Contacts of the helix formed by residues 50 - 60 (chain A) in PDB entry 1RUV
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 SER 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A MET* 4.0 0.2 - - - -
15A SER* 4.0 6.5 - - - -
49A GLU* 1.3 80.3 + - - +
51A LEU* 1.3 67.8 - - - +
52A ALA* 3.8 8.2 + - - +
53A ASP* 3.1 39.2 + - - +
54A VAL* 3.2 12.5 + - - +
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Residues in contact with LEU 51 (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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8A PHE* 5.5 3.4 - - + -
9A GLU* 3.5 45.5 - - + +
13A MET* 3.9 26.0 - - + -
15A SER* 3.8 6.7 + - - +
49A GLU 3.6 1.8 + - - -
50A SER* 1.3 76.5 - - - +
52A ALA* 1.3 56.7 + - - +
54A VAL* 3.1 4.3 + - + -
55A GLN* 2.8 60.3 + - + +
117A PRO* 6.3 0.4 - - + -
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Residues in contact with ALA 52 (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 SER* 3.2 8.0 + - - +
51A LEU* 1.3 78.3 - - - +
53A ASP* 1.4 60.8 + - - +
55A GLN* 3.8 15.1 - - - +
56A ALA* 2.9 29.1 + - - +
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Residues in contact with ASP 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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49A GLU* 4.4 13.9 - - + +
50A SER* 3.1 27.1 + - - +
52A ALA* 1.4 81.7 - - - +
54A VAL* 1.3 64.4 - - - +
56A ALA* 3.4 16.8 - - - +
57A VAL* 3.7 10.9 + - - +
60A GLN* 4.7 1.7 + - - -
79A MET* 3.8 14.7 - - + +
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Residues in contact with VAL 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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8A PHE* 3.8 34.8 - - + -
13A MET* 3.7 16.8 - - + -
47A VAL* 3.6 29.6 - - + -
49A GLU* 4.1 6.3 - - + -
50A SER 3.2 11.8 + - - +
51A LEU* 3.1 7.9 + - + +
53A ASP* 1.3 77.3 - - - +
55A GLN* 1.3 67.6 - - - +
57A VAL* 3.0 24.3 + - - +
58A CYS 4.3 0.2 + - - -
79A MET* 4.2 6.7 - - - -
106A ILE* 4.2 13.7 - - + -
108A VAL* 5.0 1.1 - - + +
117A PRO* 3.8 10.9 - - + +
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Residues in contact with GLN 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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9A GLU* 4.5 5.3 + - - -
51A LEU* 2.8 54.3 + - + +
52A ALA* 3.8 15.9 - - - +
54A VAL* 1.3 74.1 - - - +
56A ALA* 1.3 61.6 + - - +
57A VAL 3.1 1.2 + - - -
58A CYS* 3.1 22.2 + - - +
59A SER* 4.6 0.3 + - - -
115A TYR 4.5 3.6 - - - +
116A VAL* 4.4 20.0 - - + +
117A PRO* 3.8 23.3 - - + -
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Residues in contact with ALA 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 ALA 2.9 18.2 + - - +
53A ASP* 3.4 12.3 - - - +
54A VAL 3.1 0.2 - - - -
55A GLN* 1.3 78.4 - - - +
57A VAL* 1.3 59.4 + - - +
58A CYS 3.0 1.3 - - - -
59A SER* 2.7 29.9 + - - +
60A GLN* 3.3 17.7 + - - +
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Residues in contact with VAL 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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53A ASP 3.7 11.7 - - - +
54A VAL* 3.0 17.8 + - - +
56A ALA* 1.3 76.6 - - - +
58A CYS* 1.3 56.6 - - - +
59A SER 3.0 0.2 - - - -
60A GLN* 2.8 29.9 + - - +
73A TYR* 3.1 39.8 - - - +
74A GLN 3.8 1.8 - - - -
75A SER* 3.6 38.4 - - - +
79A MET* 3.8 11.0 - - + -
106A ILE* 4.4 10.1 - - + +
108A VAL* 4.0 14.1 - - + -
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Residues in contact with CYS 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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55A GLN 3.1 10.6 + - - +
56A ALA 3.0 1.2 - - - -
57A VAL* 1.3 77.2 - - - +
59A SER* 1.3 56.3 + - - +
60A GLN 3.5 0.4 - - - -
73A TYR* 3.5 21.3 - - - -
108A VAL* 4.7 0.2 - - - -
110A CYS* 2.0 54.1 - - + -
115A TYR* 3.6 29.7 - - + +
116A VAL* 3.5 22.2 - - - -
117A PRO* 3.5 13.0 - - - -
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Residues in contact with SER 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 GLN 4.6 0.2 + - - -
56A ALA* 2.7 24.3 + - - +
57A VAL 3.0 0.2 - - - -
58A CYS* 1.3 78.6 - - - +
60A GLN* 1.3 67.1 + - - +
73A TYR* 4.9 1.1 - - - -
76A TYR* 4.4 4.9 + - - -
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Residues in contact with GLN 60 (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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53A ASP 4.7 1.6 + - - -
56A ALA* 3.3 34.7 + - - +
57A VAL* 2.8 19.9 + - - +
58A CYS 3.5 0.8 - - - -
59A SER* 1.3 85.2 + - - +
61A LYS* 1.3 64.0 + - - +
62A ASN* 3.3 4.0 + - - +
73A TYR* 3.8 8.7 - - - -
74A GLN 3.5 8.1 - - - +
75A SER* 3.3 9.9 - - - -
76A TYR* 2.8 67.3 + - + +
77A SER 4.6 0.7 + - - -
79A MET* 5.7 1.3 - - - +
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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