Contacts of the strand formed by residues 198 - 207 (chain F) in PDB entry 4BEI
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 ALA 198 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164F LEU* 4.3 19.7 - - + -
192F ASN* 3.4 22.8 - - + +
194F ARG* 3.5 26.7 - - - +
197F GLU* 1.3 74.0 - - - +
199F ASN* 1.3 62.4 + - - +
200F VAL* 3.9 3.0 + - + +
222F TRP 3.5 2.6 - - - +
223F VAL* 3.6 1.6 - - - +
224F ILE* 2.9 37.6 + - + +
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Residues in contact with ASN 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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194F ARG* 4.8 2.0 - - - +
197F GLU* 3.9 22.3 + - - +
198F ALA* 1.3 75.6 - - - +
200F VAL* 1.3 64.4 - - - +
222F TRP 3.4 3.5 - - - +
223F VAL* 3.3 29.1 - - - +
255F ASP* 3.5 7.0 + - - +
256F ILE* 2.9 43.5 + - + -
257F VAL* 4.7 19.2 - - + +
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Residues in contact with VAL 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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164F LEU* 3.3 32.1 - - + -
190F LEU* 4.5 9.2 - - + -
198F ALA* 4.7 3.1 - - + -
199F ASN* 1.3 83.1 - - - +
201F GLU* 1.3 60.1 + - - +
202F PHE* 5.2 1.8 - - + -
220F GLU 3.9 0.3 - - - +
221F LYS* 3.5 2.3 - - - -
222F TRP* 2.8 57.8 + - + +
224F ILE* 4.1 17.0 - - + -
253F VAL* 3.8 17.0 - - + -
254F VAL 3.1 12.3 - - - +
255F ASP* 4.3 7.9 - - + +
256F ILE* 3.5 8.8 - - - +
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Residues in contact with GLU 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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92E ALA* 5.5 2.1 - - - +
121E PRO* 4.1 3.5 - - - +
123E TYR* 2.6 45.1 + - + +
124E MET* 3.8 7.6 - - - +
200F VAL* 1.3 74.5 - - - +
202F PHE* 1.3 64.0 + - - +
203F TRP* 3.7 22.2 - - + -
219F ARG* 3.8 29.7 + - + +
220F GLU 3.2 14.8 - - - +
221F LYS* 4.0 14.7 + - + +
253F VAL* 3.4 4.5 - - - +
254F VAL* 2.8 35.3 + - + +
256F ILE* 3.8 8.6 - - + +
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Residues in contact with PHE 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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168F ILE* 4.5 4.3 - - + -
188F VAL* 4.0 24.0 - - + -
190F LEU* 4.4 16.4 - - + -
200F VAL* 5.2 2.7 - - + -
201F GLU* 1.3 77.4 - - - +
203F TRP* 1.3 71.3 + - - +
204F MET* 3.8 37.2 - - + -
217F ASN* 3.5 26.7 - - - -
218F ALA 3.4 2.6 - - - +
219F ARG* 3.5 0.5 - - - -
220F GLU* 2.8 43.5 + - + +
222F TRP* 5.2 3.4 - + + -
230F TYR* 4.3 24.0 - + - -
232F LYS* 4.6 3.8 - - - -
251F ALA* 4.5 9.0 - - + -
252F GLN 3.4 12.8 - - - +
253F VAL* 3.8 17.0 - - + -
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Residues in contact with TRP 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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86E ILE* 5.3 1.3 - - + -
87E TYR 2.9 26.9 + - - -
88E PHE* 3.7 20.2 - + + -
89E PRO* 4.1 4.7 - - + -
124E MET* 3.5 26.5 - - + -
201F GLU* 3.7 25.1 - - + -
202F PHE* 1.3 87.2 - - - +
204F MET* 1.3 74.0 - - - +
205F THR* 4.8 0.2 - - + -
217F ASN* 3.5 14.1 - - - +
218F ALA 4.0 1.1 - - - +
219F ARG* 3.6 32.5 - - + -
250F ASN* 5.5 0.4 - - - -
251F ALA* 3.4 0.2 - - - -
252F GLN* 2.8 68.2 + - + +
254F VAL* 3.3 31.0 - - + -
261F ARG* 4.6 2.2 - - - -
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Residues in contact with MET 204 (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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89E PRO* 4.1 0.7 - - - +
168F ILE* 4.3 15.3 - - + -
186F PHE* 4.5 13.0 - - + -
188F VAL* 4.2 13.2 - - + -
202F PHE* 3.8 21.8 - - + -
203F TRP* 1.3 83.6 - - - +
205F THR* 1.3 68.1 + - - +
215F PRO* 4.0 0.9 - - - +
216F VAL* 2.9 21.5 + - + -
217F ASN* 2.9 45.3 + - + +
234F ARG* 4.5 8.3 - - - +
249F ILE* 4.0 25.6 - - + -
250F ASN 3.2 5.6 - - - +
251F ALA* 3.7 24.2 - - + -
266F MET* 5.2 0.2 - - + -
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Residues in contact with THR 205 (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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79E SER* 5.7 0.4 - - - +
87E TYR* 3.7 33.5 - - - +
88E PHE* 4.1 2.2 - - - -
89E PRO* 4.0 22.2 - - + -
203F TRP* 4.8 1.1 - - + -
204F MET* 1.3 79.9 - - - +
206F ALA* 1.3 58.4 + - - +
207F VAL* 3.9 9.5 - - - +
213F ILE* 3.9 20.4 - - + -
214F ILE 3.2 11.2 - - - +
215F PRO* 4.7 1.6 - - + -
216F VAL* 3.7 6.5 - - - +
248F THR 3.7 0.2 - - - +
249F ILE* 3.6 2.8 - - - +
250F ASN* 2.7 44.1 + - - +
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Residues in contact with ALA 206 (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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205F THR* 1.3 71.8 - - - +
207F VAL* 1.3 63.0 + - - +
208F GLY* 3.5 2.8 + - - -
212F LEU 3.7 0.5 - - - +
213F ILE* 3.7 0.7 - - - -
214F ILE* 2.7 44.9 + - + +
216F VAL* 3.6 11.9 - - + +
236F ILE* 4.0 11.7 - - + -
247F TYR* 4.5 11.2 - - + -
248F THR 3.5 5.2 - - - -
249F ILE* 3.5 27.1 - - + -
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Residues in contact with VAL 207 (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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87E TYR* 3.6 41.3 - - + -
1272E O4B 4.0 15.5 - - - +
205F THR* 3.9 10.5 - - - +
206F ALA* 1.3 73.0 - - - +
208F GLY* 1.3 60.7 + - - +
212F LEU 3.5 9.2 - - - +
213F ILE* 4.5 4.5 - - + +
246F GLU 3.8 1.2 - - - +
247F TYR* 3.5 1.2 - - - -
248F THR* 2.7 45.2 + - - +
250F ASN* 4.9 2.2 - - + -
1272F O4B 3.7 40.9 - - - +
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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