Contacts of the strand formed by residues 508 - 514 (chain B) in PDB entry 5X1V
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 VAL 508 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423B CYS* 3.8 34.8 - - + +
425B SER* 3.5 6.2 - - - -
426B GLY 3.2 21.3 + - - -
506B GLY 5.0 2.9 - - - +
507B ASP* 1.3 79.2 - - - +
509B VAL* 1.3 61.7 + - - +
527B VAL* 3.7 29.4 - - + -
528B VAL 3.5 8.7 - - - +
529B PRO* 5.1 1.8 - - + -
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Residues in contact with VAL 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B SER* 4.0 2.7 - - - -
426B GLY* 4.1 1.8 - - - +
427B ALA* 3.6 28.9 - - + +
429B ILE* 4.2 8.5 - - + -
494B MET* 3.8 28.9 - - + -
503B PHE* 3.8 27.6 - - + -
507B ASP 5.3 0.2 - - - -
508B VAL* 1.3 76.4 - - - +
510B ILE* 1.3 67.5 + - - +
511B VAL* 4.4 4.5 - - + -
527B VAL* 3.7 3.8 - - - +
528B VAL* 2.8 42.8 + - - +
530B VAL* 3.9 14.4 - - + -
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Residues in contact with ILE 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B ALA* 3.9 28.3 - - + +
419B ALA* 3.9 24.5 - - + -
420B SER* 3.8 19.3 - - - +
423B CYS* 4.1 12.8 - - - -
425B SER* 3.7 15.9 - - - +
427B ALA 3.0 9.1 + - - +
428B ILE* 3.4 12.5 - - + -
429B ILE* 2.6 36.0 + - - +
509B VAL* 1.3 76.9 - - - +
511B VAL* 1.3 59.5 + - - +
512B LEU* 4.3 0.7 - - + -
525B MET* 3.9 18.2 - - + -
526B ARG 3.5 1.8 - - - -
527B VAL* 4.0 19.3 - - + -
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Residues in contact with VAL 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429B ILE* 3.4 21.8 - - + +
490B VAL* 3.8 41.7 - - + -
494B MET* 4.4 1.1 - - + -
509B VAL* 4.4 1.6 - - + -
510B ILE* 1.3 78.6 - - - +
512B LEU* 1.3 64.6 + - - +
513B THR* 4.2 13.2 + - + -
524B THR 3.6 1.0 - - - +
525B MET* 3.5 3.8 - - - -
526B ARG* 2.8 54.5 + - + +
528B VAL* 3.8 32.1 - - + -
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Residues in contact with LEU 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B THR* 3.9 12.8 - - + -
413B ALA* 4.8 3.8 - - + +
416B ALA* 3.8 15.0 - - + -
428B ILE* 4.3 4.3 - - + -
429B ILE 2.6 14.5 + - - +
430B VAL* 3.8 20.1 - - + -
431B LEU* 3.1 27.4 + - - +
437B SER 4.9 2.0 - - - +
441B VAL* 3.7 29.6 - - + -
510B ILE* 4.6 0.9 - - + -
511B VAL* 1.3 77.4 - - - +
513B THR* 1.3 65.4 + - - +
522B THR* 4.0 24.0 - - + -
524B THR 3.3 12.3 - - - +
525B MET* 3.7 23.6 - - + -
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Residues in contact with THR 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B LEU* 4.1 20.2 - - + -
486B VAL* 3.8 23.1 - - + -
490B VAL* 4.5 1.8 - - + -
511B VAL* 4.2 9.6 + - + -
512B LEU* 1.3 77.7 - - - +
514B GLY* 1.3 63.7 + - - +
522B THR* 3.6 10.5 - - - +
523B ASN 3.3 4.9 + - - -
524B THR* 3.1 43.8 + - - +
526B ARG* 3.3 32.0 + - - +
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Residues in contact with GLY 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B TRP* 3.3 19.6 - - - -
513B THR* 1.3 79.9 + - - +
515B TRP* 1.3 63.5 + - - -
516B ARG 3.4 4.7 - - - -
521B PHE* 3.3 20.0 - - - -
522B THR* 3.8 6.3 + - - +
523B ASN* 3.6 4.0 - - - -
524B THR* 4.2 4.5 + - - -
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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