Contacts of the helix formed by residues 504 - 518 (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 THR 504 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A GLU* 4.8 5.4 + - - +
30A ARG* 2.6 34.9 + - - +
33A ALA* 4.9 8.4 - - - +
500B HIS 4.5 2.4 + - - -
501B HIS* 3.0 32.6 + - - +
502B TYR 3.4 2.4 - - - +
503B ASN* 1.3 80.4 - - - +
505B GLY* 1.3 68.2 + - - +
506B TRP* 4.0 3.5 + - - +
507B VAL* 3.5 22.2 - - + +
508B LEU* 3.4 17.5 + - - +
534B ILE* 4.7 2.5 - - - -
535B GLU* 4.1 5.1 + - - -
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Residues in contact with GLY 505 (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 4.0 0.4 + - - -
504B THR* 1.3 74.6 + - - +
506B TRP* 1.3 59.4 + - - +
508B LEU* 3.4 6.0 + - - +
509B CYS* 2.8 32.3 + - - +
531B VAL* 4.5 9.0 - - - +
534B ILE* 4.4 7.2 - - - +
535B GLU* 3.1 35.4 + - - -
538B ARG* 4.3 5.5 + - - -
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Residues in contact with TRP 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.5 24.7 - + - -
29A GLU* 3.9 18.4 - - - +
30A ARG* 4.4 5.8 - - - +
149B TRP* 3.6 37.0 - + - -
153B GLU* 4.6 10.3 + - - -
475B MET* 3.5 37.9 - - + -
479B TYR* 4.3 12.3 - + + -
504B THR* 3.4 4.4 + - + -
505B GLY* 1.3 75.0 - - - +
507B VAL* 1.3 95.4 + - + +
509B CYS* 3.2 1.4 + - - +
510B GLN* 3.0 61.5 + - + +
535B GLU* 4.2 1.4 + - - -
538B ARG* 3.4 37.4 - - - +
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Residues in contact with VAL 507 (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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475B MET* 3.8 17.7 - - + -
494B LEU* 4.2 21.3 - - + +
497B LEU* 5.7 0.2 - - + -
501B HIS 3.1 26.2 - - - +
502B TYR* 3.5 20.9 - - + +
504B THR* 3.5 9.0 - - + +
505B GLY 3.4 0.2 - - - -
506B TRP* 1.3 96.0 - - + +
508B LEU* 1.3 68.1 + - - +
510B GLN* 3.1 7.0 + - - +
511B ILE* 3.0 36.7 + - + +
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Residues in contact with LEU 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B TYR* 4.0 7.4 + - + +
503B ASN* 5.8 1.1 - - - -
504B THR 3.4 15.9 + - - +
505B GLY* 3.7 4.5 - - - +
507B VAL* 1.3 79.4 - - - +
509B CYS* 1.3 51.3 + - - +
511B ILE* 3.1 14.1 + - - +
512B GLY* 2.7 33.8 + - - -
527B ILE* 4.3 15.8 - - + +
528B PHE* 5.3 0.4 - - - -
530B GLU* 5.9 2.2 - - + -
531B VAL* 4.2 20.0 - - + +
534B ILE* 6.4 1.1 - - + -
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Residues in contact with CYS 509 (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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505B GLY 2.8 15.8 + - - +
506B TRP 3.3 10.3 - - - +
507B VAL 3.1 0.2 - - - -
508B LEU* 1.3 76.3 - - - +
510B GLN* 1.3 57.8 + - - +
512B GLY 3.2 0.9 + - - +
513B ARG* 2.6 36.8 + - - +
528B PHE* 4.0 14.6 - - - -
531B VAL* 4.8 4.2 - - + +
538B ARG* 3.6 15.5 - - - +
540B GLU 3.4 25.8 - - - -
541B GLY* 3.5 26.0 - - - -
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Residues in contact with GLN 510 (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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479B TYR* 3.6 26.1 - - + -
482B LEU* 5.3 11.1 - - + +
506B TRP* 3.0 74.2 + - + +
507B VAL* 3.1 5.6 + - - +
509B CYS* 1.3 84.4 - - - +
511B ILE* 1.3 54.9 + - + +
513B ARG* 3.2 10.8 - - - +
514B ALA* 2.8 32.7 + - - +
538B ARG* 4.2 4.0 - - - +
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Residues in contact with ILE 511 (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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490B ALA 5.6 1.3 - - - +
491B ILE* 4.8 21.3 - - + +
494B LEU* 4.9 6.1 - - + +
495B SER* 5.2 2.0 - - - +
502B TYR* 3.5 41.7 - - + +
507B VAL* 3.0 33.2 + - + +
508B LEU* 3.3 10.3 - - - +
510B GLN* 1.3 75.2 - - + +
512B GLY* 1.3 60.6 + - - +
514B ALA* 3.0 8.7 + - - +
515B TYR* 2.9 55.5 + - + -
527B ILE* 4.5 9.0 - - + -
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Residues in contact with GLY 512 (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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508B LEU 2.7 18.6 + - - -
509B CYS 3.5 3.1 - - - -
511B ILE* 1.3 71.3 - - - +
513B ARG* 1.3 61.2 + - - +
515B TYR* 3.5 6.3 + - - +
516B PHE 3.4 15.6 + - - -
524B ALA* 4.1 2.9 - - - +
527B ILE* 4.1 15.5 - - - +
528B PHE* 3.4 33.0 - - - -
544B ILE* 3.9 1.2 - - - +
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Residues in contact with ARG 513 (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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482B LEU* 6.1 3.1 - - + -
509B CYS* 2.6 19.4 + - - +
510B GLN* 3.2 20.4 - - - +
512B GLY* 1.3 73.4 - - - +
514B ALA* 1.3 62.8 + - - +
516B PHE* 3.3 13.7 + - - +
517B GLU* 3.4 10.8 + - - +
528B PHE* 3.7 0.8 - - - -
544B ILE* 3.5 19.3 - - + +
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Residues in contact with ALA 514 (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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482B LEU* 5.6 5.6 - - + +
487B CYS* 3.9 30.0 - - + +
490B ALA* 5.1 4.9 - - + -
491B ILE* 4.9 10.5 - - + +
510B GLN 2.8 16.4 + - - +
511B ILE* 3.3 12.6 - - - +
513B ARG* 1.3 73.4 - - - +
515B TYR* 1.3 57.6 + - + +
517B GLU* 2.8 23.5 + - - +
518B LEU* 2.8 19.2 + - + +
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Residues in contact with TYR 515 (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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491B ILE* 5.3 10.1 - - + +
511B ILE* 2.9 50.4 + - + +
512B GLY* 3.8 2.2 - - - +
513B ARG 3.5 0.2 - - - -
514B ALA* 1.3 72.1 - - + +
516B PHE* 1.3 57.0 + - - +
518B LEU* 3.7 20.4 - - + -
519B SER 3.3 0.9 + - - -
520B GLU* 2.7 56.6 + - + +
523B GLN* 3.4 42.9 + - + +
524B ALA* 3.7 20.9 - - + -
527B ILE* 4.9 2.2 - - + -
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Residues in contact with PHE 516 (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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512B GLY 3.4 4.4 + - - +
513B ARG 3.3 10.4 + - - +
514B ALA 3.1 1.2 - - - -
515B TYR* 1.3 79.1 - - - +
517B GLU* 1.3 58.6 + - - +
519B SER* 2.9 20.1 + - - +
520B GLU 5.4 0.4 - - - -
521B TYR* 5.8 1.6 - - - +
524B ALA* 4.7 4.5 - - + -
544B ILE* 3.6 24.9 - - + +
548B THR* 4.3 13.0 - - - +
677B LEU* 5.3 8.3 - - - +
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Residues in contact with GLU 517 (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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485B TYR* 4.8 21.8 - - + +
487B CYS* 4.5 10.3 - - + -
513B ARG 3.4 8.6 + - - +
514B ALA* 2.8 14.5 + - - +
516B PHE* 1.3 77.2 - - - +
518B LEU* 1.3 58.2 + - - +
519B SER* 3.1 5.3 + - - -
641B TYR* 6.0 2.0 - - - -
671B ASN* 5.3 8.8 + - - +
673B GLN* 4.6 16.8 - - - +
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Residues in contact with LEU 518 (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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487B CYS* 3.5 24.9 - - + +
488B LYS* 3.7 25.6 - - + +
491B ILE* 5.6 4.0 - - + -
514B ALA* 2.8 18.8 + - + +
515B TYR* 3.7 37.2 - - + +
517B GLU* 1.3 75.2 - - - +
519B SER* 1.3 65.0 + - - +
520B GLU* 3.0 10.6 + - + +
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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