Contacts of the strand formed by residues 520 - 530 (chain A) in PDB entry 2Y74
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 HIS 520 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A ALA* 5.3 0.7 - - + -
371A ILE 3.0 17.0 - - - +
372A TYR* 3.5 35.1 + + + -
471A T0I 4.9 1.3 - + - -
495A ILE* 5.3 7.4 - - + -
496A SER 5.7 1.6 - - - -
518A THR 2.9 23.8 + - - -
519A VAL* 1.3 76.7 - - - +
521A THR* 1.3 67.0 + - - +
522A HIS* 2.6 30.6 + + - -
683A LEU* 3.5 5.0 - - - +
684A HIS* 2.8 51.7 + + - +
686A PRO* 4.3 5.4 - - + -
801A CU 1.9 29.2 - - - -
562B LEU* 4.1 3.4 - - - -
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Residues in contact with THR 521 (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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369A LEU 3.6 0.3 - - - +
370A ALA* 3.2 7.4 - - - +
371A ILE* 2.9 42.4 + - + +
520A HIS* 1.3 77.8 - - - +
522A HIS* 1.3 65.2 + - - +
523A SER* 4.5 4.5 + - - -
612A GLY* 4.7 7.6 - - - -
613A GLU 4.6 5.1 + - - +
628A GLU* 4.2 12.1 + - - -
682A PHE 3.5 13.0 - - - +
683A LEU* 4.3 4.7 - - + -
684A HIS 4.7 0.4 - - - +
544B MET* 3.9 35.4 - - + -
546B PHE* 5.8 0.4 - - + -
562B LEU* 4.7 3.4 - - + -
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Residues in contact with HIS 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LEU 3.3 4.5 - - - +
370A ALA* 4.5 4.4 - - + +
471A T0I 3.4 33.4 - + - -
473A TYR* 3.9 20.2 + - + +
489A PHE* 4.6 10.8 - - + -
491A ALA* 4.7 8.2 - - + +
520A HIS* 2.6 23.0 + + - -
521A THR* 1.3 73.1 - - - +
523A SER* 1.3 63.9 + - - +
681A GLY* 3.2 20.5 - - - -
682A PHE* 3.2 47.6 + + + +
684A HIS* 4.0 2.7 - - + -
801A CU 1.8 32.3 - - - -
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Residues in contact with SER 523 (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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368A ALA* 3.4 2.9 - - - +
369A LEU* 2.7 49.0 + - - +
489A PHE* 4.6 5.1 - - - -
521A THR* 4.5 4.5 + - - -
522A HIS* 1.3 76.8 + - - +
524A ALA* 1.3 59.9 + - - +
627A TRP* 3.8 21.2 - - - -
628A GLU* 3.9 13.8 + - - +
679A THR* 4.4 7.6 - - - -
680A ALA 3.3 11.2 - - - -
681A GLY* 4.6 2.5 - - - -
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Residues in contact with ALA 524 (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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365A LEU* 4.2 6.5 - - + -
367A GLU 3.2 10.8 - - - +
368A ALA* 4.5 1.1 - - - -
475A TRP* 4.3 7.0 - - + -
489A PHE* 3.9 25.5 - - + -
523A SER* 1.3 75.4 - - - +
525A HIS* 1.3 61.1 + - - +
526A PHE* 3.9 19.2 - - + -
627A TRP* 3.9 3.8 - - - -
678A VAL 3.8 0.7 - - - +
679A THR* 3.5 4.5 - - - +
680A ALA 3.0 29.6 + - - +
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Residues in contact with HIS 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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365A LEU* 3.2 7.6 - - - +
366A GLN* 2.7 38.7 + - + +
367A GLU 2.8 13.4 + - - +
524A ALA* 1.3 73.4 - - - +
526A PHE* 1.3 56.4 + - - +
627A TRP* 3.4 47.2 - + + +
630A TYR* 5.9 1.0 - - - +
644A SER* 2.7 30.8 + - - -
660A PHE* 3.9 8.2 - + - -
677A TRP* 3.6 40.0 + + + +
678A VAL 3.5 8.7 - - - -
679A THR* 3.1 27.5 + - - -
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Residues in contact with PHE 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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363A ILE* 5.6 1.3 - - + -
364A SER 3.4 3.8 - - - +
365A LEU* 3.9 21.8 - - + -
366A GLN* 4.1 4.0 - - - -
475A TRP* 4.4 2.7 - + - -
487A ILE* 3.8 17.5 - - + -
489A PHE* 4.1 20.6 - - + -
524A ALA* 3.9 29.6 - - + -
525A HIS* 1.3 78.0 - - - +
527A LYS* 1.3 61.2 + - - +
528A VAL* 3.9 1.3 + - + -
676A ALA 3.8 0.2 - - - +
677A TRP* 3.3 9.4 - - - +
678A VAL* 2.8 45.1 + - + +
680A ALA* 4.4 15.0 - - + -
702A GLY* 4.9 3.4 - - - -
703A PHE* 3.7 34.8 - + + -
806A IMD 3.8 26.7 - + - -
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Residues in contact with LYS 527 (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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362A GLU* 3.0 36.4 + - - +
363A ILE* 3.2 7.8 - - - +
364A SER* 2.7 34.8 + - - +
366A GLN* 3.2 29.3 - - - +
526A PHE* 1.3 72.5 - - - +
528A VAL* 1.3 62.1 + - - +
529A ASP* 3.9 3.1 - - - +
637A ARG* 3.7 19.7 - - - +
638A LYS 5.9 0.2 + - - -
641A GLU 4.6 3.0 + - - -
642A PRO* 2.9 30.9 + - - +
675A VAL* 3.9 20.0 - - + -
676A ALA 3.7 2.2 - - - -
677A TRP* 3.5 26.7 - - + -
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Residues in contact with VAL 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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362A GLU 3.8 1.6 - - - -
363A ILE* 4.4 8.7 - - + +
526A PHE 4.3 4.3 - - - +
527A LYS* 1.3 77.1 - - - +
529A ASP* 1.3 58.9 + - - +
530A LEU* 3.2 23.9 + - + +
589A LEU* 5.3 0.2 - - - +
605A ILE* 5.2 1.1 - - + -
675A VAL* 3.6 1.7 - - - -
676A ALA* 2.6 49.8 + - + +
678A VAL* 4.1 16.6 - - + -
703A PHE* 3.6 29.6 - - + -
705A LEU* 3.7 34.5 - - + -
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Residues in contact with ASP 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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106A LYS* 3.3 17.2 + - - -
360A VAL* 3.3 5.1 - - - +
361A TYR* 2.7 41.7 + - - +
362A GLU* 2.6 31.6 + - + +
527A LYS* 3.9 1.9 - - - -
528A VAL* 1.3 68.2 - - - +
530A LEU* 1.3 58.2 + - - +
531A ASP* 3.3 0.2 - - - +
637A ARG* 3.2 30.1 + - - -
673A ASP* 3.9 0.3 - - - +
674A LEU 3.4 3.8 - - - +
675A VAL* 4.0 16.4 - - + +
803A CA 2.2 33.0 - - - -
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Residues in contact with LEU 530 (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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359A LEU* 3.4 18.6 - - + +
360A VAL* 3.5 19.7 - - + -
528A VAL* 3.2 25.9 + - + +
529A ASP* 1.3 73.6 - - - +
531A ASP* 1.3 57.9 + - - +
532A VAL* 3.6 9.2 - - + -
537A ASN* 3.4 7.6 + - - -
589A LEU* 4.1 29.0 - - + +
603A TYR* 4.1 38.1 - - + +
605A ILE* 4.7 7.0 - - + -
674A LEU 3.3 5.1 + - - +
675A VAL* 5.0 0.2 - - - +
705A LEU* 4.3 15.7 - - + -
803A CA 2.1 28.1 - - - -
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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