Contacts of the strand formed by residues 176 - 184 (chain A) in PDB entry 2FBW
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 TYR 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A VAL* 3.6 16.7 - - + +
48A THR* 3.0 4.8 + - - -
49A LYS* 3.1 22.4 + - - +
173A PHE* 3.3 46.3 - + + +
174A VAL 3.3 18.2 - - - -
175A GLU* 1.3 80.6 - - - +
177A PHE* 1.3 61.5 + - - +
178A ALA 3.8 2.1 + - - -
193A ALA* 4.7 2.5 - - + -
194A LEU 3.3 7.0 - - - +
195A CYS* 3.6 41.6 - - + -
196A ILE* 4.8 0.2 - - - -
198A ASP* 5.4 0.3 + - - -
202A HIS* 3.6 35.3 - + + -
204A PHE* 4.1 17.0 - + - -
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Residues in contact with PHE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LYS* 4.0 18.6 - - + -
175A GLU 4.3 0.2 - - - -
176A TYR* 1.3 72.0 - - - +
178A ALA* 1.3 81.4 + - - +
179A LEU* 3.4 16.5 + - + +
193A ALA* 3.2 2.6 - - - -
194A LEU* 2.8 44.1 + - + +
196A ILE* 4.2 15.7 - - + +
232A ASP* 3.5 27.8 - - - -
520A VAL* 3.7 31.9 - - + -
523A LEU* 4.0 29.4 - - + -
524A GLU* 3.7 20.6 - - + -
527A ASN* 4.0 9.0 - - - -
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Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 3.7 34.8 - - + -
47A VAL* 5.0 4.2 - - + +
176A TYR 3.8 3.6 + - - -
177A PHE* 1.3 88.8 - - - +
179A LEU* 1.3 59.3 + - - +
191A VAL* 4.8 6.5 - - + -
192A ILE 3.7 8.1 - - - +
193A ALA* 3.8 6.9 - - + +
232A ASP* 5.0 7.8 - - + +
236A MET* 3.9 20.3 - - + +
239A ARG* 5.6 0.3 + - - -
527A ASN* 5.4 1.2 + - - -
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PHE* 3.7 20.0 - - + +
178A ALA* 1.3 72.2 - - - +
180A ASP* 1.3 72.8 + - - +
192A ILE* 2.8 18.5 + - + +
193A ALA* 4.0 8.7 - - - +
194A LEU* 4.0 18.6 - - + +
201A ILE* 4.3 8.5 - - + -
236A MET* 3.8 3.1 - - - -
239A ARG* 3.1 18.9 + - - +
449A SER* 4.2 29.2 - - - +
450A VAL 5.3 0.7 - - - +
453A LEU* 4.2 23.1 - - + -
523A LEU* 3.7 37.5 - - + -
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Residues in contact with ASP 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LEU* 1.3 83.6 - - - +
181A LEU* 1.3 67.6 + - - +
191A VAL* 3.3 7.1 - - - +
192A ILE* 3.0 29.9 + - + +
236A MET* 3.5 19.7 - - - +
239A ARG* 2.7 43.3 + - - +
449A SER* 2.7 34.3 + - - +
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ASP* 1.3 84.2 + - - +
182A LEU* 1.3 64.0 + - - +
183A MET* 3.6 32.7 + - + +
188A CYS* 4.2 10.1 - - - -
190A GLY 3.6 4.3 - - - +
191A VAL* 4.2 15.3 - - + -
209A THR* 4.5 0.2 - - + -
211A ILE* 3.9 27.6 - - + -
236A MET* 4.2 24.6 + - + +
237A VAL* 4.6 10.5 - - + -
240A ALA* 4.3 14.6 - - + -
242A LEU* 4.8 0.4 - - + -
392A LEU* 3.9 29.4 - - + -
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Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A LEU* 1.3 73.3 - - - +
183A MET* 1.3 59.3 + - - +
188A CYS* 3.6 0.9 - - - -
189A ARG* 2.7 37.5 + - - +
190A GLY* 2.8 22.4 + - - +
191A VAL 3.9 23.6 - - - +
192A ILE* 4.2 19.1 - - + -
203A ARG* 4.3 11.4 - - + -
204A PHE 4.2 7.0 - - - +
205A ARG* 4.8 1.1 - - + -
441A ILE* 4.0 35.4 - - + -
445A ALA* 4.2 11.7 - - + +
446A GLY* 4.2 25.4 - - - +
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Residues in contact with MET 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A LEU* 3.6 28.9 + - + +
182A LEU* 1.3 74.3 - - - +
184A GLU* 1.3 70.4 + - - +
186A GLY* 3.9 26.0 - - - +
187A GLU 3.2 14.1 - - - +
188A CYS* 3.7 25.1 - - - +
240A ALA* 4.0 24.9 - - + +
242A LEU* 4.3 23.8 - - + -
389A VAL* 4.4 4.5 - - + -
392A LEU* 5.2 0.4 - - - -
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Residues in contact with GLU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LEU 4.1 0.6 + - - -
183A MET* 1.3 82.1 - - - +
185A ASN* 1.3 93.4 + - - +
186A GLY 3.3 0.9 - - - -
187A GLU* 2.8 27.3 + - - +
189A ARG* 3.9 33.4 + - + +
440A SER 4.6 6.1 - - - +
441A ILE* 4.9 12.6 - - + -
442A LYS* 2.3 50.0 + - - +
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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