Contacts of the helix formed by residues 52 - 59 (chain A) in PDB entry 4RQO
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 GLY 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A TYR* 1.3 71.3 - - - +
53A SER* 1.3 57.8 + - - -
55A ALA* 3.1 3.0 + - - +
56A LEU* 2.9 34.8 + - - +
116A LEU 3.5 6.5 + - - -
117A GLN 4.2 7.6 - - - +
119A GLU 3.2 20.5 + - - -
120A LEU* 4.0 16.4 - - - -
125A SER 3.6 5.6 - - - -
451A LEU* 4.7 1.1 - - - -
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Residues in contact with SER 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A HIS* 2.8 16.7 + - - -
52A GLY* 1.3 73.2 - - - -
54A LEU* 1.3 58.0 + - - +
56A LEU* 3.9 9.4 - - - +
57A THR* 3.1 16.3 + - - -
125A SER* 3.0 30.2 + - - -
126A ASN* 2.3 32.0 + - - -
444A LYS* 6.2 0.4 - - - -
451A LEU* 3.7 17.4 - - - +
455A LEU* 3.9 9.8 - - - +
457A GLU* 4.6 11.6 - - - +
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER 4.3 3.6 - - - +
19A HIS* 3.5 26.9 - - + +
23A PRO* 4.0 15.9 - - + -
50A LEU* 4.2 14.5 - - + +
51A TYR 3.1 13.0 + - - +
52A GLY 3.0 0.4 - - - -
53A SER* 1.3 76.2 - - - +
55A ALA* 1.3 58.1 + - - +
58A GLY* 2.9 30.0 + - - -
63A THR* 3.9 13.4 + - + +
126A ASN* 3.2 23.4 - - + +
127A GLY 3.7 12.6 - - - +
128A MSE 3.2 43.3 - - + -
147A SER* 5.2 0.2 - - - -
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 3.5 31.3 - - + +
51A TYR 3.4 2.0 + - - -
52A GLY 3.1 8.1 + - - +
54A LEU* 1.3 77.6 - - - +
56A LEU* 1.3 68.3 + - - +
57A THR 3.1 0.7 + - - -
58A GLY 3.4 6.2 + - - -
59A LYS* 4.6 1.0 + - - +
115A PHE* 3.5 24.6 - - - -
116A LEU 3.8 5.2 - - - +
117A GLN* 3.8 30.4 + - + +
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLY 2.9 20.2 + - - +
53A SER* 3.9 7.9 - - - +
54A LEU 3.4 0.4 - - - -
55A ALA* 1.3 79.6 - - - +
57A THR* 1.3 67.7 + - + +
59A LYS* 5.4 0.9 + - - +
117A GLN* 3.5 44.2 + - + +
447A SER 5.3 3.4 - - - +
448A MSE 3.6 27.4 - - - +
449A GLY* 3.8 19.1 - - - +
451A LEU* 4.1 25.6 - - + -
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Residues in contact with THR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A HIS* 3.1 6.2 + - - -
53A SER 3.1 13.6 + - - -
56A LEU* 1.3 87.8 - - + +
58A GLY* 1.3 66.5 + - - +
59A LYS* 3.2 3.1 - - - -
60A GLY* 3.2 8.0 + - - +
61A HIS* 3.1 28.2 + - - -
389A LEU 4.7 4.5 - - - +
390A GLY* 4.0 23.6 - - - -
444A LYS* 6.0 0.2 - - - +
448A MSE 5.5 9.2 - - + +
457A GLU* 2.6 33.8 + - - +
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Residues in contact with GLY 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A HIS* 4.3 3.1 - - - -
54A LEU 2.9 18.8 + - - -
55A ALA 3.4 4.9 + - - -
57A THR* 1.3 77.7 - - - +
59A LYS* 1.3 57.0 + - - +
61A HIS 3.1 0.8 + - - -
62A GLY 2.8 9.9 + - - -
63A THR* 2.7 52.1 + - - -
64A ASP 5.0 0.9 - - - -
115A PHE* 4.5 5.2 - - - -
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Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ALA 4.6 1.0 + - - +
56A LEU 6.0 0.7 - - - +
57A THR 3.2 0.8 - - - -
58A GLY* 1.3 75.6 - - - +
60A GLY* 1.3 62.9 + - - +
62A GLY* 2.9 15.1 + - - -
64A ASP* 3.8 25.9 - - - +
88A MSE 6.4 1.3 - - - -
115A PHE* 3.9 24.1 - - + -
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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