Contacts of the strand formed by residues 193 - 197 (chain C) in PDB entry 3CQ6
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 ILE 193 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PRO* 3.8 20.0 - - + -
105C LEU* 4.9 4.3 - - + -
109C PHE* 3.8 33.9 - - + -
162C PRO 5.4 0.2 - - - +
163C ASP 2.8 8.5 + - - +
164C ILE* 3.3 24.1 - - + -
165C VAL* 2.9 24.8 + - - +
190C ALA* 4.9 1.3 - - - +
192C GLY* 1.3 77.6 - - - +
194C VAL* 1.3 66.0 + - - +
195C ILE* 4.0 25.1 - - + -
218C THR 4.3 1.6 - - - +
219C LYS 3.2 10.1 - - - +
221C VAL* 4.8 5.8 - - + -
246C PHE* 3.9 30.7 - - + -
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Residues in contact with VAL 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C VAL* 3.3 16.8 - - + +
167C VAL* 4.1 17.3 - - + -
183C VAL* 5.3 0.9 - - + -
186C ILE* 4.6 5.4 - - + -
187C ILE* 4.0 32.1 - - + -
190C ALA* 3.5 31.2 - - + -
193C ILE* 1.3 75.3 - - - +
195C ILE* 1.3 62.7 + - - +
196C VAL* 4.0 20.6 - - + -
219C LYS* 2.7 14.2 + - + +
220C LEU* 3.6 4.8 - - + +
221C VAL 3.0 25.5 + - - +
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Residues in contact with ILE 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LEU* 3.8 24.5 - - + +
105C LEU* 4.1 30.7 - - + -
106C LEU* 5.7 0.9 - - + +
164C ILE* 3.8 18.6 - - + -
165C VAL 2.8 7.9 + - - -
166C PHE* 3.5 34.3 - - + -
167C VAL 3.0 23.7 + - - -
193C ILE* 4.0 19.9 - - + -
194C VAL* 1.3 73.9 - - - +
196C VAL* 1.3 63.0 + - - +
197C ASP* 3.5 3.7 + - + +
221C VAL* 3.4 13.0 - - + +
223C SER* 4.2 13.9 - - - -
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Residues in contact with VAL 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C VAL* 3.2 11.9 - - + +
169C THR* 3.5 31.4 - - + -
183C VAL* 4.1 19.1 - - + -
194C VAL* 4.0 12.1 - - + -
195C ILE* 1.3 73.0 - - - +
197C ASP* 1.3 57.8 + - - +
198C GLU* 3.2 16.8 + - + +
209C ALA* 4.0 17.0 - - + -
220C LEU* 3.5 27.4 - - + -
221C VAL 2.9 8.6 + - - +
222C VAL* 3.7 3.6 - - - -
223C SER 2.9 24.5 + - - +
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Residues in contact with ASP 197 (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 0.3 + - - -
102C LEU* 4.2 4.9 - - + +
123C TYR* 4.0 0.3 - - - -
126C HIS* 2.9 37.2 + - + +
167C VAL 2.8 9.4 + - - +
168C THR* 3.6 11.6 - - - +
169C THR 3.0 25.7 + - - +
170C PRO 4.5 0.2 - - - +
195C ILE* 3.5 6.9 + - + +
196C VAL* 1.3 68.5 - - - +
198C GLU* 1.3 60.3 + - - +
199C ALA* 3.3 14.4 + - - +
223C SER* 4.0 18.9 + - - +
224C ARG 6.0 0.2 - - - -
228C LLP 2.7 42.2 + - - -
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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