Contacts of the strand formed by residues 493 - 500 (chain A) in PDB entry 3BA6
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 SER 493 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487A PHE* 3.9 4.8 - - - -
488A SER 3.5 15.1 + - - -
491A ARG* 3.1 30.3 + - - +
492A LYS* 1.3 81.2 - - - +
494A MET* 1.3 61.9 - - - +
514A VAL* 4.6 2.9 - - - -
515A LYS 3.4 12.6 - - - -
516A GLY* 3.8 6.1 - - - -
521A VAL* 4.2 6.7 - - - -
524A ARG* 3.3 21.0 + - - -
588A GLU* 2.6 25.9 + - - -
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Residues in contact with MET 494 (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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420A CYS* 3.3 11.3 - - - -
421A ASN 4.2 11.9 - - - +
422A ASP* 3.6 26.7 - - - +
442A GLU* 3.2 28.3 - - - +
484A THR* 4.5 12.8 - - - +
485A LEU 3.8 6.7 - - - +
486A GLU* 5.0 0.4 - - - -
487A PHE* 3.5 24.2 - - + +
491A ARG* 3.9 1.3 - - - +
493A SER* 1.3 78.5 + - - +
495A SER* 1.3 66.3 + - - +
496A VAL* 6.1 1.3 - - + -
514A VAL* 3.3 4.3 - - - +
515A LYS* 2.8 48.2 + - - +
588A GLU* 3.5 2.5 - - - -
1001A AN2 3.3 21.5 - - + +
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Residues in contact with SER 495 (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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420A CYS* 4.0 2.7 - - - -
484A THR* 3.6 5.0 + - - -
485A LEU* 2.9 52.2 + - - +
494A MET* 1.3 79.5 - - - +
496A VAL* 1.3 65.0 + - - +
512A MET* 3.4 11.6 - - - +
513A PHE 3.2 10.8 - - - -
514A VAL* 3.9 8.5 - - - -
588A GLU* 2.7 32.0 + - - -
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Residues in contact with VAL 496 (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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419A LEU 3.7 16.2 - - - +
420A CYS* 4.2 8.7 - - - +
421A ASN 5.4 0.2 - - - +
481A LYS* 3.3 44.4 - - + +
483A PHE 3.9 5.6 - - - +
484A THR* 4.0 10.5 - - - +
485A LEU* 6.0 0.4 - - - -
494A MET* 6.1 1.8 - - + -
495A SER* 1.3 77.0 - - - +
497A TYR* 1.3 59.5 + - - +
498A CYS* 3.5 19.4 + - - -
511A LYS 3.6 0.3 - - - +
512A MET* 2.9 9.2 - - - -
513A PHE* 2.9 46.2 + - + +
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Residues in contact with TYR 497 (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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481A LYS 3.6 0.3 - - - -
482A GLU* 2.7 53.4 + - + +
483A PHE* 3.0 49.6 + + + +
485A LEU* 6.2 0.4 - - - +
496A VAL* 1.3 72.3 - - - +
498A CYS* 1.3 56.1 + - - +
510A ASN* 3.6 38.8 + - + +
511A LYS 3.4 1.8 - - - -
512A MET* 3.5 21.7 - - + +
570A PRO* 3.7 22.1 - - + +
571A PRO 3.2 20.3 + - - -
572A LYS* 4.3 1.4 - - - -
573A ARG* 3.5 29.0 + - + +
576A MET* 4.0 10.5 - - - -
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Residues in contact with CYS 498 (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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419A LEU* 4.4 11.4 - - - -
479A MET* 3.9 15.3 - - + +
480A LYS 3.1 6.7 - - - +
481A LYS* 3.9 19.7 - - - -
482A GLU* 4.5 2.7 - - - -
496A VAL* 3.5 25.8 - - - -
497A TYR* 1.3 81.9 - - - +
499A SER* 1.3 59.7 + - - +
510A ASN* 3.5 4.5 - - - +
511A LYS 2.7 40.7 + - - +
513A PHE* 3.8 24.7 - - + -
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Residues in contact with SER 499 (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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479A MET* 3.3 10.9 - - - +
480A LYS* 2.7 45.2 + - - +
482A GLU* 3.2 29.0 + - - +
498A CYS* 1.3 73.7 - - - +
500A PRO* 1.3 70.7 + - - +
510A ASN* 3.0 21.1 - - - -
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Residues in contact with PRO 500 (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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478A LEU 4.6 0.7 - - - +
479A MET* 4.1 11.0 - - - -
480A LYS* 4.7 1.4 - - - +
499A SER* 1.3 96.6 + - - +
501A ALA* 1.3 68.6 + - - +
503A SER* 3.6 11.5 + - - +
504A SER* 5.3 1.6 - - - +
505A ARG 3.2 31.2 - - - +
506A ALA* 4.8 4.7 - - - -
507A ALA 5.0 2.5 - - - +
508A VAL* 4.1 13.5 - - + -
509A GLY 3.6 15.9 - - - +
510A ASN* 3.6 9.4 - - - +
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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