Contacts of the strand formed by residues 201 - 208 (chain C) in PDB entry 7CN9
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 PHE 201 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86C PHE* 6.1 1.6 - + - -
106C PHE* 3.7 20.9 - + - -
117C LEU* 5.1 16.8 - - + -
119C ILE* 4.0 28.7 - - + -
194C PHE* 3.2 57.2 - + + -
195C LYS 3.6 1.6 - - - -
196C ASN* 4.2 20.4 - - + +
199C GLY 3.9 2.9 + - - +
200C TYR* 1.3 67.8 - - - +
202C LYS* 1.3 54.8 + - - +
203C ILE* 3.3 29.4 - - + +
227C VAL* 2.7 27.3 - - + +
228C ASP* 4.1 4.1 + - - -
229C LEU* 4.3 10.3 - - + +
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Residues in contact with LYS 202 (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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193C VAL 3.6 1.7 - - - +
195C LYS* 2.8 37.7 + - + +
197C ILE* 4.2 16.7 - - + +
200C TYR* 3.5 41.3 - - + +
201C PHE* 1.3 73.7 - - - +
203C ILE* 1.3 61.1 + - - +
204C TYR* 4.2 22.9 + - + +
225C PRO* 5.0 8.5 - - + -
227C VAL 3.5 8.7 - - - +
228C ASP* 4.5 12.4 + - + -
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Residues in contact with ILE 203 (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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192C PHE* 4.8 8.7 - - + -
193C VAL 3.4 7.0 - - - +
194C PHE* 3.4 35.7 - - + -
201C PHE* 3.3 37.7 - - + +
202C LYS* 1.3 86.1 - - - +
204C TYR* 1.3 66.3 + - - +
205C SER* 4.1 6.4 + - - -
224C GLU 2.9 12.4 - - - +
225C PRO* 3.0 17.0 - - - +
226C LEU* 3.1 20.6 + - + +
227C VAL* 4.2 17.7 + - + -
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Residues in contact with TYR 204 (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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37C TYR* 3.2 44.6 - + + -
38C TYR 3.5 8.3 - - - -
39C PRO 3.6 13.2 + - - -
191C GLU* 4.3 1.0 - - - +
192C PHE* 3.8 0.3 + - - -
193C VAL* 3.0 47.4 + - + +
195C LYS* 5.3 8.7 - - + -
202C LYS* 4.7 23.3 - - + +
203C ILE* 1.3 74.1 - - - +
205C SER* 1.3 58.3 + - - +
223C LEU* 3.3 30.8 - - + +
224C GLU* 3.0 13.9 - - - +
225C PRO* 3.2 42.9 - - + +
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Residues in contact with SER 205 (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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191C GLU 3.4 6.7 - - - -
192C PHE* 3.1 31.4 - - - -
203C ILE* 4.9 4.9 - - - -
204C TYR* 1.3 76.2 - - - +
206C LYS* 1.3 77.3 + - - +
207C HIS 4.9 0.2 + - - -
222C ALA 3.6 9.5 - - - +
223C LEU* 4.4 2.7 - - - -
224C GLU* 3.5 24.4 + - - +
226C LEU* 4.8 18.4 - - - -
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Residues in contact with LYS 206 (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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190C ARG* 3.2 3.9 - - - +
191C GLU* 2.9 32.1 + - + +
192C PHE* 5.2 0.4 - - - -
205C SER* 1.3 85.1 + - - +
207C HIS* 1.3 100.9 + - + +
208C THR* 3.6 3.8 + - + +
209C PRO* 3.7 12.9 - - - +
221C SER* 3.1 32.8 - - - +
222C ALA* 3.3 13.5 - - + +
223C LEU* 3.9 3.1 - - + +
224C GLU* 6.1 0.4 - - - +
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Residues in contact with HIS 207 (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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175C PHE 5.9 0.7 - - - +
176C LEU* 5.1 19.8 - - + +
188C ASN* 3.0 23.0 + - + +
189C LEU 3.2 13.2 - - - -
190C ARG* 3.6 9.4 - - + -
192C PHE* 5.6 0.6 - - - -
206C LYS* 1.3 118.8 + - + +
208C THR* 1.3 76.7 + - - +
209C PRO* 3.1 29.3 - - + +
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Residues in contact with THR 208 (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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34C ARG* 5.5 2.2 - - - +
188C ASN* 2.2 28.8 + - - -
189C LEU* 2.8 54.6 + - + +
190C ARG* 3.0 6.8 + - - -
191C GLU* 3.8 23.3 - - + +
206C LYS* 3.6 6.6 + - - +
207C HIS* 1.3 78.2 - - - +
209C PRO* 1.3 55.2 - - - +
210C ILE* 5.5 0.4 - - - -
217C PRO* 5.0 11.0 - - + -
221C SER* 4.7 12.6 - - - -
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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