Contacts of the helix formed by residues 554 - 567 (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 LYS 554 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549B LEU* 3.3 19.1 + - + +
552B LEU* 3.3 10.6 + - + +
553B GLN* 1.3 73.0 - - - +
555B ASP* 1.3 64.9 + - - +
556B VAL* 3.0 13.5 - - + -
557B ALA* 2.9 17.1 + - + -
558B LEU* 2.9 21.3 + - - +
585B LEU* 4.1 0.6 - - - +
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Residues in contact with ASP 555 (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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553B GLN 3.6 4.4 + - - -
554B LYS* 1.3 74.6 - - - +
556B VAL* 1.3 56.9 + - - +
558B LEU* 4.0 4.6 - - - +
559B SER* 2.9 31.7 + - - -
582B CYS* 4.7 6.3 - - - +
585B LEU* 3.7 29.1 - - + +
586B GLN* 5.5 4.3 - - + +
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Residues in contact with VAL 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B LYS* 4.1 16.8 - - + -
555B ASP* 1.3 80.4 - - - +
557B ALA* 1.3 71.4 + - + +
559B SER* 3.5 6.2 - - - -
560B VAL* 3.4 22.5 + - + +
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Residues in contact with ALA 557 (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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545B TYR* 5.8 4.9 - - + +
549B LEU* 5.1 6.3 - - + -
554B LYS* 2.9 19.0 + - + +
556B VAL* 1.3 79.9 - - + +
558B LEU* 1.3 60.6 + - - +
559B SER 3.1 1.6 - - - -
560B VAL* 3.2 10.4 + - - +
561B LEU* 2.9 30.4 + - - +
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Residues in contact with LEU 558 (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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546B SER* 5.2 6.1 - - - +
549B LEU* 4.2 22.7 - - + +
550B TRP* 5.9 0.7 - - + -
554B LYS 2.9 16.0 + - - +
555B ASP* 4.0 8.7 - - - +
557B ALA* 1.3 76.8 - - - +
559B SER* 1.3 56.4 + - - +
561B LEU* 3.9 7.4 - - - +
562B SER* 3.1 30.1 + - - -
578B ALA 4.9 1.8 - - - +
581B ASN* 5.8 1.8 - - + -
582B CYS* 3.7 21.1 - - + +
585B LEU* 4.9 4.5 - - + -
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Residues in contact with SER 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B ASP 2.9 19.1 + - - -
556B VAL* 3.5 7.4 - - - -
557B ALA 3.1 0.2 - - - -
558B LEU* 1.3 74.9 - - - +
560B VAL* 1.3 67.0 + - - +
562B SER* 3.3 2.4 + - - -
563B LYS* 3.0 27.4 + - - +
582B CYS* 3.8 15.9 - - - -
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Residues in contact with VAL 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B VAL* 3.4 13.6 + - + +
557B ALA* 3.2 12.0 + - - +
559B SER* 1.3 77.3 - - - +
561B LEU* 1.3 65.1 + - - +
563B LYS* 3.9 4.4 - - - +
564B ASP* 3.2 36.7 + - - +
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Residues in contact with LEU 561 (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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545B TYR* 5.2 16.8 - - + -
546B SER* 5.9 7.4 - - - -
557B ALA 2.9 17.0 + - - +
558B LEU* 3.9 8.7 - - - +
560B VAL* 1.3 82.5 - - + +
562B SER* 1.3 57.6 + - - +
564B ASP* 3.5 4.6 + - - +
565B LEU* 3.0 30.3 + - - +
578B ALA* 5.2 5.4 - - + -
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Residues in contact with SER 562 (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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558B LEU 3.1 15.7 + - - -
559B SER* 3.3 8.0 + - - -
561B LEU* 1.3 77.5 - - - +
563B LYS* 1.3 59.8 + - - +
565B LEU* 4.8 0.4 - - - -
566B THR* 2.4 41.0 + - - +
578B ALA* 4.0 14.6 - - - +
579B ALA* 3.7 33.0 - - - +
582B CYS* 4.0 11.4 - - - +
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Residues in contact with LYS 563 (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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559B SER 3.0 14.6 + - - +
560B VAL* 3.9 4.5 - - - +
562B SER* 1.3 81.6 + - - +
564B ASP* 1.3 62.4 + - - +
566B THR* 2.6 19.2 + - - -
567B ASP* 3.4 12.6 + - - +
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Residues in contact with ASP 564 (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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59A ARG* 6.0 0.2 + - - -
560B VAL* 3.2 31.2 + - - +
561B LEU* 3.6 5.8 - - - +
563B LYS* 1.3 80.4 - - - +
565B LEU* 1.3 57.8 + - - +
567B ASP* 3.9 1.0 - - - +
568B MET* 3.1 29.3 + - - +
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Residues in contact with LEU 565 (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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539B VAL* 5.2 11.1 - - + +
561B LEU 3.0 17.4 + - - +
562B SER* 4.1 3.1 - - - +
564B ASP* 1.3 75.2 - - - +
566B THR* 1.3 67.8 + - - +
568B MET* 3.7 5.5 - - - +
569B ASP* 3.0 21.0 + - - +
575B ALA* 3.4 28.5 - - + +
578B ALA* 4.9 4.9 - - + -
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Residues in contact with THR 566 (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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562B SER 2.4 30.8 + - - +
563B LYS* 2.6 19.6 + - - -
565B LEU* 1.3 78.7 - - - +
567B ASP* 1.3 57.3 + - - +
569B ASP 3.3 0.7 - - - -
570B LYS* 3.1 31.2 + - - +
575B ALA* 3.7 24.9 - - - +
576B TRP* 4.1 24.5 - - + -
579B ALA* 3.9 17.3 - - + -
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Residues in contact with ASP 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 5.8 0.3 + - - -
563B LYS 3.4 12.3 + - - +
564B ASP 3.9 1.8 - - - +
566B THR* 1.3 78.5 + - - +
568B MET* 1.3 60.0 + - - +
570B LYS* 5.2 1.1 - - - +
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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