Contacts of the helix formed by residues 32 - 45 (chain V) in PDB entry 5XS0
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 32 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208T CYS* 4.2 3.6 - - - -
203U ALA 4.4 0.2 + - - -
207U SER* 3.0 42.0 + - - +
30V GLN 3.4 6.4 + - - +
31V TYR* 1.3 74.6 - - - +
33V ALA* 1.3 58.3 + - - +
34V GLU* 3.6 20.3 + - - +
35V GLU* 3.2 12.0 + - - +
36V TYR* 2.7 31.4 + - - +
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Residues in contact with ALA 33 (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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205T TYR* 3.5 45.2 - - + +
208T CYS* 3.6 26.9 - - + +
32V THR* 1.3 72.9 - - - +
34V GLU* 1.3 70.5 + - - +
36V TYR* 3.5 0.7 + - - +
37V GLN* 2.9 27.4 + - - +
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Residues in contact with GLU 34 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205T TYR* 4.7 14.1 + - - +
203U ALA* 3.5 23.5 - - + +
206U ASN* 4.9 12.1 - - - +
32V THR* 3.2 20.6 + - - +
33V ALA* 1.3 85.1 + - - +
35V GLU* 1.3 56.9 + - - +
37V GLN* 3.9 3.0 - - - +
38V ALA* 2.9 30.8 + - - +
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Residues in contact with GLU 35 (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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200U VAL 4.9 2.5 - - - +
203U ALA* 3.5 16.5 - - + +
204U ARG* 3.2 43.3 + - + +
207U SER* 3.2 21.8 + - - -
31V TYR* 3.5 23.9 - - + -
32V THR* 3.2 16.8 + - - +
34V GLU* 1.3 75.5 - - - +
36V TYR* 1.3 66.7 + - - +
38V ALA* 3.8 1.8 - - - +
39V ILE* 2.9 39.5 + - + +
79V PHE 4.9 0.7 - - - +
116V LYS* 3.2 18.6 + - - -
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Residues in contact with TYR 36 (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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201T GLU* 3.2 29.9 + - - -
204T ARG* 2.4 55.8 + - + -
205T TYR* 4.7 9.4 - - - -
208T CYS* 4.3 18.8 - - - -
80U GLY* 4.4 3.4 - - - -
81U TYR* 3.3 34.2 - + - -
82U ASN* 3.6 20.9 - - - +
31V TYR* 4.0 13.5 - - + +
32V THR 2.7 22.5 + - - +
33V ALA 3.9 5.4 - - - +
35V GLU* 1.3 73.9 - - - +
37V GLN* 1.3 62.5 + - + +
40V GLN* 2.9 35.1 + - + +
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Residues in contact with GLN 37 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201T GLU* 4.0 16.9 + - - +
205T TYR* 2.9 36.2 + - + +
33V ALA 2.9 17.4 + - - +
34V GLU* 3.9 3.9 - - - +
36V TYR* 1.3 84.5 - - + +
38V ALA* 1.3 63.8 + - - +
40V GLN* 3.4 2.7 + - + +
41V LYS* 3.0 57.4 + - + +
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Residues in contact with ALA 38 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199U SER* 3.8 20.6 - - - +
200U VAL* 3.5 31.0 - - + +
203U ALA* 4.4 3.4 - - + -
34V GLU 2.9 17.7 + - - +
35V GLU 3.8 3.1 - - - +
37V GLN* 1.3 76.0 - - - +
39V ILE* 1.3 57.0 - - - +
41V LYS* 3.9 3.9 - - - +
42V ALA* 2.9 31.4 + - - +
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Residues in contact with ILE 39 (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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81U TYR* 3.3 41.3 - - + +
200U VAL* 3.5 22.0 - - + -
31V TYR* 3.5 25.4 - - + +
35V GLU* 2.9 31.2 + - + +
38V ALA* 1.3 75.5 - - - +
40V GLN* 1.3 57.5 + - - +
42V ALA 3.3 0.2 + - - -
43V LEU* 2.8 38.7 + - + +
78V MET* 3.6 33.2 - - + +
79V PHE* 4.1 7.9 - - + -
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Residues in contact with GLN 40 (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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201T GLU* 4.1 11.2 + - - +
204T ARG* 3.8 4.0 - - - +
76U ASN* 3.1 30.6 + - - +
77U GLU* 4.3 12.8 + - - +
80U GLY* 3.5 13.5 - - - -
81U TYR* 3.9 26.6 + - + +
36V TYR* 2.9 31.7 + - + +
37V GLN* 3.8 4.5 - - - +
39V ILE* 1.3 76.9 - - - +
41V LYS* 1.3 63.6 + - + +
43V LEU* 3.2 8.1 + - - +
44V ARG* 3.1 44.9 + - - +
158V PHE 5.3 0.7 - - - +
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Residues in contact with LYS 41 (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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201T GLU* 5.5 4.0 - - - -
37V GLN* 3.0 53.0 + - + +
38V ALA* 4.0 4.0 - - - +
40V GLN* 1.3 76.7 - - - +
42V ALA* 1.3 63.6 + - - +
44V ARG* 3.0 46.3 + - - +
45V GLN* 3.7 6.9 + - - +
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Residues in contact with ALA 42 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197U GLU* 3.3 33.0 - - - +
200U VAL* 3.9 4.0 - - + -
38V ALA 2.9 18.8 + - - +
39V ILE 3.8 3.1 - - - +
41V LYS* 1.3 76.9 - - - +
43V LEU* 1.3 61.0 + - - +
45V GLN* 3.0 35.0 + - - +
78V MET* 3.8 14.6 - - + -
161V ALA* 3.3 6.8 - - - +
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Residues in contact with LEU 43 (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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81U TYR* 3.6 27.1 - - + -
39V ILE* 2.8 33.5 + - + +
40V GLN* 3.6 8.7 - - - +
41V LYS 3.2 0.2 - - - -
42V ALA* 1.3 74.1 - - - +
44V ARG* 1.3 61.7 + - - +
45V GLN 3.2 0.2 - - - -
78V MET* 3.6 17.7 - - + -
79V PHE* 4.6 2.9 - - + -
158V PHE* 3.5 31.2 - - + +
159V GLY* 3.9 1.1 - - - -
160V ASN 3.2 10.4 + - - -
161V ALA* 3.0 36.8 + - + -
162V LEU* 4.0 30.3 - - + +
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Residues in contact with ARG 44 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196T LEU* 3.6 21.3 - - - +
201T GLU* 4.3 13.9 + - - +
77U GLU* 2.8 49.5 + - - +
40V GLN* 3.1 30.6 + - - +
41V LYS* 3.0 49.6 + - - +
43V LEU* 1.3 77.6 - - - +
45V GLN* 1.3 64.3 + - - +
46V ARG* 3.3 6.4 + - - +
160V ASN* 3.5 21.8 + - - +
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Residues in contact with GLN 45 (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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190U LYS 5.2 8.0 - - - +
192U LYS* 3.5 37.9 + - + +
197U GLU* 2.4 33.6 + - - +
41V LYS 4.1 4.7 - - - +
42V ALA* 3.0 24.6 + - - +
44V ARG* 1.3 77.7 - - - +
46V ARG* 1.3 60.9 + - - +
78V MET* 5.3 0.4 - - - -
160V ASN 3.4 0.7 - - - -
161V ALA* 3.1 30.2 + - + +
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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