Contacts of the helix formed by residues 158 - 167 (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 PHE 158 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76U ASN* 3.5 15.4 + - - +
81U TYR* 3.6 29.2 - + + +
40V GLN* 5.3 0.5 - - - +
43V LEU* 3.5 25.3 - - + +
79V PHE* 4.3 4.5 - + - -
113V VAL* 3.9 29.6 - - + -
115V LEU* 3.6 41.1 - - + -
119V SER* 4.2 6.3 - - - -
120V TYR 4.8 0.9 - - - -
121V HIS* 3.3 35.9 - + + -
154V ALA 4.3 4.5 - - - -
155V LEU* 3.6 30.7 - - + +
156V ARG 3.0 1.8 + - - -
157V SER* 1.3 78.8 - - - +
159V GLY* 1.3 56.5 + - - +
162V LEU* 3.8 15.9 - - + -
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Residues in contact with GLY 159 (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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73U ASN* 4.2 7.0 - - - -
76U ASN* 3.8 11.2 - - - -
43V LEU* 4.1 8.9 - - - +
155V LEU 4.7 0.2 + - - -
156V ARG 3.4 6.1 + - - +
157V SER 3.4 1.6 - - - -
158V PHE* 1.3 80.8 - - - +
160V ASN* 1.3 67.3 + - - -
161V ALA 3.3 2.7 - - - -
162V LEU* 3.3 9.3 + - - +
163V GLY 3.5 0.2 + - - -
164V ASN* 3.2 22.9 + - - +
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Residues in contact with ASN 160 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69U HIS* 5.9 0.2 + - - -
73U ASN* 3.4 31.4 - - - +
43V LEU 3.2 6.3 + - - -
44V ARG* 3.5 23.0 + - - +
45V GLN 3.4 14.4 - - - +
46V ARG* 4.4 9.7 + - - +
47V LEU* 3.1 13.3 - - - +
159V GLY* 1.3 72.4 - - - -
161V ALA* 1.3 63.6 + - - +
163V GLY 3.0 11.8 + - - -
164V ASN* 4.0 0.4 - - - -
165V CYS* 3.3 40.6 + - + +
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Residues in contact with ALA 161 (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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192U LYS* 4.7 8.7 - - + -
42V ALA 3.3 26.9 - - - +
43V LEU* 3.0 22.2 + - + -
45V GLN* 3.1 14.6 + - + +
47V LEU* 3.5 23.7 - - - +
74V LEU* 3.6 15.4 - - - +
78V MET* 4.6 9.4 - - + -
159V GLY 3.3 0.4 - - - -
160V ASN* 1.3 76.0 - - - +
162V LEU* 1.3 59.1 + - - +
163V GLY 3.4 0.2 - - - -
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Residues in contact with LEU 162 (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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43V LEU* 4.0 13.2 - - + +
66V ILE* 4.9 4.5 - - - +
71V VAL* 4.3 18.3 - - + +
74V LEU* 3.7 33.7 - - + +
75V ALA* 3.7 19.3 - - + +
78V MET* 4.6 3.1 - - + -
79V PHE* 3.5 31.2 - - + -
152V LYS 4.8 1.2 - - - +
155V LEU* 3.4 36.5 - - + +
156V ARG* 3.8 13.6 + - - +
158V PHE* 3.8 14.8 - - + -
159V GLY 3.3 7.1 + - - +
160V ASN 3.1 0.6 - - - -
161V ALA* 1.3 76.5 - - - +
163V GLY* 1.3 56.7 + - - +
164V ASN 3.9 0.9 - - - -
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Residues in contact with GLY 163 (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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47V LEU* 4.3 1.3 - - - +
66V ILE* 3.8 22.7 - - - -
156V ARG* 3.8 14.3 + - - +
160V ASN 3.0 8.3 + - - -
161V ALA 3.4 0.8 + - - -
162V LEU* 1.3 81.4 - - - +
164V ASN* 1.3 63.8 + - - +
165V CYS 3.3 2.5 - - - -
166V ILE* 3.1 26.1 - - - +
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Residues in contact with ASN 164 (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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69U HIS* 3.0 38.9 - - - +
72U ILE* 3.6 22.4 - - - +
73U ASN* 2.9 26.7 + - - +
156V ARG* 3.5 29.2 - - - +
159V GLY* 3.2 25.5 + - - +
160V ASN* 3.7 2.4 + - - +
163V GLY* 1.3 76.3 - - - +
165V CYS* 1.3 66.7 + - - +
167V LEU* 3.0 23.6 + - - +
168V ASP 4.3 0.2 + - - -
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Residues in contact with CYS 165 (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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69U HIS* 5.7 1.6 - - - -
46V ARG* 4.2 15.7 - - + +
47V LEU* 3.5 31.9 - - - -
52V ILE* 5.8 0.9 - - - -
66V ILE* 5.9 0.2 - - - -
160V ASN* 3.3 43.6 + - + +
163V GLY* 4.8 0.7 - - - -
164V ASN* 1.3 78.4 - - - +
166V ILE* 1.3 66.1 + - - +
167V LEU 2.9 0.9 - - - -
168V ASP* 2.9 21.0 + - + +
171V TYR* 3.2 30.5 - - + -
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Residues in contact with ILE 166 (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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52V ILE* 3.6 34.3 - - + -
64V CYS* 3.8 39.9 - - + +
65V TYR* 4.3 9.9 - - - +
66V ILE* 4.8 9.6 - - + -
156V ARG* 4.7 10.5 - - - +
163V GLY 3.1 23.9 + - - +
164V ASN 3.0 0.8 + - - -
165V CYS* 1.3 81.5 - - - +
167V LEU* 1.3 76.2 + - + +
168V ASP 3.3 0.7 + - - -
171V TYR* 4.2 10.3 - - + -
172V LEU* 3.7 21.7 - - + +
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Residues in contact with LEU 167 (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 GLU* 4.5 1.9 - - - +
68U GLY* 5.6 0.9 - - - -
69U HIS* 3.6 31.0 + - + +
72U ILE* 5.9 0.9 - - + -
156V ARG* 3.6 43.5 - - - +
164V ASN* 3.0 20.9 + - - +
165V CYS 2.9 1.6 - - - -
166V ILE* 1.3 91.1 - - + +
168V ASP* 1.3 60.6 + - - +
169V LYS* 3.5 9.7 + - - +
172V LEU* 5.3 2.3 - - - +
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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