Contacts of the strand formed by residues 542 - 550 (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 ILE 542 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A VAL* 6.3 0.4 - - + -
463A ILE* 5.5 6.1 - - + -
488A LEU* 5.7 1.3 - - + -
489A ASP* 3.3 31.2 - - + +
491A ASN* 3.4 2.7 - - - +
499A ARG* 3.3 41.5 - - + +
500A PHE* 4.2 30.1 - - + -
541A PRO* 1.3 72.6 - - - +
543A GLN* 1.3 61.9 + - - +
544A ILE* 4.1 21.9 - - + +
581A LYS 4.2 0.2 - - - +
582A THR* 3.8 0.3 - - - -
583A ILE* 3.2 47.5 + - + +
585A PHE* 5.0 6.2 - - + -
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Residues in contact with GLN 543 (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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489A ASP* 3.2 5.9 + - - +
490A VAL* 3.0 32.5 + - + +
491A ASN* 3.2 29.5 + - - +
541A PRO 5.1 1.3 - - - +
542A ILE* 1.3 73.7 - - - +
544A ILE* 1.3 64.5 + - - +
545A GLU* 5.5 4.4 - - + +
580A LYS* 5.0 14.6 - - + +
581A LYS 3.2 7.4 - - - +
582A THR* 3.7 29.3 + - - +
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Residues in contact with ILE 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A LEU* 4.4 19.4 - - + +
442A HIS* 4.7 12.6 - - + +
463A ILE* 6.1 1.3 - - + -
465A LEU* 4.0 33.7 - - + -
486A MET* 4.9 4.0 - - + -
487A SER 3.3 15.5 - - - +
488A LEU* 3.7 25.4 - - + -
542A ILE* 4.1 17.0 - - + +
543A GLN* 1.3 79.6 - - - +
545A GLU* 1.3 62.9 + - - +
579A MET 3.6 1.7 - - - +
580A LYS* 3.6 2.6 - - - +
581A LYS* 2.8 51.8 + - + +
583A ILE* 5.9 1.6 - - + -
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Residues in contact with GLU 545 (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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440A LEU* 5.6 0.4 - - - -
485A ASN 3.8 0.3 - - - +
486A MET* 3.4 4.6 - - - +
487A SER* 3.0 37.4 + - - +
490A VAL* 3.6 30.7 - - + +
543A GLN* 5.5 5.2 - - + +
544A ILE* 1.3 76.1 - - - +
546A ALA* 1.3 61.5 + - - +
547A ALA 4.3 0.2 - - - -
578A ILE* 4.6 10.1 - - + +
579A MET 3.5 3.6 - - - +
580A LYS* 3.4 43.5 + - + +
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Residues in contact with ALA 546 (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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440A LEU* 4.1 18.2 - - + -
467A LEU* 4.2 11.9 - - + -
485A ASN 3.3 11.7 - - - +
486A MET* 4.3 8.5 - - + -
545A GLU* 1.3 76.2 - - - +
547A ALA* 1.3 61.6 + - - +
548A TYR* 5.0 0.2 - - - -
577A ASP 4.1 0.5 - - - +
578A ILE* 3.5 2.9 - - - +
579A MET* 2.9 59.7 + - + +
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Residues in contact with ALA 547 (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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484A TYR* 3.5 2.3 - - - +
485A ASN* 3.0 42.9 + - - +
545A GLU* 4.3 0.8 - - - +
546A ALA* 1.3 74.7 - - - +
548A TYR* 1.3 66.2 + - - +
577A ASP 3.4 6.3 - - - +
578A ILE* 3.6 28.5 - - + -
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Residues in contact with TYR 548 (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* 4.0 35.2 + - + +
438A ALA* 4.0 23.8 + - + +
469A PHE* 4.2 22.2 - + + -
482A LEU* 4.4 12.8 - - + -
483A PHE 3.1 15.5 - - - +
484A TYR* 4.2 9.9 - - + -
547A ALA* 1.3 83.4 - - - +
549A HIS* 1.3 71.5 + - - +
570A LEU* 4.2 8.6 - - + +
573A LYS* 5.8 0.2 + - - -
577A ASP* 3.5 56.7 + - + +
579A MET* 4.3 17.9 - - + -
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Residues in contact with HIS 549 (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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482A LEU* 3.4 8.2 - - - +
483A PHE* 2.9 62.7 + + + +
485A ASN* 6.3 0.4 - - - -
548A TYR* 1.3 80.7 + - - +
550A LEU* 1.3 82.2 + - - +
570A LEU* 3.6 16.2 - - + -
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Residues in contact with LEU 550 (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* 4.1 11.9 - - + -
480A ILE* 3.6 27.4 - - + -
481A VAL 3.7 3.1 - - - +
482A LEU* 4.3 6.3 - - + -
483A PHE* 4.7 0.2 - - - -
549A HIS* 1.3 93.1 - - - +
551A GLY* 1.3 66.7 + - - +
552A PRO* 3.8 6.9 - - + +
553A HIS* 4.3 19.3 - - + -
567A GLN* 6.0 0.7 - - + -
568A PRO* 3.1 33.0 - - + +
569A ILE* 4.1 4.3 - - + -
570A LEU* 3.6 35.4 - - + +
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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