Contacts of the strand formed by residues 524 - 529 (chain A) in PDB entry 3INB
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 524 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467A ILE* 4.0 17.7 - - + -
482A LEU* 4.4 5.0 - - + +
483A PHE* 3.3 30.0 - + - -
514A LEU* 3.2 24.5 - - + -
515A VAL 3.1 17.0 - - - +
516A ILE* 3.8 13.5 - - + -
517A LEU* 3.7 7.0 - - - +
522A LEU* 3.2 32.5 - - + -
523A GLN* 1.3 76.1 - - - +
525A VAL* 1.3 63.8 + - - +
526A LEU* 5.1 2.5 - - + -
541A TYR 3.9 0.9 - - - +
542A VAL* 6.1 0.2 - - - +
543A TYR* 3.0 70.1 + + + +
545A PRO* 4.0 6.2 - - + +
35D PHE* 4.1 10.6 - - - -
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Residues in contact with VAL 525 (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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513A ASN 4.4 0.3 - - - +
514A LEU* 3.9 2.4 - - - +
515A VAL* 3.0 40.2 + - + +
517A LEU* 3.1 30.7 - - + +
524A TYR* 1.3 74.6 - - - +
526A LEU* 1.3 74.0 + - - +
540A TYR* 4.0 22.2 - - + -
541A TYR 3.4 17.3 - - - +
542A VAL* 3.7 13.0 - - + -
568A VAL* 5.6 2.6 - - + +
570A CYS* 4.2 12.1 - - + -
577A LEU* 3.7 18.4 - - + -
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Residues in contact with LEU 526 (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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458A PRO* 4.2 25.6 - - + -
465A GLY 5.7 0.9 - - - +
483A PHE* 6.2 2.5 - - + -
511A SER* 5.9 1.6 - - - -
512A SER* 4.1 0.7 - - - +
513A ASN 4.1 11.4 - - - +
514A LEU* 4.0 27.4 - - + -
524A TYR* 4.2 2.4 + - + -
525A VAL* 1.3 80.6 - - - +
527A ALA* 1.3 70.4 + - - +
541A TYR* 3.0 60.5 + - + +
543A TYR* 3.5 19.3 - - + +
568A VAL* 5.3 2.7 - - - -
37D ILE* 5.6 6.3 - - + -
38D PRO* 4.6 11.0 - - + -
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Residues in contact with ALA 527 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511A SER* 3.4 4.0 - - - -
512A SER* 2.6 47.1 + - - +
526A LEU* 1.3 83.0 - - - +
528A THR* 1.3 59.9 + - - +
538A VAL* 4.3 9.0 - - + -
539A VAL 3.0 18.8 - - - +
540A TYR* 3.8 24.9 - - + -
541A TYR* 4.5 0.4 - - - +
566A LEU* 4.7 2.7 - - + -
568A VAL* 4.9 4.3 - - + -
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Residues in contact with THR 528 (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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460A LYS* 4.4 2.2 - - - +
509A LYS* 4.0 11.1 - - - +
510A LEU 2.8 18.7 + - - -
511A SER* 3.9 9.6 - - - +
527A ALA* 1.3 79.3 - - - +
529A TYR* 1.3 61.7 + - - +
530A ASP 3.9 6.9 + - - +
531A THR* 6.3 0.9 - - + -
537A ALA 4.1 0.5 - - - +
538A VAL* 3.5 1.6 - - - -
539A VAL* 3.0 51.6 + - + +
541A TYR* 3.3 18.8 - - + +
566A LEU* 4.1 4.3 - - - -
38D PRO* 4.8 9.2 - - + -
39D PRO* 6.1 0.9 - - - +
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Residues in contact with TYR 529 (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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509A LYS* 3.3 1.4 - - - +
510A LEU* 2.7 36.9 + - + +
528A THR* 1.3 73.4 - - - +
530A ASP* 1.3 73.3 + - + +
536A HIS* 2.4 57.4 + + + +
537A ALA* 3.0 28.0 - - - -
538A VAL* 4.1 6.5 - - + -
555A PHE* 5.4 7.6 - - + -
557A LEU* 3.7 9.1 - - + +
559A ILE* 4.3 1.4 - - + +
563A PRO* 3.1 36.4 - - + +
566A LEU* 3.6 19.9 - - + +
583A CYS* 4.2 22.0 - - - -
585A LEU* 5.3 3.3 - - + +
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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