Contacts of the helix formed by residues 562 - 571 (chain B) in PDB entry 3RWR
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 562 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560B ALA 3.7 1.1 + - - +
561B MET* 1.3 86.3 - - + +
563B LYS* 1.3 54.7 + - - +
564B GLY* 2.8 20.3 + - - +
565B LYS* 2.9 12.3 + - + +
566B TYR* 2.8 31.0 + - - +
92H GLU* 4.9 8.1 - - - +
109H ARG* 5.7 1.9 + - - +
116H PRO* 4.8 1.0 - - - +
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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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529B GLU* 5.4 7.6 - - + -
552B ILE* 3.0 19.6 + - + +
553B SER* 2.7 35.5 + - - +
556B ALA* 3.1 16.1 - - - +
557B ASP* 3.1 19.9 + - - -
561B MET 3.7 4.2 + - - -
562B GLU* 1.3 71.3 - - - +
564B GLY* 1.3 61.5 + - - +
565B LYS 3.2 0.8 + - - -
566B TYR* 3.5 28.6 + - + -
567B VAL* 4.0 23.8 + - + +
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Residues in contact with GLY 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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562B GLU* 2.8 17.0 + - - +
563B LYS* 1.3 79.4 - - - +
565B LYS* 1.3 64.8 + - - +
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Residues in contact with LYS 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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561B MET* 4.7 10.1 - - + -
562B GLU* 2.9 12.5 + - + +
564B GLY* 1.3 79.7 - - - +
566B TYR* 1.3 64.8 + - - +
567B VAL 3.6 0.7 - - - -
568B GLY* 3.6 8.0 + - - +
569B GLU* 3.2 27.1 + - + +
111H GLU* 4.9 16.5 + - - +
114H GLY* 5.3 5.4 - - - +
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Residues in contact with TYR 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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552B ILE* 3.4 39.1 - - + +
555B GLU* 3.2 29.2 - - + +
556B ALA* 3.4 24.7 - - + -
561B MET* 4.0 22.4 - - + -
562B GLU 2.8 16.4 + - - +
563B LYS* 3.5 20.1 + - + -
565B LYS* 1.3 74.4 - - - +
567B VAL* 1.3 63.7 + - + +
568B GLY 2.9 1.3 - - - -
569B GLU* 2.7 31.0 + - + +
570B LEU* 3.3 37.0 + - + +
608B LEU* 4.3 14.9 + - + -
64H ARG* 5.1 4.9 - - - -
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Residues in contact with VAL 567 (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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527B THR* 6.1 0.4 - - + -
528B LEU* 3.6 36.2 - - + +
529B GLU* 4.2 19.3 - - + +
552B ILE* 3.9 19.1 - - + -
563B LYS* 4.0 21.0 + - + +
566B TYR* 1.3 82.3 - - + +
568B GLY* 1.3 62.1 + - - +
570B LEU* 3.4 23.7 + - - +
571B ARG* 3.7 16.0 + - - +
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Residues in contact with GLY 568 (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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564B GLY 5.6 0.6 + - - -
565B LYS* 3.6 10.4 + - - +
566B TYR 2.9 1.6 + - - -
567B VAL* 1.3 77.5 - - - +
569B GLU* 1.3 64.2 + - - +
571B ARG* 3.0 33.0 + - - +
572B LYS* 3.9 3.1 + - - +
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Residues in contact with GLU 569 (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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561B MET* 4.4 14.1 - - - -
565B LYS* 3.2 20.6 + - + +
566B TYR* 2.7 18.2 + - + +
568B GLY* 1.3 71.8 - - - +
570B LEU* 1.3 61.8 + - - +
572B LYS* 2.9 18.0 + - - +
573B ALA* 3.3 12.7 + - - +
584B TYR* 2.6 31.3 + - + +
599B LYS* 2.8 30.4 + - - +
608B LEU* 6.1 5.1 - - + +
113H SER 5.1 2.4 - - - +
114H GLY* 5.3 4.9 - - - +
115H LEU* 4.2 9.6 - - + +
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Residues in contact with LEU 570 (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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528B LEU* 3.9 17.0 - - + -
532B PHE* 5.5 5.6 - - + -
552B ILE* 3.9 15.5 - - + -
566B TYR* 3.3 44.8 + - + +
567B VAL* 3.4 23.1 - - - +
568B GLY 3.2 0.2 - - - -
569B GLU* 1.3 78.5 - - - +
571B ARG* 1.3 56.2 + - - +
573B ALA* 3.7 2.5 - - - +
574B LEU* 3.0 61.1 + - + +
575B LEU* 4.1 1.4 - - - +
597B PHE* 4.6 13.7 - - + -
608B LEU* 5.4 2.7 - - + +
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Residues in contact with ARG 571 (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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524B TRP* 4.7 18.4 - - - -
526B LYS 5.5 2.0 + - - -
527B THR* 5.5 1.4 - - - +
528B LEU* 3.3 48.8 - - + +
567B VAL* 3.7 15.9 + - - +
568B GLY* 3.0 21.8 + - - +
570B LEU* 1.3 79.0 - - - +
572B LYS* 1.3 57.2 + - + +
573B ALA 3.4 0.2 - - - -
575B LEU* 3.1 33.5 + - + +
576B SER 3.0 16.6 - - - +
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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