Contacts of the helix formed by residues 466 - 484 (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 466 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465B ALA* 1.3 78.7 - - - +
467B GLY* 1.3 57.3 + - - +
469B MET* 4.1 6.5 - - - +
470B SER* 3.0 31.6 + - - -
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Residues in contact with GLY 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B ALA 3.1 4.2 - - - +
466B GLU* 1.3 77.4 - - - +
468B LEU* 1.3 62.7 + - - +
470B SER* 2.9 18.5 + - - -
471B LEU* 3.2 12.6 + - - +
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Residues in contact with LEU 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 6.1 5.4 - - + -
27A LEU* 5.9 6.3 - - + -
465B ALA* 3.0 13.0 + - - +
467B GLY* 1.3 73.4 - - - +
469B MET* 1.3 57.7 + - + +
471B LEU* 3.0 8.1 + - - +
472B LEU* 2.7 47.7 + - + +
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Residues in contact with MET 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B PRO* 5.1 11.0 - - + +
168B PHE* 3.3 29.2 - - + +
169B LYS* 5.3 1.3 - - - -
170B PHE* 4.5 19.3 - - + +
465B ALA* 3.2 16.0 + - + +
466B GLU* 4.1 6.1 - - - +
468B LEU* 1.3 76.9 - - + +
470B SER* 1.3 53.4 + - - +
472B LEU* 3.5 12.9 - - + +
473B ARG* 2.6 38.8 + - - +
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Residues in contact with SER 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B GLU 3.0 17.7 + - - -
467B GLY* 2.9 22.5 + - - -
469B MET* 1.3 75.4 - - - +
471B LEU* 1.3 59.9 + - - +
473B ARG* 3.9 6.5 - - - +
474B GLU* 3.5 21.3 + - - +
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Residues in contact with LEU 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B GLY 3.2 9.4 + - - +
468B LEU* 3.0 10.9 + - - +
470B SER* 1.3 80.2 + - - +
472B LEU* 1.3 67.3 + - + +
474B GLU* 3.2 5.4 + - - +
475B MET* 3.0 38.0 + - - +
501B HIS* 6.3 7.0 - - + +
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Residues in contact with LEU 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 4.3 27.1 - - + -
27A LEU* 5.2 11.0 - - + -
30A ARG* 5.1 9.0 - - + -
146B PRO 3.4 26.0 - - - +
147B PHE* 4.4 13.7 - - - +
148B LEU 6.1 0.4 - - - -
149B TRP* 4.2 10.4 - - + -
168B PHE* 4.2 20.3 - - + -
468B LEU* 2.7 30.4 + - + +
469B MET* 3.5 13.2 - - + +
471B LEU* 1.3 74.9 - - + +
473B ARG* 1.3 52.1 + - - +
475B MET* 3.4 8.0 + - - +
476B GLY* 2.7 35.2 + - - -
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Residues in contact with ARG 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B PRO* 3.2 35.2 - - + +
165B ASP* 4.6 6.7 - - - +
168B PHE* 4.2 8.9 - - + -
469B MET 2.6 21.5 + - - +
470B SER* 3.9 8.5 - - - +
472B LEU* 1.3 73.5 - - - +
474B GLU* 1.3 57.0 + - - +
477B LYS* 2.9 26.7 + - - +
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Residues in contact with GLU 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B SER 3.5 10.8 + - - +
471B LEU* 3.2 10.1 + - - +
473B ARG* 1.3 76.0 - - - +
475B MET* 1.3 66.4 + - + +
477B LYS* 3.5 6.9 + - - +
478B GLY* 3.1 18.2 + - - -
493B ILE* 4.5 17.5 - - - +
494B LEU* 4.9 2.7 - - - +
497B LEU* 6.0 7.4 - - + -
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Residues in contact with MET 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 4.1 7.6 - - + -
30A ARG* 3.5 35.7 - - - +
149B TRP* 4.0 8.0 - - + -
471B LEU* 3.0 29.9 + - - +
472B LEU* 3.8 8.1 - - - +
474B GLU* 1.3 74.5 - - + +
476B GLY* 1.3 61.6 + - - +
478B GLY* 3.2 3.4 + - - -
479B TYR* 3.0 27.4 + - - +
494B LEU* 5.2 10.1 - - + +
497B LEU* 5.4 11.7 - - + -
501B HIS* 5.3 10.3 - - - +
506B TRP* 3.5 40.3 - - + -
507B VAL* 3.8 17.3 - - + -
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Residues in contact with GLY 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B TRP* 3.6 8.7 - - - -
152B PHE* 3.3 37.5 - - - -
164B PRO* 4.4 0.7 - - - -
168B PHE* 4.6 2.7 - - - -
472B LEU 2.7 21.1 + - - -
473B ARG 3.8 0.9 - - - -
475B MET* 1.3 71.3 - - - +
477B LYS* 1.3 62.8 + - - +
479B TYR 3.3 0.5 + - - -
480B LEU* 3.0 21.3 + - - +
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Residues in contact with LYS 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B PRO* 3.8 13.7 - - + +
473B ARG 2.9 19.4 + - - +
474B GLU* 3.7 7.4 - - - +
476B GLY* 1.3 74.4 - - - +
478B GLY* 1.3 61.4 + - - +
480B LEU* 3.8 8.9 + - - +
481B ALA* 3.3 20.6 + - - +
493B ILE* 5.4 7.6 - - + +
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Residues in contact with GLY 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B GLU 3.1 14.0 + - - -
475B MET 3.2 4.0 + - - -
476B GLY 3.1 1.0 - - - -
477B LYS* 1.3 74.4 - - - +
479B TYR* 1.3 63.9 + - - +
481B ALA* 3.1 9.7 + - - +
482B LEU* 3.1 17.9 + - - +
490B ALA* 3.5 22.2 - - - +
493B ILE* 4.8 6.3 - - - +
494B LEU* 4.6 10.1 - - - -
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Residues in contact with TYR 479 (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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149B TRP* 3.9 24.2 - + + -
153B GLU* 3.5 37.4 + - + +
156B CYS* 4.1 11.2 - - + -
157B GLU* 3.1 25.8 + - - +
475B MET 3.0 14.7 + - - +
476B GLY 3.9 3.8 - - - +
478B GLY* 1.3 74.8 - - - +
480B LEU* 1.3 57.3 + - - +
482B LEU* 3.2 11.7 + - + +
483B CYS* 2.8 54.5 + - - -
506B TRP* 4.3 15.0 - + + -
510B GLN* 3.6 31.0 - - + -
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Residues in contact with LEU 480 (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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152B PHE* 4.6 7.0 - - + -
156B CYS* 3.9 22.3 - - + -
160B GLU 5.2 1.8 - - - +
161B LYS* 4.5 18.8 - - + -
162B PRO* 3.0 35.4 - - + +
163B ASP* 5.3 0.4 - - - -
164B PRO* 5.1 3.4 - - + -
476B GLY 3.0 15.7 + - - +
477B LYS* 3.8 9.6 - - - +
479B TYR* 1.3 75.9 - - - +
481B ALA* 1.3 53.7 + - - +
483B CYS* 3.1 3.9 + - + +
484B SER* 2.6 50.7 + - - +
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Residues in contact with ALA 481 (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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477B LYS 3.3 11.2 + - - +
478B GLY* 3.1 10.4 + - - +
480B LEU* 1.3 76.9 - - - +
482B LEU* 1.3 60.7 + - - +
484B SER* 3.1 5.6 + - - +
485B TYR 2.8 24.6 + - - -
486B ASN* 3.1 25.9 + - + +
489B GLU* 4.5 6.7 - - + -
490B ALA* 3.5 21.1 - - + +
493B ILE* 6.2 0.7 - - + -
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Residues in contact with LEU 482 (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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478B GLY 3.1 9.3 + - - +
479B TYR* 3.5 19.3 - - + +
481B ALA* 1.3 78.5 - - - +
483B CYS* 1.3 58.9 + - - +
485B TYR* 3.1 29.8 + - - +
486B ASN 5.0 0.7 - - - -
487B CYS* 5.0 5.3 - - - +
490B ALA* 3.5 13.6 - - + +
510B GLN* 5.3 14.8 - - + +
513B ARG* 6.1 2.7 - - + -
514B ALA* 5.6 6.1 - - + +
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Residues in contact with CYS 483 (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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156B CYS* 3.6 35.1 - - + +
157B GLU* 4.2 7.6 - - - -
479B TYR* 2.8 53.1 + - - +
480B LEU* 3.1 8.3 + - + +
482B LEU* 1.3 74.4 - - - +
484B SER* 1.3 57.0 + - - +
485B TYR* 3.0 29.6 - - - -
670B ILE 4.9 0.2 - - - +
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Residues in contact with SER 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LYS* 5.3 3.3 - - - +
480B LEU* 2.6 39.4 + - - +
481B ALA* 3.1 5.6 + - - -
483B CYS* 1.3 70.6 - - - +
485B TYR* 1.3 68.5 + - - +
486B ASN* 3.2 20.5 + - - +
670B ILE 4.4 4.8 - - - +
672B PRO* 5.4 1.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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