Contacts of the strand formed by residues 184 - 187 (chain C) in PDB entry 2Q2U
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 LEU 184 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C LEU* 3.9 35.2 - - + +
9C ALA* 3.1 31.9 - - + +
10C ALA 2.9 20.8 + - - -
98C PHE* 6.4 0.2 - - + -
164C MET* 3.6 25.4 - - + -
165C ILE 3.4 6.7 - - - +
166C ARG* 3.9 33.0 - - + +
177C SER* 3.4 9.8 + - - -
183C ILE* 1.3 81.0 - - - +
185C LEU* 1.3 77.2 + - - +
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Residues in contact with LEU 185 (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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9C ALA* 4.0 3.8 - - - -
10C ALA* 3.4 20.2 - - + +
12C LEU* 4.5 24.0 - - + -
17C ASP 5.2 1.8 - - - +
18C VAL* 4.8 14.1 - - + -
19C GLN 5.9 0.2 - - - +
163C VAL 3.8 0.2 - - - +
164C MET* 3.3 5.9 - - - -
165C ILE* 2.6 60.2 + - + +
178C THR 4.2 3.8 - - - +
179C LEU* 3.8 41.7 - - + +
182C GLY* 4.5 15.5 - - - -
184C LEU* 1.3 82.4 - - - +
186C LYS* 1.3 60.7 + - - +
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Residues in contact with LYS 186 (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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9C ALA* 3.4 26.6 - - + +
10C ALA 2.8 19.8 + - - +
11C THR* 3.0 28.1 - - + +
12C LEU* 2.9 26.8 + - - +
27C LYS* 5.7 2.5 - - + -
164C MET* 3.8 23.6 - - + -
176C ARG* 3.6 19.7 - - - +
185C LEU* 1.3 71.8 - - - +
187C MET* 1.3 61.4 + - - +
188C LYS* 3.9 14.5 + - + +
32J C 4.0 22.0 + - - -
33J A 3.5 21.7 + - - +
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Residues in contact with MET 187 (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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12C LEU* 3.8 33.0 - - + +
15C ILE* 4.2 10.3 - - + -
27C LYS* 6.3 0.2 - - - +
148C LEU* 3.5 31.2 - - + -
149C LEU* 5.0 1.3 - - + -
152C GLU* 3.0 45.1 - - + +
162C GLY* 3.4 6.4 - - - -
163C VAL* 2.9 59.7 + - + +
164C MET* 4.9 0.2 - - - -
165C ILE* 3.9 6.1 - - + -
185C LEU 4.0 0.2 + - - -
186C LYS* 1.3 71.0 - - - +
188C LYS* 1.3 62.9 + - - +
189C GLN* 5.6 1.6 - - - +
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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