Contacts of the helix formed by residues 55 - 59 (chain C) in PDB entry 1C9T
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 ALA 55 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C SER* 1.3 79.1 + - - +
56C ALA* 1.3 59.0 + - - +
57C HIS* 3.8 14.6 - - + +
58C CYS* 2.8 30.7 + - - +
102C ASP* 3.2 29.8 - - - +
104C MET* 3.6 6.0 - - - +
196C GLY* 3.3 28.0 - - - +
212C ILE* 3.7 2.9 - - + +
213C VAL 3.9 3.1 - - - +
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Residues in contact with ALA 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C SER 3.5 4.2 + - - -
55C ALA* 1.3 70.6 - - - +
57C HIS* 1.3 57.1 + - - +
58C CYS 3.0 0.2 - - - -
59C TYR* 3.0 26.9 + - - +
90C VAL* 3.8 14.3 - - + +
94C TYR* 3.8 30.3 - - + -
102C ASP* 3.1 6.3 + - - +
103C ILE 3.5 32.5 - - - +
104C MET* 3.4 12.3 - - - -
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Residues in contact with HIS 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ALA* 3.1 8.9 - - + +
56C ALA* 1.3 76.4 - - - +
58C CYS* 1.3 61.6 + - - +
59C TYR* 3.1 7.0 + - - +
94C TYR* 3.7 23.7 - - + +
99C LEU* 4.5 5.5 - - + +
102C ASP* 2.9 38.6 + - - +
195C SER* 2.6 31.4 + - - -
214C SER* 3.4 19.7 + - - -
33I CYS* 3.3 11.2 - - + +
35I VAL* 3.5 27.6 - - + +
52I CYS* 3.6 19.2 - - - -
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Residues in contact with CYS 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 4.3 9.4 - - + -
41C PHE* 3.1 20.3 - - - -
42C CYS* 2.0 53.4 - - + -
54C SER* 4.4 2.2 - - - +
55C ALA* 2.8 21.4 + - - +
57C HIS* 1.3 80.4 - - - +
59C TYR* 1.3 64.6 + - - +
63C ILE* 3.4 10.9 - - - +
104C MET* 4.2 2.5 - - + -
195C SER* 3.5 25.8 - - - -
196C GLY* 4.1 1.3 - - - -
35I VAL* 5.2 0.4 - - - -
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Residues in contact with TYR 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ALA 3.0 18.2 + - - +
57C HIS 3.1 4.9 - - - +
58C CYS* 1.3 79.0 - - - +
60C LYS* 1.3 82.7 + - - +
61C SER* 4.3 7.4 - - - -
63C ILE* 4.3 0.9 - - + -
88C SER* 3.7 31.0 - - - -
90C VAL* 3.4 22.7 - - + -
104C MET* 3.6 20.1 - - - -
37F SER* 3.4 34.7 - - - -
38F GLY* 3.5 16.2 + - - -
62F GLY 4.2 11.6 + - - -
64F GLN* 4.5 6.9 + - - -
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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