Contacts of the strand formed by residues 185 - 188 (chain C) in PDB entry 3C6Q
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 185 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116C MET* 3.4 31.0 - - - -
120C LEU* 4.0 5.4 - - + -
125C LYS 3.5 2.4 + - - -
126C VAL* 3.3 12.3 - - + -
127C VAL 3.1 22.2 + - - -
183C LEU* 3.7 6.6 - - - +
184C ASP* 1.3 84.2 - - - +
186C PHE* 1.3 60.5 + - - +
210C VAL* 3.8 7.2 - - - +
211C LYS* 3.0 24.7 - - + +
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Residues in contact with PHE 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C MET* 3.3 6.9 - - - +
126C VAL* 4.7 0.4 - - - -
127C VAL* 3.3 42.8 - - + -
160C LEU* 5.6 0.4 - - + -
173C ALA* 3.9 33.4 - - + -
176C ALA* 4.3 5.6 - - + -
177C LEU* 4.5 13.2 - - + -
183C LEU* 3.9 14.6 - - + -
185C ALA* 1.3 73.8 - - - +
187C PHE* 1.3 60.7 + - - +
197C GLN* 3.3 42.6 - - + +
200C VAL* 5.0 2.2 - - + -
201C VAL* 3.9 20.2 - - + -
210C VAL* 3.8 15.5 - - + -
211C LYS 2.8 7.4 + - - +
212C ILE* 3.6 4.6 - - + +
213C VAL 3.1 24.3 + - - -
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Residues in contact with PHE 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C GLY* 4.9 1.1 - - - -
112C ALA* 4.0 22.4 - - + -
116C MET* 3.9 10.8 - - + -
126C VAL* 4.3 2.5 - - + -
127C VAL 2.9 13.3 + - - +
128C ILE* 3.5 20.5 - - + +
129C GLY 3.0 24.3 + - - -
141C ARG 4.1 11.7 - - - -
142C ILE* 4.9 2.9 - - + -
145C PHE* 3.6 51.6 - + + -
186C PHE* 1.3 76.7 - - - +
188C GLY* 1.3 60.0 + - - +
189C VAL* 3.6 21.1 + - + -
197C GLN* 3.6 2.9 - - - -
213C VAL* 3.1 24.0 - - + -
215C PHE* 4.0 25.6 - + - -
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Residues in contact with GLY 188 (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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187C PHE* 1.3 72.1 - - - +
189C VAL* 1.3 62.8 + - - -
190C TYR 3.4 4.0 + - - +
193C ASN* 3.5 21.3 - - - -
197C GLN* 3.4 11.8 + - - -
213C VAL 2.8 12.3 + - - -
214C CYS* 3.3 10.0 - - - +
215C PHE* 3.1 30.0 + - - -
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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