Contacts of the strand formed by residues 243 - 246 (chain C) in PDB entry 6ZGI
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 243 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79C PHE* 3.5 15.9 - - - -
99C ASN 4.7 1.3 - - - +
100C ILE* 3.2 31.2 + - + +
102C ARG* 4.2 21.3 - - + +
141C LEU* 3.3 19.5 - - + +
143C VAL* 4.6 6.1 - - + -
242C LEU* 1.3 77.0 - - - +
244C LEU* 1.3 67.2 + - - +
245C HIS* 5.7 0.9 - - + +
260C ALA 3.9 8.7 - - - +
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Residues in contact with LEU 244 (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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18C LEU* 4.2 14.4 - - + -
79C PHE* 3.4 31.2 - - + -
140C PHE* 3.6 35.0 - - + -
141C LEU 2.9 19.4 + - - +
142C GLY* 4.5 4.7 - - - -
143C VAL* 2.8 34.7 + - - +
156C GLU* 5.2 0.4 - - - +
243C ALA* 1.3 74.1 - - - +
245C HIS* 1.3 65.1 + - - +
246C ARG* 4.4 11.0 - - + +
258C TRP* 3.7 32.3 - - + -
259C THR 4.3 11.7 - - - +
260C ALA 4.9 0.4 - - - -
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Residues in contact with HIS 245 (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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98C SER* 5.2 9.3 + - - -
100C ILE* 3.5 30.6 - - + +
143C VAL* 3.3 17.6 - - + +
152C TRP* 3.4 40.5 - + + -
179C LEU 4.6 7.1 + - - -
181C GLY* 5.1 6.7 - - - -
243C ALA* 5.8 0.9 - - + +
244C LEU* 1.3 78.7 - - - +
246C ARG* 1.3 65.0 + - - +
258C TRP* 3.9 0.7 - - - +
259C THR* 3.1 50.4 + - + +
260C ALA 3.7 13.2 + - - -
261C GLY* 4.0 11.4 + - - -
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Residues in contact with ARG 246 (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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16C VAL* 5.3 1.4 - - - +
18C LEU* 4.7 0.6 - - - +
140C PHE* 4.7 7.9 - - - -
143C VAL 2.9 10.5 + - - +
144C TYR* 3.4 24.3 - - + -
145C TYR* 2.8 32.5 + - - +
156C GLU* 3.1 41.0 + - - +
244C LEU* 4.4 17.3 - - + +
245C HIS* 1.3 79.5 - - - +
247C SER* 1.3 59.5 + - - +
250C THR* 3.7 7.0 - - - +
253C ASP 5.0 0.6 + - - -
254C SER* 2.6 46.3 + - - +
257C GLY 3.3 24.5 + - - +
258C TRP* 4.1 8.8 - - + +
259C THR* 5.8 0.2 - - - -
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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