Contacts of the strand formed by residues 433 - 441 (chain A) in PDB entry 3V4V
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 433 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A TYR* 3.1 34.8 - - + +
2A ASN* 4.0 9.2 - - + -
346A ASP* 2.9 40.4 - - + +
347A ASN* 4.6 2.5 - - + +
412A TYR* 3.5 16.8 + - - +
432A PRO* 1.3 77.5 - - - +
434A VAL* 1.3 64.2 + - - +
435A ILE* 4.2 2.9 + - + -
473A GLY* 4.4 4.0 - - - -
474A LYS 4.6 0.2 + - - -
476A VAL* 3.9 6.8 - - - +
569A ILE 3.1 10.1 - - - +
571A GLN* 3.5 30.1 - - + +
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Residues in contact with VAL 434 (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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432A PRO 4.5 0.2 - - - +
433A VAL* 1.3 79.4 - - - +
435A ILE* 1.3 61.6 + - - +
436A VAL* 3.1 15.0 + - + +
471A TYR* 4.4 14.8 - - + -
472A LYS 3.7 8.5 - - - +
476A VAL* 3.5 26.5 - - + -
477A PRO* 4.8 2.0 - - + -
480A ILE* 5.1 9.0 - - + -
550A LEU* 4.1 26.2 - - + -
568A PRO* 3.8 22.0 - - + -
569A ILE 3.2 10.4 + - - +
570A LEU* 4.1 7.8 - - + -
571A GLN 3.4 15.2 + - - -
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Residues in contact with ILE 435 (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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347A ASN* 4.6 8.1 - - - +
348A ASP* 5.4 1.3 - - - -
433A VAL* 4.7 3.1 - - + -
434A VAL* 1.3 68.2 - - - +
436A VAL* 1.3 60.8 + - - +
437A ASP* 3.9 2.0 + - + +
471A TYR* 3.3 1.8 - - - -
472A LYS* 2.8 63.2 + - + +
473A GLY* 4.5 9.9 - - - -
571A GLN* 3.1 47.3 - - + +
573A LYS* 4.4 15.5 - - - +
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Residues in contact with VAL 436 (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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434A VAL* 3.1 7.9 + - + +
435A ILE* 1.3 73.2 - - - +
437A ASP* 1.3 71.9 + - - +
438A ALA 3.9 1.2 + - - -
469A PHE* 4.3 8.3 - - + -
470A SER 4.3 6.3 - - - +
471A TYR* 3.6 22.2 - - + -
480A ILE* 6.6 0.2 - - + -
482A LEU* 4.2 24.0 - - + -
548A TYR* 4.0 24.3 + - + +
570A LEU* 3.8 29.8 - - + -
571A GLN* 5.6 0.4 - - - +
573A LYS* 3.8 16.1 + - - +
577A ASP* 6.1 0.7 - - - +
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Residues in contact with ASP 437 (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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435A ILE* 3.9 3.1 + - + +
436A VAL* 1.3 73.4 - - - +
438A ALA* 1.3 72.7 + - - +
439A SER* 6.0 1.6 - - - -
468A CYS 3.8 0.7 - - - +
469A PHE* 3.6 2.3 - - - -
470A SER* 3.1 43.2 + - - +
472A LYS* 5.7 9.4 - - - +
573A LYS* 4.4 14.6 + - - +
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Residues in contact with ALA 438 (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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436A VAL* 3.9 1.7 + - + +
437A ASP* 1.3 85.5 + - - +
439A SER* 1.3 59.6 + - - +
468A CYS 3.3 5.4 - - - +
469A PHE* 3.5 33.9 - - + -
548A TYR* 4.0 18.9 + - + +
579A MET* 3.3 24.5 - - + +
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Residues in contact with SER 439 (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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437A ASP* 6.0 1.3 - - - -
438A ALA* 1.3 74.9 - - - +
440A LEU* 1.3 64.6 + - - +
441A SER* 5.0 1.0 + - - -
467A LEU* 4.0 5.4 - - - +
468A CYS* 3.2 43.2 + - - +
579A MET* 3.8 8.4 - - - +
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Residues in contact with LEU 440 (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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439A SER* 1.3 79.5 - - - +
441A SER* 1.3 73.9 + - - +
442A HIS* 3.2 10.7 + - + +
465A LEU* 4.8 1.3 - - + -
466A THR 3.4 19.7 - - - +
467A LEU* 3.6 17.9 - - + -
486A MET* 3.9 21.1 - - + -
544A ILE* 4.4 14.4 - - + +
546A ALA* 4.1 22.7 - - + -
579A MET* 4.2 18.1 - - + +
581A LYS* 3.9 39.6 - - + +
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Residues in contact with SER 441 (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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439A SER* 4.3 1.7 + - - -
440A LEU* 1.3 72.2 - - - +
442A HIS* 1.3 59.3 + - - +
443A PRO* 3.7 8.9 - - - +
464A ASP 4.7 3.4 - - - -
465A LEU* 3.8 10.7 - - - +
466A THR* 2.8 53.3 + - - +
468A CYS* 4.4 8.3 - - - -
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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