Contacts of the helix formed by residues 520 - 535 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515B TYR* 2.7 45.0 + - + +
518B LEU* 3.0 11.0 - - + +
519B SER* 1.3 70.3 - - - +
521B TYR* 1.3 57.3 + - - +
522B MET 3.4 2.5 - - - -
523B GLN* 4.1 8.7 - - + -
524B ALA* 3.0 22.7 + - - +
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Residues in contact with TYR 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516B PHE* 5.8 2.2 - - - +
519B SER* 2.9 13.2 + - - +
520B GLU* 1.3 72.2 - - - +
522B MET* 1.3 63.3 + - - +
524B ALA* 3.4 5.5 + - - -
525B GLU* 3.3 19.1 + - - +
548B THR* 3.4 24.9 - - + +
551B HIS* 5.3 7.0 - - + -
552B LEU* 5.2 15.8 - - + +
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Residues in contact with MET 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B GLU 3.4 0.4 - - - -
521B TYR* 1.3 77.9 - - - +
523B GLN* 1.3 60.8 + - - +
525B GLU* 3.8 5.8 + - - +
526B ARG* 3.4 18.0 + - - +
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Residues in contact with GLN 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B TYR* 3.4 48.0 + - + +
520B GLU* 3.6 9.1 + - + +
521B TYR 3.4 0.2 - - - -
522B MET* 1.3 77.6 - - - +
524B ALA* 1.3 64.1 + - - +
525B GLU 3.4 0.2 - - - -
526B ARG* 3.2 30.4 - - - +
527B ILE* 3.3 11.0 + - - +
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Residues in contact with ALA 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512B GLY* 4.1 10.7 - - - +
515B TYR* 3.7 24.6 - - + +
516B PHE* 4.3 2.0 - - - +
520B GLU 3.0 18.9 + - - +
521B TYR* 3.5 8.3 - - - +
522B MET 3.3 0.2 - - - -
523B GLN* 1.3 77.6 - - - +
525B GLU* 1.3 58.3 + - - +
527B ILE* 3.0 7.0 + - - +
528B PHE* 3.0 32.8 + - + -
548B THR* 4.0 18.2 - - + +
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Residues in contact with GLU 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B TYR 3.3 13.1 + - - +
522B MET* 4.2 5.6 - - - +
523B GLN 3.4 0.2 - - - -
524B ALA* 1.3 75.9 - - - +
526B ARG* 1.3 64.1 + - - +
528B PHE 4.0 0.4 - - - -
529B SER* 3.0 27.9 + - - -
545B TYR* 4.1 22.4 + - + +
548B THR* 4.0 12.9 - - + +
549B LEU* 6.3 0.4 - - - -
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Residues in contact with ARG 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B MET 3.4 13.3 + - - +
523B GLN* 3.2 30.7 + - - +
525B GLU* 1.3 78.3 - - - +
527B ILE* 1.3 61.0 + - - +
529B SER* 3.7 4.7 - - - -
530B GLU* 3.3 20.6 + - - +
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Residues in contact with ILE 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B LEU* 4.3 14.2 - - + +
511B ILE* 4.5 11.7 - - + -
512B GLY* 4.1 22.4 - - - +
515B TYR* 4.9 2.7 - - + -
523B GLN* 3.3 8.2 + - - +
524B ALA* 3.0 8.9 + - - +
526B ARG* 1.3 76.0 - - - +
528B PHE* 1.3 61.3 + - - +
530B GLU* 3.3 8.0 + - - +
531B VAL* 2.9 27.2 + - - +
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Residues in contact with PHE 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B CYS* 4.0 20.2 - - - -
512B GLY* 3.4 40.2 - - - -
513B ARG 3.7 0.4 - - - -
524B ALA* 3.0 24.8 + - + +
527B ILE* 1.3 73.9 - - - +
529B SER* 1.3 54.2 + - - +
531B VAL* 2.7 12.7 + - + +
532B ARG* 2.7 34.1 + - - +
541B GLY 3.4 19.3 - - - -
542B MET* 5.4 1.1 - - + -
544B ILE* 3.4 22.4 - - + -
545B TYR* 3.4 58.7 - + + -
548B THR* 3.9 13.5 - - - -
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Residues in contact with SER 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B GLU 3.0 19.5 + - - -
526B ARG* 3.7 5.8 - - - -
528B PHE* 1.3 76.4 - - - +
530B GLU* 1.3 61.8 + - - +
532B ARG* 3.4 9.3 - - - +
533B ARG* 3.2 19.6 + - - +
545B TYR* 3.9 16.0 + - - -
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Residues in contact with GLU 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B LEU* 5.9 2.0 - - + -
526B ARG 3.3 10.5 + - - +
527B ILE* 3.3 12.2 + - - +
528B PHE 3.0 0.8 - - - -
529B SER* 1.3 77.1 - - - +
531B VAL* 1.3 59.4 + - - +
533B ARG* 2.8 10.1 + - - +
534B ILE* 2.8 38.3 + - + +
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Residues in contact with VAL 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B GLY* 4.5 12.8 - - - +
508B LEU* 4.2 20.1 - - + +
509B CYS* 4.8 7.0 - - + +
527B ILE 2.9 13.6 + - - +
528B PHE* 2.7 22.7 + - + +
530B GLU* 1.3 71.4 - - - +
532B ARG* 1.3 55.1 + - - +
534B ILE* 4.4 7.6 - - - -
535B GLU* 2.8 34.7 + - - +
538B ARG* 5.4 5.9 - - - +
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Residues in contact with ARG 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B PHE 2.7 14.3 + - - +
529B SER* 3.4 15.0 - - - +
531B VAL* 1.3 70.5 - - - +
533B ARG* 1.3 66.6 + - - +
535B GLU 4.6 3.8 - - - -
536B ASN* 3.1 30.5 + - - +
545B TYR* 5.0 9.9 - - + -
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Residues in contact with ARG 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B SER 3.2 9.3 + - - +
530B GLU* 2.8 12.8 + - - +
532B ARG* 1.3 80.9 - - - +
534B ILE* 1.3 68.4 + - + +
536B ASN* 4.7 3.3 + - - +
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Residues in contact with ILE 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503B ASN* 3.5 31.4 - - + +
504B THR* 4.9 1.1 - - - -
505B GLY 4.4 12.6 - - - +
530B GLU* 2.8 26.0 + - + +
531B VAL* 3.9 6.1 - - - +
533B ARG* 1.3 83.7 - - + +
535B GLU* 1.3 62.8 + - + +
536B ASN* 3.9 2.5 + - - +
537B TYR* 4.8 4.9 - - - -
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Residues in contact with GLU 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLU* 4.3 10.6 - - - +
48A TYR* 4.9 0.4 + - - -
504B THR* 4.1 5.0 + - - -
505B GLY* 3.1 32.9 + - - -
506B TRP 4.2 0.9 + - - -
531B VAL 2.8 22.1 + - - +
532B ARG* 4.6 1.2 - - - -
534B ILE* 1.3 79.0 - - + +
536B ASN* 1.3 55.7 + - - +
537B TYR* 3.0 46.7 + - + +
538B ARG* 2.9 65.0 + - + +
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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