Contacts of the strand formed by residues 525 - 531 (chain A) in PDB entry 3GVJ
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 GLU 525 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A HIS* 4.3 9.9 + - + -
390A MET* 3.8 23.9 - - - +
404A GLU* 3.9 6.1 - - - +
406A ARG* 3.9 12.6 + - - +
411A ASN* 5.6 3.1 + - - -
523A VAL* 3.9 2.2 - - - +
524A THR* 1.3 88.7 - - + +
526A VAL* 1.3 68.0 + - - +
527A HIS* 4.9 3.0 - - + +
541A TYR* 3.3 22.9 - - - +
542A HIS* 3.3 23.7 + - + +
581A GLU* 2.7 39.3 - - - +
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Residues in contact with VAL 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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390A MET* 3.5 20.1 + - - +
391A SER* 4.0 4.6 + - - -
402A MET* 3.8 43.8 - - + +
404A GLU* 2.9 22.5 + - - +
416A CYS* 4.7 8.5 - - - -
520A ILE* 5.1 0.7 - - + -
523A VAL* 4.0 16.6 - - + -
525A GLU* 1.3 74.0 - - - +
527A HIS* 1.3 62.2 + - - +
539A MET* 3.8 22.2 - - + -
540A GLY 3.3 15.7 - - - +
541A TYR* 4.5 5.2 - - + -
554A PHE* 4.5 9.2 - - + -
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Residues in contact with HIS 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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330A GLN* 3.1 45.6 + - + -
331A ASP* 3.8 11.3 - - + +
390A MET* 3.4 25.0 - - + +
391A SER* 4.1 0.2 - - - -
525A GLU* 4.9 5.4 - - + +
526A VAL* 1.3 77.0 - - - +
528A SER* 1.3 73.5 + - - +
540A GLY* 2.8 34.1 + - - +
541A TYR* 5.3 0.2 - - - -
542A HIS* 5.8 0.2 - - + -
581A GLU* 3.5 37.8 + - + +
582A PRO* 2.7 31.8 + - + +
583A CYS* 3.8 9.5 - - - -
630A THR* 3.9 3.8 - - + +
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Residues in contact with SER 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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331A ASP* 2.7 40.8 + - - -
390A MET 3.0 12.7 + - - -
391A SER* 2.7 19.1 + - - -
527A HIS* 1.3 80.8 - - - +
529A PHE* 1.3 64.3 + - - +
539A MET* 3.3 1.0 - - - -
540A GLY 3.3 13.3 + - - -
582A PRO 3.3 16.6 - - - -
584A ILE* 2.9 24.5 + - - -
585A LYS* 3.5 4.0 + - - -
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Residues in contact with PHE 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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331A ASP 4.1 2.8 + - - +
391A SER* 4.0 2.2 - - - +
392A MET 3.4 22.0 - - - +
393A GLY* 3.6 38.1 - - - -
394A VAL 3.8 7.4 - - - -
395A CYS* 4.6 0.2 - - + -
400A PHE* 3.9 17.7 - - + -
528A SER* 1.3 79.6 + - - +
530A ALA* 1.3 63.2 + - - +
531A THR* 3.3 31.2 - - - -
537A PHE* 3.5 40.4 - + + -
538A ALA 3.5 4.9 - - - -
539A MET* 3.9 21.3 - - + -
584A ILE* 3.3 13.2 - - - +
585A LYS* 3.4 14.1 + - - +
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Residues in contact with ALA 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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529A PHE* 1.3 76.1 - - - +
531A THR* 1.3 64.9 + - - +
532A ILE* 3.4 2.9 + - + +
537A PHE* 3.3 0.7 - - - -
538A ALA* 2.9 33.3 + - + +
584A ILE* 3.7 29.6 - - + +
585A LYS* 3.9 15.0 - - - +
586A TYR* 4.1 9.9 - - + +
591A LEU* 4.1 11.9 - - + -
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Residues in contact with THR 531 (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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394A VAL 2.8 28.4 + - - +
395A CYS* 4.5 9.0 - - + -
396A ARG 5.6 0.2 - - - +
529A PHE* 3.3 12.6 - - - -
530A ALA* 1.3 71.7 - - - +
532A ILE* 1.3 63.0 + - - +
533A ASP* 3.9 19.5 - - - +
536A GLY 4.2 2.7 - - - +
537A PHE* 4.0 7.6 - - - -
586A TYR* 3.6 19.2 - - - +
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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