Contacts of the strand formed by residues 192 - 201 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190F PRO* 3.3 5.3 + - - +
191F LEU* 1.3 79.2 - - - +
193F ALA* 1.3 54.1 + - - +
194F LEU 4.2 0.2 - - - -
212F ILE 3.8 0.3 - - - -
213F LYS* 2.8 36.0 + - + +
214F ASN* 2.8 41.0 + - + +
273F THR* 4.8 7.2 - - - +
274F LEU 3.5 2.2 - - - -
281F ALA* 3.7 15.2 - - + +
283F LYS 3.0 27.1 + - - +
284F ALA 4.6 0.2 - - - -
285F LEU* 4.2 34.2 - - + +
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Residues in contact with ALA 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191F LEU* 4.2 6.5 - - + -
192F GLN* 1.3 74.5 - - - +
194F LEU* 1.3 60.7 + - - +
195F ILE* 3.6 1.7 + - - +
210F ILE* 3.4 29.4 - - + -
211F ARG 3.3 4.9 - - - +
212F ILE* 4.1 11.0 - - + -
217F LEU* 5.6 1.3 - - + -
273F THR* 3.1 5.7 - - - -
274F LEU* 2.6 56.5 + - + +
285F LEU* 4.3 1.7 - - - +
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Residues in contact with LEU 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F ARG* 3.5 36.3 - - - +
93F ALA* 3.9 27.4 - - + +
94F ALA* 4.0 11.4 - - + +
193F ALA* 1.3 70.5 - - - +
195F ILE* 1.3 65.3 + - - +
196F ILE* 3.1 8.7 + - + +
210F ILE* 3.6 3.5 - - - -
211F ARG* 2.8 37.1 + - + +
213F LYS* 4.5 8.7 - - + -
271F GLY* 3.6 32.3 - - - +
272F ASP 3.7 2.7 - - - +
285F LEU* 3.9 25.7 - - + +
286F PRO 5.6 1.6 - - - +
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Residues in contact with ILE 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F ARG* 4.8 1.0 - - - +
193F ALA 4.2 0.7 - - - +
194F LEU* 1.3 70.4 - - - +
196F ILE* 1.3 61.9 + - - +
197F ASP 4.0 8.5 - - - +
198F SER* 3.6 22.9 - - - +
208F SER* 4.6 15.0 - - - +
209F LEU 3.9 3.4 - - - +
210F ILE* 5.1 2.7 - - + +
225F VAL* 4.8 4.3 - - + -
268F ALA* 3.9 7.2 - - + +
269F PRO 3.2 21.3 - - - +
270F VAL* 3.9 7.6 - - - +
271F GLY* 2.9 28.8 + - - -
272F ASP* 2.9 44.4 + - + +
273F THR 4.0 2.9 - - - +
274F LEU* 3.7 37.0 - - + +
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Residues in contact with ILE 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F ILE* 4.7 8.3 - - + -
87F GLU* 5.1 3.3 - - - +
90F ARG* 4.6 8.9 - - - +
91F SER* 3.2 38.1 + - - +
94F ALA* 3.9 18.8 - - + -
194F LEU* 3.6 10.8 - - + +
195F ILE* 1.3 73.7 - - - +
197F ASP* 1.3 66.0 + - + +
209F LEU* 2.9 34.0 + - + +
210F ILE 3.7 28.3 - - - +
211F ARG* 3.7 10.8 - - + +
255F VAL* 4.3 7.4 - - + -
270F VAL* 3.4 19.1 - - - +
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Residues in contact with ASP 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F GLN* 2.9 29.5 + - - +
87F GLU* 5.2 10.8 - - - +
195F ILE* 3.6 4.3 - - - +
196F ILE* 1.3 85.7 - - + +
198F SER* 1.3 79.8 + - - +
199F TRP* 3.9 15.1 - - + +
208F SER* 3.1 5.5 - - - -
209F LEU* 2.8 31.4 + - + +
270F VAL* 4.9 7.0 - - - +
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Residues in contact with SER 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F ILE* 3.6 4.4 - - - +
197F ASP* 1.3 85.8 + - - +
199F TRP* 1.3 62.3 + - - +
206F VAL* 4.7 1.8 - - - -
207F VAL 3.2 7.2 - - - -
208F SER* 2.8 24.4 + - - -
265F ILE* 3.9 32.5 - - - +
268F ALA* 2.8 29.7 + - - -
270F VAL* 5.5 2.7 - - - +
320F ASN 5.0 2.6 - - - +
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Residues in contact with TRP 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F GLN* 4.0 24.2 - - - -
197F ASP* 3.9 13.0 - - + +
198F SER* 1.3 80.8 - - - +
200F PHE* 1.3 73.7 + - - +
201F ASP* 4.2 8.9 + - - +
206F VAL* 3.5 3.8 - - - -
207F VAL* 2.9 70.0 + - + +
208F SER 4.5 0.2 - - - -
209F LEU* 3.8 31.9 - - + -
240F PHE* 4.0 31.6 - + - -
244F GLN* 6.1 0.4 - - - -
257F TRP* 4.9 0.4 - - + -
265F ILE* 3.6 10.7 - - - +
320F ASN* 3.4 16.2 - - - +
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Residues in contact with PHE 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E ASN 5.0 5.8 - - - -
199F TRP* 1.3 79.2 - - - +
201F ASP* 1.3 76.1 + - - +
202F ASN* 4.0 24.5 + - - +
205F GLY* 3.8 17.5 - - - -
206F VAL* 4.0 21.8 - - + -
262F ILE 5.8 0.2 - - - -
263F LYS 4.6 9.2 - - - -
264F ASP* 5.6 1.3 - - - -
265F ILE* 4.0 1.4 - - + +
319F LEU* 3.6 50.0 - - + +
320F ASN* 2.8 26.8 + - - +
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Residues in contact with ASP 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316E LYS* 4.9 5.9 + - - -
199F TRP* 4.0 8.1 + - - +
200F PHE* 1.3 77.8 - - - +
202F ASN* 1.3 60.9 + - - +
203F TYR* 2.8 20.3 + - - +
204F LEU* 2.8 50.1 + - + +
205F GLY* 2.8 45.3 + - - +
207F VAL* 3.9 10.2 - - + +
244F GLN* 5.3 2.3 + - - -
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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