Contacts of the helix formed by residues 520 - 535 (chain A) in PDB entry 4RG7
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 520 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515A TYR* 3.0 21.1 + - + +
518A LEU* 3.3 8.3 + - + -
519A SER* 1.3 74.5 - - - +
521A TYR* 1.3 58.9 + - - +
522A MET 3.4 2.5 - - - -
523A GLN* 3.5 17.9 + - + +
524A ALA* 3.0 27.9 + - - +
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Residues in contact with TYR 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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516A PHE* 4.4 20.0 - + - -
519A SER* 3.2 34.4 + - - -
520A GLU* 1.3 72.3 - - - +
522A MET* 1.3 58.7 + - - +
524A ALA* 3.4 5.8 + - - +
525A GLU* 2.9 29.6 + - - +
548A THR* 4.7 7.9 + - - +
551A HIS* 3.6 38.7 + + + -
552A LEU* 3.4 36.7 - - + +
676A VAL 4.6 0.3 + - - -
677A LEU* 4.2 11.8 - - + -
680A HIS* 3.4 50.1 - + - +
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Residues in contact with MET 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A GLU 3.4 0.2 - - - -
521A TYR* 1.3 76.6 - - - +
523A GLN* 1.3 65.6 + - - +
524A ALA 3.2 0.2 - - - -
525A GLU* 4.1 3.3 - - - +
526A ARG* 3.3 22.2 + - - +
552A LEU* 4.2 13.0 - - + +
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Residues in contact with GLN 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A TYR* 3.7 35.2 - - + -
520A GLU* 3.5 14.4 + - + +
522A MET* 1.3 79.2 - - - +
524A ALA* 1.3 62.8 + - - +
526A ARG* 3.7 11.4 - - - +
527A ILE* 3.6 14.9 - - - +
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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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512A GLY 4.1 7.4 - - - +
515A TYR* 3.7 17.8 - - + +
516A PHE* 4.0 15.9 - - + +
520A GLU 3.0 18.1 + - - +
521A TYR* 3.4 8.5 - - - +
522A MET 3.2 0.2 - - - -
523A GLN* 1.3 74.6 - - - +
525A GLU* 1.3 66.0 + - - +
526A ARG 3.1 2.0 + - - -
527A ILE* 3.0 26.9 + - - +
528A PHE* 3.2 13.9 + - + -
548A THR* 4.8 6.1 - - + -
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Residues in contact with GLU 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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521A TYR 2.9 19.5 + - - +
522A MET* 3.6 5.1 + - - +
524A ALA* 1.3 73.9 - - - +
526A ARG* 1.3 58.5 + - - +
528A PHE* 3.9 7.6 - - - -
529A SER* 2.7 34.8 + - - +
545A TYR* 4.5 9.4 - - + -
548A THR* 4.3 11.1 + - - +
549A LEU* 5.0 6.5 - - + -
552A LEU* 4.3 15.7 - - + -
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Residues in contact with ARG 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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522A MET 3.3 13.3 + - - +
523A GLN* 3.7 14.1 - - - +
524A ALA 3.1 0.2 + - - -
525A GLU* 1.3 78.7 - - - +
527A ILE* 1.3 63.6 + - + +
529A SER* 3.7 5.1 + - - -
530A GLU* 3.3 20.3 + - - +
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Residues in contact with ILE 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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502A TYR* 5.0 11.4 - - + +
508A LEU* 3.9 21.5 - - + +
511A ILE* 4.2 8.7 - - + -
512A GLY* 3.3 36.8 - - - +
515A TYR* 4.3 12.3 - - + -
523A GLN 3.6 10.8 - - - +
524A ALA* 3.0 26.5 - - - +
526A ARG* 1.3 78.3 - - + +
528A PHE* 1.3 61.7 + - - +
530A GLU* 3.2 16.7 - - + +
531A VAL* 3.0 24.1 + - - +
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Residues in contact with PHE 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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509A CYS* 3.8 29.4 - - - -
512A GLY* 3.4 28.3 - - - -
524A ALA* 3.2 24.1 + - + +
525A GLU 4.2 0.4 - - - +
527A ILE* 1.3 77.8 - - + +
529A SER* 1.3 64.6 + - - +
530A GLU 3.0 1.3 - - - -
531A VAL* 3.1 30.3 - - + +
532A ARG* 3.3 14.7 + - - +
541A GLY 3.7 15.3 - - - -
542A MET* 5.5 0.2 - - - -
544A ILE* 3.3 40.8 - - + -
545A TYR* 3.4 46.2 - + + -
548A THR* 4.4 6.1 - - + -
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Residues in contact with SER 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A GLU* 2.7 25.0 + - - +
526A ARG* 3.8 5.6 - - - -
528A PHE* 1.3 76.4 - - - +
530A GLU* 1.3 58.9 + - - +
532A ARG* 3.6 6.9 - - - +
533A ARG* 3.3 21.1 + - - +
545A TYR* 3.2 19.7 + - - -
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Residues in contact with GLU 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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503A ASN* 4.9 7.3 - - - +
508A LEU* 3.5 23.9 - - + +
526A ARG 3.3 6.5 + - - +
527A ILE* 3.2 28.7 - - + +
528A PHE 3.0 0.6 - - - -
529A SER* 1.3 76.1 - - - +
531A VAL* 1.3 65.0 + - - +
532A ARG 3.0 1.9 + - - -
533A ARG* 2.4 46.7 + - - +
534A ILE* 3.0 30.7 + - - +
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Residues in contact with VAL 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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505A GLY* 3.6 33.2 - - - +
508A LEU* 4.4 11.7 - - + -
509A CYS* 3.8 13.9 - - - +
527A ILE 3.0 6.5 + - - +
528A PHE* 3.1 43.1 - - + +
530A GLU* 1.3 77.0 - - - +
532A ARG* 1.3 59.5 + - + +
534A ILE* 3.2 7.8 - - - +
535A GLU* 3.0 28.1 + - - +
536A ASN 3.8 0.3 + - - -
538A ARG* 3.9 14.6 - - + +
541A GLY 6.3 0.2 - - - -
542A MET* 6.6 0.2 - - - -
545A TYR* 5.7 1.1 - - + -
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Residues in contact with ARG 532 (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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528A PHE 3.3 13.4 + - - +
529A SER* 3.6 11.4 - - - +
530A GLU 3.0 0.6 - - - -
531A VAL* 1.3 80.3 - - + +
533A ARG* 1.3 61.5 + - - +
534A ILE 3.2 1.6 - - - -
536A ASN* 3.0 63.8 + - - +
538A ARG 4.9 11.5 + - - +
542A MET* 5.6 4.9 - - + -
545A TYR* 4.2 20.9 - - + -
560A VAL* 5.3 3.2 - - - +
561A LEU* 4.7 12.9 - - - +
564A ASP* 3.1 46.9 + - - +
565A LEU* 5.1 13.7 - - - +
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Residues in contact with ARG 533 (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 SER 3.3 10.1 + - - +
530A GLU* 2.4 59.7 + - - +
532A ARG* 1.3 79.1 - - - +
534A ILE* 1.3 73.3 + - - +
536A ASN* 5.1 3.2 - - - +
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Residues in contact with ILE 534 (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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503A ASN* 3.9 30.7 - - + +
504A THR* 5.8 0.2 - - - -
505A GLY* 4.8 0.7 - - - -
508A LEU* 4.6 4.0 - - + -
530A GLU* 3.0 28.0 + - - +
531A VAL* 3.2 16.8 - - + +
533A ARG* 1.3 93.0 - - + +
535A GLU* 1.3 74.3 + - + +
537A TYR* 5.4 0.9 - - - -
64B HIS* 5.8 2.3 + - - -
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Residues in contact with GLU 535 (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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504A THR* 5.4 1.0 + - - -
505A GLY* 3.2 32.9 + - - +
506A TRP 4.1 1.0 + - - -
531A VAL* 3.0 12.0 + - + +
534A ILE* 1.3 94.9 - - + +
536A ASN* 1.3 66.9 + - - +
537A TYR* 2.4 67.4 + - + +
538A ARG* 3.5 30.2 + - + -
29B GLU* 5.1 6.9 - - - +
48B TYR* 4.6 2.4 + - - -
59B ARG* 5.3 2.1 - - - +
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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