Contacts of the strand formed by residues 195 - 203 (chain F) in PDB entry 4BQ7
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 LEU 195 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190F ILE* 3.5 21.1 - - + +
192F ASN* 3.0 35.9 + - - +
194F TYR* 1.3 81.7 - - + +
196F SER* 1.3 62.8 + - - +
197F VAL* 3.9 25.6 - - + -
218F ILE* 3.8 8.5 - - + -
219F ILE 3.4 12.6 - - - +
220F PHE* 3.5 38.8 - - + -
221F LYS* 4.1 3.8 - - - +
276F ILE* 4.5 5.4 - - + -
278F THR* 4.2 21.5 - - + -
280F VAL* 4.8 5.6 - - + -
293F ILE* 5.0 0.7 - - + -
295F MET* 4.5 12.3 - - + -
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Residues in contact with SER 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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1044B ASN 3.0 25.7 + - - -
1045B ARG* 4.4 4.0 - - - +
1046B LEU* 5.8 4.5 - - - -
190F ILE 3.4 7.0 - - - -
191F ASP* 4.4 9.5 + - - -
195F LEU* 1.3 71.4 + - - +
197F VAL* 1.3 63.1 + - - +
198F GLN* 4.1 2.0 - - - -
217F THR 3.8 0.6 - - - +
218F ILE* 3.3 5.4 - - - +
219F ILE* 2.7 52.3 + - - +
221F LYS* 3.4 14.8 + - - +
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Residues in contact with VAL 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188F PRO* 3.6 2.4 - - - +
189F LEU* 2.8 42.9 + - + -
190F ILE* 2.8 44.8 + - + +
195F LEU* 3.9 16.6 - - + -
196F SER* 1.3 77.1 - - - +
198F GLN* 1.3 58.4 + - - +
199F VAL* 4.8 3.4 - - + -
216F ILE* 4.8 1.3 - - + -
217F THR 3.4 6.7 - - - +
218F ILE* 4.2 16.6 - - + -
280F VAL* 5.4 1.3 - - + -
291F LEU* 3.6 30.3 - - + -
293F ILE* 4.3 7.9 - - + -
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Residues in contact with GLN 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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1007B ASN* 4.0 9.3 - - - +
1008B TRP 3.4 23.6 + - - +
1009B GLN* 3.9 11.6 + - - +
1046B LEU* 2.7 62.7 + - + +
1047B THR* 4.7 0.5 - - - +
186F ALA* 4.1 0.4 - - + +
187F TRP 3.7 18.6 - - - +
188F PRO* 3.2 26.8 - - - +
190F ILE 5.2 0.5 - - - +
196F SER* 4.1 3.4 - - - -
197F VAL* 1.3 73.2 - - - +
199F VAL* 1.4 67.1 + - - +
216F ILE 3.7 0.2 - - - -
217F THR* 2.8 42.8 + - - +
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Residues in contact with VAL 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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1009B GLN* 3.2 6.5 + - - -
165E LEU* 3.7 24.5 - - + -
185F GLY 3.4 1.2 - - - +
186F ALA* 3.2 3.1 - - - -
187F TRP* 2.8 41.1 + - + +
189F LEU* 3.5 37.2 - - + -
197F VAL* 4.3 1.5 - - + -
198F GLN* 1.4 77.2 - - - +
200F THR* 1.3 57.7 + - - +
201F ASN* 3.8 16.6 - - - +
213F THR* 4.1 6.5 - - + -
215F LYS 3.3 11.4 - - - +
216F ILE* 3.9 18.2 - - + -
291F LEU* 4.4 6.3 - - + -
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Residues in contact with THR 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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991B ASP* 2.9 30.6 + - + +
1009B GLN* 2.3 43.1 + - - +
185F GLY* 3.3 15.3 - - - +
186F ALA* 4.1 1.2 - - - +
199F VAL* 1.3 70.8 + - - +
201F ASN* 1.3 67.3 + - - +
202F VAL* 5.9 0.7 - - + -
213F THR* 3.4 5.9 - - - +
214F ASN* 3.0 43.9 + - - +
215F LYS* 3.1 13.2 + - - -
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Residues in contact with ASN 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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165E LEU* 5.0 0.8 - - - +
169F PRO* 3.6 12.6 - - - +
183F VAL* 2.8 42.6 + - - +
184F GLU* 3.7 6.3 - - - +
185F GLY* 2.9 31.7 + - - -
187F TRP* 4.5 2.4 - - - +
199F VAL* 3.8 20.7 - - - +
200F THR* 1.3 78.8 - - - +
202F VAL* 1.3 61.6 + - - +
211F THR* 3.9 14.6 - - - +
212F ALA 3.2 6.7 - - - +
213F THR* 2.7 29.6 + - - +
311F LEU* 5.7 0.2 - - - +
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Residues in contact with VAL 202 (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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200F THR* 5.9 0.9 - - + -
201F ASN* 1.3 74.7 - - - +
203F PRO* 1.4 85.4 - - + +
204F VAL* 3.3 0.9 + - - -
211F THR* 3.9 3.6 - - - -
212F ALA* 2.8 37.0 + - - +
214F ASN* 4.0 27.4 - - + +
288F TYR* 3.8 22.2 - - + +
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Residues in contact with PRO 203 (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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184F GLU* 3.6 39.7 - - + +
202F VAL* 1.4 100.2 - - + +
204F VAL* 1.3 64.2 + - - +
205F VAL* 3.3 20.8 + - - +
206F PRO* 4.8 1.8 - - + -
207F GLY* 4.7 6.3 - - - +
208F SER 3.6 19.3 - - - +
210F ALA 3.4 8.3 - - - +
211F THR* 3.9 5.5 - - + -
288F TYR* 4.8 0.5 + - - -
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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