Contacts of the strand formed by residues 192 - 201 (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 GLN 192 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190C PRO 4.3 3.1 - - - +
191C LEU* 1.3 81.8 - - - +
193C ALA* 1.3 55.7 + - - +
212C ILE 3.7 0.3 - - - -
213C LYS* 2.7 41.2 + - + +
214C ASN* 2.9 33.3 + - + +
273C THR* 5.2 5.6 - - - +
274C LEU 3.4 2.5 - - - -
281C ALA* 3.9 12.2 - - + +
283C LYS* 2.9 28.1 + - - +
284C ALA 4.2 0.6 - - - -
285C LEU* 3.7 37.0 - - + +
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Residues in contact with ALA 193 (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* 3.9 13.7 - - + -
192C GLN* 1.3 73.2 - - - +
194C LEU* 1.3 60.6 + - - +
195C ILE* 3.6 1.6 + - - +
210C ILE* 3.7 23.3 - - + -
211C ARG 2.9 10.8 - - - +
212C ILE* 4.2 5.8 - - + -
217C LEU* 5.5 1.6 - - + -
273C THR* 3.1 6.1 - - - -
274C LEU* 2.7 54.9 + - + +
285C LEU* 4.3 1.1 - - - +
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Residues in contact with LEU 194 (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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90C ARG* 3.6 32.8 - - - +
93C ALA* 3.8 28.9 - - + +
94C ALA* 4.0 8.7 - - + +
193C ALA* 1.3 71.4 - - - +
195C ILE* 1.3 66.2 + - - +
196C ILE* 3.3 7.0 + - + +
210C ILE* 3.4 4.6 - - - -
211C ARG* 2.7 39.8 + - + +
213C LYS* 4.6 9.2 - - + -
271C GLY* 3.6 29.8 - - - +
272C ASP 3.5 5.6 - - - +
285C LEU* 3.9 27.9 - - + +
286C PRO 5.4 1.1 - - - +
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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
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90C ARG* 4.7 0.9 - - - +
193C ALA 4.1 0.7 - - - +
194C LEU* 1.3 72.3 - - - +
196C ILE* 1.3 60.7 + - - +
197C ASP 3.7 21.5 - - - +
198C SER* 3.8 3.1 - - - +
208C SER* 4.5 8.1 - - - -
209C LEU 3.8 3.6 - - - +
210C ILE* 4.6 9.9 - - + -
225C VAL* 5.1 2.9 - - + -
268C ALA* 3.6 21.3 - - + +
269C PRO 3.5 20.6 - - - +
270C VAL* 4.0 2.8 - - - +
271C GLY* 2.7 31.0 + - - -
272C ASP* 2.8 47.5 + - + +
273C THR 3.9 0.7 - - - +
274C LEU* 3.7 38.4 - - + +
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Residues in contact with ILE 196 (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* 5.1 1.8 - - - +
76C ILE* 4.1 22.0 - - + -
87C GLU* 5.0 2.1 - - - +
90C ARG* 4.6 10.3 - - - +
91C SER* 3.5 32.3 + - - +
94C ALA* 3.7 30.5 - - + -
194C LEU* 4.0 7.9 - - + +
195C ILE* 1.3 74.7 - - - +
197C ASP* 1.3 65.2 + - + +
209C LEU* 2.9 31.5 + - + +
210C ILE 4.0 24.7 - - - +
211C ARG* 4.0 3.4 - - + +
255C VAL* 4.3 4.3 - - + -
270C VAL* 3.2 22.4 - - - +
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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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57C GLN* 3.7 33.1 + - - +
87C GLU* 4.7 11.6 - - - +
195C ILE* 3.5 7.5 - - - +
196C ILE* 1.3 85.7 - - + +
198C SER* 1.3 82.7 + - - +
199C TRP* 3.9 11.6 - - + +
208C SER* 3.4 0.9 - - - -
209C LEU* 3.0 30.8 + - + +
270C VAL* 4.7 8.9 - - - +
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Residues in contact with SER 198 (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* 3.8 1.0 - - - +
197C ASP* 1.3 90.4 + - - +
199C TRP* 1.3 64.5 + - - +
206C VAL* 4.9 1.1 - - - -
207C VAL 3.4 7.6 - - - -
208C SER* 3.1 18.9 + - - -
265C ILE* 3.7 31.2 - - - +
268C ALA* 3.0 28.6 + - - +
270C VAL* 5.5 2.5 - - - +
320C ASN* 5.0 4.0 + - - +
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Residues in contact with TRP 199 (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* 3.9 16.8 - - - -
197C ASP* 3.9 14.4 - - - +
198C SER* 1.3 79.6 - - - +
200C PHE* 1.3 72.1 + - - +
201C ASP* 4.3 9.2 + - + +
206C VAL* 3.5 3.6 - - - -
207C VAL* 2.9 67.5 + - + +
208C SER 4.5 0.7 - - - -
209C LEU* 3.9 36.8 - - + -
240C PHE* 3.7 32.1 - + - -
244C GLN* 5.9 0.8 - - - +
265C ILE* 3.7 8.8 - - - +
320C ASN* 3.3 17.5 - - - +
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Residues in contact with PHE 200 (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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202B ASN 5.2 7.6 - - - -
199C TRP* 1.3 78.4 - - - +
201C ASP* 1.3 72.4 + - - +
202C ASN* 4.2 24.2 + - - +
205C GLY* 3.7 26.2 - - - -
206C VAL* 3.9 15.0 - - + -
263C LYS 4.6 9.9 - - - -
264C ASP* 5.7 1.3 - - - -
265C ILE* 4.9 0.9 - - + -
319C LEU* 3.5 51.4 + - + +
320C ASN* 3.1 25.9 + - - +
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Residues in contact with ASP 201 (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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316B LYS* 5.1 6.7 + - - -
199C TRP* 3.9 10.6 + - + -
200C PHE* 1.3 79.5 - - - +
202C ASN* 1.3 61.5 + - - +
203C TYR* 3.0 19.2 + - - +
204C LEU* 3.2 24.4 + - + +
205C GLY* 2.6 43.9 + - - +
207C VAL* 3.8 16.6 - - + +
244C GLN* 5.4 3.3 + - - -
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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