Contacts of the helix formed by residues 76 - 81 (chain V) in PDB entry 1UW9
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 76 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112M ASN* 3.7 9.3 + - - +
113M GLN* 4.0 27.3 + - - -
75V THR* 1.3 81.5 + - - +
77V LEU* 1.3 64.1 + - - +
78V ASP* 3.8 9.0 + - - +
79V ARG* 3.0 35.2 + - - +
80V TYR* 3.3 18.7 - - - -
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Residues in contact with LEU 77 (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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176O PRO* 4.5 8.1 - - + -
178O LEU 5.5 0.2 - - - +
23V THR* 4.0 17.5 - - + -
24V TYR* 4.1 5.6 - - - +
63V THR* 3.8 31.2 - - + +
72V ASP* 3.5 46.8 + - + +
75V THR* 3.8 7.7 + - + +
76V SER* 1.3 72.6 - - - +
78V ASP* 1.3 58.5 + - - +
80V TYR* 4.5 2.5 - - + +
81V LYS* 2.8 44.3 + - + +
1478V EDO 3.8 16.6 - - - -
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Residues in contact with ASP 78 (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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76V SER* 3.2 10.0 - - - +
77V LEU* 1.3 76.7 - - - +
79V ARG* 1.3 61.3 + - - +
80V TYR 3.6 0.3 + - - -
81V LYS* 3.8 21.8 + - - +
83V ARG* 3.0 33.2 + - - +
104V HYP 4.8 2.1 + - - -
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Residues in contact with ARG 79 (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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113M GLN 4.0 18.5 + - - -
352R ASP* 4.2 18.9 + - - +
370R SER* 3.1 31.5 + - - +
32V ARG* 5.9 3.1 + - - +
76V SER* 3.0 25.9 + - - +
78V ASP* 1.3 81.7 - - - +
80V TYR* 1.3 91.5 + - + +
104V HYP 3.4 23.1 + - - -
106V ASP* 3.7 9.8 + - - +
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Residues in contact with TYR 80 (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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115M GLN* 5.0 2.8 + - - -
178O LEU 4.6 0.2 - - - +
179O GLY* 3.7 20.8 + - - -
211O PHE* 3.6 29.6 - + + +
63V THR* 3.6 17.3 - - + +
75V THR* 3.4 24.9 - - + -
76V SER* 3.3 23.2 + - - +
77V LEU* 3.1 5.3 + - + +
79V ARG* 1.3 118.1 + - + +
81V LYS* 1.3 67.8 + - - +
104V HYP 3.7 3.1 - - - -
106V ASP* 3.7 28.6 + - + -
107V LEU* 3.2 42.5 - - + +
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Residues in contact with LYS 81 (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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23V THR* 2.8 47.8 + - + +
24V TYR* 3.6 18.2 - - + -
26V THR* 4.3 6.5 - - - +
63V THR* 3.6 13.4 - - - +
77V LEU* 2.8 28.7 + - + +
78V ASP* 3.8 17.4 + - - +
79V ARG 3.8 0.4 - - - -
80V TYR* 1.3 75.0 - - - +
82V GLY* 1.3 67.2 + - - +
83V ARG* 3.6 47.9 + - + +
104V HYP 3.5 15.6 + - - -
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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