Contacts of the strand formed by residues 205 - 214 (chain C) in PDB entry 3CB4
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 GLY 205 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200C PHE* 3.8 18.2 - - - -
201C ASP* 2.6 46.0 + - - +
203C TYR 3.5 1.4 - - - -
204C LEU* 1.3 78.3 - - - +
206C VAL* 1.3 62.5 + - - -
207C VAL* 3.7 0.3 - - - +
261C ALA* 6.5 0.2 - - - -
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Residues in contact with VAL 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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198C SER* 4.9 0.4 - - - -
199C TRP 3.5 9.0 - - - +
200C PHE* 3.9 13.9 - - + -
204C LEU 4.2 0.2 + - - -
205C GLY* 1.3 71.1 - - - -
207C VAL* 1.3 67.6 + - - +
208C SER* 4.5 9.4 + - - +
258C LEU 4.0 5.9 - - - +
259C VAL* 4.3 8.1 - - - +
260C CYS 4.0 14.1 + - - +
261C ALA* 5.9 1.8 - - - +
262C ILE* 3.3 38.5 + - + +
263C LYS 3.8 4.7 - - - +
264C ASP* 3.6 33.7 - - - +
265C ILE* 3.9 18.4 - - + +
268C ALA* 4.8 4.0 - - + -
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Residues in contact with VAL 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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198C SER* 3.4 3.1 - - - -
199C TRP* 2.9 71.0 + - + +
201C ASP* 3.8 12.6 - - + +
204C LEU* 4.3 9.9 - - + -
205C GLY 3.7 11.4 - - - +
206C VAL* 1.3 77.8 - - - +
208C SER* 1.3 64.2 + - - +
240C PHE* 5.2 1.1 - - + -
244C GLN* 5.3 2.9 - - - +
257C TRP* 3.9 19.3 - - + -
258C LEU 3.6 11.4 - - - +
259C VAL* 3.9 20.9 - - + -
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Residues in contact with SER 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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195C ILE* 4.5 10.5 - - - -
197C ASP 3.4 6.1 - - - -
198C SER* 3.1 18.5 + - - -
199C TRP* 4.4 3.4 - - - -
206C VAL* 4.4 4.5 + - - +
207C VAL* 1.3 76.2 - - - +
209C LEU* 1.3 61.1 + - - +
210C ILE* 3.8 12.4 + - - -
257C TRP* 3.2 4.4 - - - -
258C LEU* 2.9 39.0 + - - +
262C ILE* 4.7 5.0 - - - +
268C ALA* 3.3 18.8 - - - +
274C LEU* 6.0 0.9 - - - -
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Residues in contact with LEU 209 (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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57C GLN* 3.8 21.8 - - - +
58C SER* 3.4 37.7 - - - +
76C ILE* 4.8 4.9 - - + -
195C ILE* 3.8 4.0 - - - -
196C ILE* 2.9 53.3 + - + -
197C ASP* 3.0 15.6 + - + +
199C TRP* 3.9 17.9 - - + -
208C SER* 1.3 70.7 - - - +
210C ILE* 1.3 61.2 + - - +
240C PHE* 4.2 16.6 - - + -
255C VAL* 4.3 8.1 - - + -
256C GLY* 3.2 27.4 - - - +
257C TRP* 4.5 0.7 - - - +
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Residues in contact with ILE 210 (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 ALA* 3.7 22.7 - - + -
194C LEU 3.4 7.9 - - - +
195C ILE* 4.6 9.2 - - + -
196C ILE* 4.0 4.3 - - - -
208C SER* 4.4 7.2 - - - +
209C LEU* 1.3 78.9 - - - +
211C ARG* 1.3 67.7 + - - +
212C ILE* 3.8 15.0 - - + -
217C LEU* 4.6 5.4 - - + -
250C LEU* 4.6 8.5 - - + -
255C VAL* 3.3 9.5 - - - +
256C GLY 2.8 37.1 + - - +
258C LEU* 3.6 29.2 - - + -
274C LEU* 3.5 31.4 - - + -
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Residues in contact with ARG 211 (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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6C ASN* 3.8 9.6 - - - +
94C ALA* 3.6 44.2 + - + +
96C GLU* 2.8 40.6 + - - -
183C PRO* 3.3 12.1 - - - +
184C GLU 4.4 4.8 + - - +
193C ALA* 2.9 4.3 - - - -
194C LEU* 2.7 47.2 + - + +
196C ILE* 4.0 3.8 - - + +
210C ILE* 1.3 76.0 - - - +
212C ILE* 1.3 97.5 + - - +
213C LYS* 3.5 35.6 + - + +
253C GLY* 3.5 12.3 - - - -
254C GLU 3.6 7.9 - - - -
255C VAL* 3.7 13.5 - - + -
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Residues in contact with ILE 212 (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 LEU* 4.3 5.2 - - + -
192C GLN 3.9 2.2 - - - -
193C ALA* 4.2 7.4 - - + +
210C ILE* 3.8 21.5 - - + -
211C ARG* 1.3 93.7 + - - +
213C LYS* 1.3 52.2 + - - +
214C ASN 3.6 14.6 - - - +
215C GLY 3.5 27.1 - - - +
216C THR* 4.6 0.4 - - - +
217C LEU* 3.9 17.0 - - + -
250C LEU* 3.6 30.5 - - + +
251C LYS 3.4 26.2 - - - +
252C CYS* 3.8 2.9 - - - -
253C GLY* 2.9 17.9 + - - +
254C GLU 3.1 12.4 + - - +
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Residues in contact with LYS 213 (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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93C ALA* 3.1 28.8 + - - -
94C ALA* 4.9 0.4 - - - +
95C CYS 5.4 0.6 + - - -
96C GLU* 4.5 5.3 + - - -
184C GLU 3.3 17.0 - - - +
192C GLN* 2.7 17.7 + - + +
194C LEU* 4.6 11.7 - - + -
211C ARG* 3.5 36.6 + - - +
212C ILE* 1.3 74.4 - - - +
214C ASN* 1.3 65.8 + - + +
252C CYS* 3.3 14.4 - - - -
285C LEU* 3.9 37.9 - - + -
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Residues in contact with ASN 214 (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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185C GLY* 3.6 5.5 - - - -
186C ASP* 3.5 34.7 + - - +
189C GLY* 4.1 7.5 - - - -
190C PRO* 3.5 21.1 + - - +
191C LEU* 3.4 8.3 - - - +
192C GLN* 2.9 45.1 + - + +
212C ILE* 3.6 2.7 - - - +
213C LYS* 1.3 84.5 - - - +
215C GLY* 1.3 63.2 + - - +
252C CYS* 3.8 3.6 - - - -
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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