Contacts of the helix formed by residues 52 - 61 (chain V) in PDB entry 6QXT
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 THR 52 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43U LEU* 5.5 5.6 - - - -
45U THR 3.9 17.9 - - - -
46U THR* 3.7 10.7 + - - -
48U ILE* 3.1 26.5 + - - -
50U LEU 5.9 0.2 - - - +
67U PHE* 6.1 5.3 - - - +
68U CYS 5.0 5.1 - - - +
51V THR* 1.3 73.3 - - - +
53V MET* 1.3 57.3 + - - +
55V VAL* 3.3 10.6 + - - +
56V LYS* 2.9 27.2 + - - +
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Residues in contact with MET 53 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46U THR* 3.0 34.0 + - - +
17V TYR* 4.7 7.6 - - + +
51V THR* 3.2 6.2 - - - -
52V THR* 1.3 74.8 - - - +
54V LEU* 1.3 59.6 + - - +
56V LYS* 3.2 4.9 + - - +
57V ARG* 2.9 28.8 + - - +
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Residues in contact with LEU 54 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15V LEU* 4.9 4.0 - - + +
16V SER* 4.4 7.4 - - - +
17V TYR* 3.8 31.9 - - + +
50V LEU* 5.7 2.9 - - + -
51V THR* 3.1 19.8 + - - +
53V MET* 1.3 78.9 - - - +
55V VAL* 1.3 58.3 + - - +
57V ARG* 3.5 3.5 + - - +
58V LEU* 2.9 28.2 + - - +
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Residues in contact with VAL 55 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67U PHE* 5.5 11.0 - - + -
76U ALA* 6.0 0.3 - - - +
50V LEU* 6.4 0.7 - - + -
51V THR 3.1 12.3 + - - +
52V THR* 3.5 13.2 - - - +
53V MET 3.2 0.2 - - - -
54V LEU* 1.3 76.3 - - - +
56V LYS* 1.3 58.7 + - - +
58V LEU* 3.3 6.9 + - - +
59V VAL* 2.9 27.7 + - - +
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Residues in contact with LYS 56 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46U THR* 5.4 3.4 - - - -
68U CYS 4.6 4.9 - - - +
69U ASP* 4.5 26.0 - - + -
70U ASP 5.5 0.7 - - - +
75U THR* 5.7 4.7 - - - -
52V THR 2.9 14.0 + - - +
53V MET* 3.2 10.5 + - - +
55V VAL* 1.3 77.9 - - - +
57V ARG* 1.3 57.0 + - - +
59V VAL* 3.2 7.8 + - - +
60V ASP* 2.9 29.2 + - - +
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Residues in contact with ARG 57 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17V TYR* 4.8 10.1 - - + -
53V MET 2.9 16.0 + - - +
54V LEU* 3.8 7.6 - - - +
56V LYS* 1.3 76.1 - - - +
58V LEU* 1.3 57.4 + - - +
60V ASP* 3.8 6.9 - - - +
61V GLU* 2.9 30.0 + - - +
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Residues in contact with LEU 58 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54V LEU 2.9 17.2 + - - +
55V VAL* 3.6 9.0 - - - +
56V LYS 3.2 0.2 - - - -
57V ARG* 1.3 75.5 - - - +
59V VAL* 1.3 59.8 + - - +
61V GLU* 3.4 5.5 + - - -
62V ASN 3.0 21.7 + - - -
63V ILE* 3.0 32.4 + - + +
65V VAL* 5.6 7.9 - - + -
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Residues in contact with VAL 59 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75U THR* 4.4 20.2 - - - -
76U ALA* 4.6 15.9 - - + -
55V VAL 2.9 16.5 + - - +
56V LYS* 3.2 8.5 + - - +
58V LEU* 1.3 75.6 - - - +
60V ASP* 1.3 63.4 + - - +
62V ASN* 3.2 13.1 + - - +
63V ILE 5.5 0.4 - - - -
80V PRO* 4.9 15.7 - - + +
83V ALA* 6.2 0.3 - - - -
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Residues in contact with ASP 60 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56V LYS 2.9 16.7 + - - +
57V ARG* 3.9 7.2 - - - +
59V VAL* 1.3 77.1 - - - +
61V GLU* 1.3 58.9 + - - +
62V ASN* 3.2 2.6 + - - +
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Residues in contact with GLU 61 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35V LEU* 5.1 20.9 - - + +
57V ARG 2.9 19.1 + - - +
58V LEU* 3.9 6.3 - - - +
59V VAL 3.3 0.2 - - - -
60V ASP* 1.3 74.7 - - - +
62V ASN* 1.3 71.0 + - - +
63V ILE* 3.5 8.2 + - + +
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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