - +
397A ALA* 3.2 5.1 - - - -
398A ASP* 2.9 33.5 + - + +
400A PHE* 4.5 4.7 - - + -
410A ILE* 3.6 27.8 - - + -
423A TYR* 3.6 29.8 - - + +
425A LEU* 4.7 9.0 - - + -
430A THR* 3.8 25.8 - - + -
432A CYS 3.7 2.5 - - - -
433A VAL* 4.3 9.6 - - + -
510A VAL* 4.0 11.7 - - + -
511A VAL* 1.3 77.0 - - - +
513A LEU* 1.3 64.4 + - - +
514A SER* 4.0 3.2 + - - -
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Residues in contact with LEU 513 (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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338A PHE* 4.9 10.1 - - + -
342A PHE* 3.9 20.2 - - + -
358A ILE* 5.1 0.4 - - + -
365A TYR* 6.4 2.2 - - + -
368A LEU* 5.9 0.4 - - + -
395A VAL* 4.5 11.0 - - + -
396A TYR 3.3 4.3 - - - +
397A ALA* 3.7 24.9 - - + -
430A THR* 3.2 11.5 - - - +
431A GLY* 3.1 21.8 + - - -
432A CYS* 3.0 31.4 + - + +
434A ILE* 3.8 25.8 - - + -
511A VAL* 3.9 13.7 - - + +
512A VAL* 1.3 74.2 - - - +
514A SER* 1.3 60.1 + - - +
515A PHE* 4.5 16.8 - - + -
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Residues in contact with SER 514 (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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355A ARG* 4.9 10.9 + - - -
395A VAL* 3.3 3.5 - - - -
396A TYR* 2.7 63.8 + - - +
430A THR* 5.3 5.2 - - - +
431A GLY 4.4 4.5 - - - +
512A VAL* 5.2 4.0 - - - -
513A LEU* 1.3 74.9 - - - +
515A PHE* 1.3 63.6 + - - +
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Residues in contact with PHE 515 (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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365A TYR* 3.6 24.2 - + - -
382A VAL* 6.0 1.3 - - + -
387A LEU* 3.9 24.5 - - + -
392A PHE* 3.5 43.7 - + + -
394A ASN 3.3 3.4 - - - -
395A VAL* 3.4 36.8 - - + -
396A TYR* 5.4 1.3 - - - -
429A PHE* 4.0 18.3 - + + -
431A GLY* 3.5 34.1 - - - -
432A CYS* 5.3 2.9 - - - -
513A LEU* 4.5 13.2 - - + -
514A SER* 1.3 76.7 + - - +
516A GLU* 1.3 61.0 + - - +
517A LEU* 3.6 14.1 + - + +
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Residues in contact with GLU 516 (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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392A PHE* 3.7 7.3 - - - +
393A THR* 2.8 36.7 + - + -
394A ASN* 2.7 41.8 + - + +
396A TYR* 4.7 8.2 - - + -
514A SER 4.3 0.2 + - - -
515A PHE* 1.3 71.9 - - - +
517A LEU* 1.3 59.7 + - - +
519A HIS* 5.1 7.9 - - + -
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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