Contacts of the strand formed by residues 187 - 195 (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 GLU 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A MET* 3.2 6.8 - - - -
184A GLU 2.8 34.7 + - - +
185A ASN* 3.8 12.1 - - - +
186A GLY* 1.3 81.5 - - - +
188A CYS* 1.3 65.1 + - - +
189A ARG* 3.1 32.0 + - + +
390A PRO* 3.6 36.7 - - + +
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Residues in contact with CYS 188 (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* 4.2 13.7 - - - -
182A LEU 3.7 4.5 - - - -
183A MET* 3.7 13.7 - - - +
186A GLY 4.4 0.2 + - - -
187A GLU* 1.3 75.2 - - - +
189A ARG* 1.3 65.9 + - - +
190A GLY 3.4 24.9 - - - -
206A ALA 4.4 0.2 - - - +
207A LYS 4.2 13.5 - - - +
209A THR* 3.8 21.5 - - - -
389A VAL* 4.8 0.8 - - - +
390A PRO 3.1 12.1 + - - +
391A GLY* 4.0 14.3 - - - +
392A LEU* 4.1 23.6 - - + -
439A PRO* 5.1 0.7 - - - +
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Residues in contact with ARG 189 (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* 2.7 19.7 + - - +
184A GLU* 3.9 24.4 + - + +
185A ASN* 3.5 22.6 - - - +
187A GLU* 3.1 34.7 + - + +
188A CYS* 1.3 77.9 - - - +
190A GLY* 1.3 55.0 - - - +
205A ARG* 3.4 12.1 - - - +
206A ALA 3.2 29.5 + - - +
439A PRO* 3.2 31.0 - - + +
440A SER* 2.7 47.0 + - - +
441A ILE* 4.0 12.5 - - + +
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Residues in contact with GLY 190 (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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22A VAL* 4.5 1.8 - - - -
181A LEU* 3.6 1.0 - - - -
182A LEU* 2.8 25.9 + - - -
188A CYS* 3.4 13.0 - - - -
189A ARG* 1.3 79.8 - - - +
191A VAL* 1.3 69.6 + - - +
204A PHE 3.0 12.6 - - - -
206A ALA 4.3 2.7 - - - -
209A THR* 3.5 13.9 + - - -
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Residues in contact with VAL 191 (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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22A VAL* 4.4 7.2 - - + -
24A VAL* 3.9 24.7 - - + -
47A VAL* 5.1 3.1 - - + -
178A ALA* 4.8 9.4 - - + -
180A ASP 3.3 12.3 - - - +
181A LEU* 4.2 9.6 - - + -
182A LEU* 3.9 7.7 - - - +
190A GLY* 1.3 80.7 - - - +
192A ILE* 1.3 65.3 + - - +
193A ALA* 5.0 2.0 - - + -
203A ARG* 3.7 1.0 - - - -
204A PHE* 2.9 53.8 + - + +
209A THR* 3.7 26.0 - - + +
236A MET* 5.4 0.9 - - + -
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Residues in contact with ILE 192 (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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14A VAL* 6.0 0.2 - - + -
178A ALA* 3.7 2.4 - - - +
179A LEU* 2.8 27.9 + - + -
180A ASP* 3.0 20.2 + - + +
182A LEU* 4.2 15.7 - - + +
191A VAL* 1.3 73.7 - - - +
193A ALA* 1.3 67.7 + - - +
201A ILE* 3.6 26.7 - - + -
202A HIS 3.4 10.5 - - - +
203A ARG* 3.8 16.2 - - + +
445A ALA 4.5 0.4 - - - +
446A GLY* 3.7 28.7 - - - +
449A SER* 3.8 25.4 - - - +
450A VAL* 4.0 9.0 - - + -
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Residues in contact with ALA 193 (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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47A VAL* 4.4 11.0 - - + -
176A TYR* 4.7 3.1 - - + -
177A PHE 3.2 18.4 - - - +
178A ALA* 3.8 9.4 - - + +
179A LEU* 4.0 8.1 - - - -
191A VAL* 5.0 0.9 - - + -
192A ILE* 1.3 79.3 - - - +
194A LEU* 1.3 62.1 + - - +
201A ILE* 3.5 4.7 - - - +
202A HIS* 2.8 37.1 + - - +
204A PHE* 4.3 18.8 - - + -
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Residues in contact with LEU 194 (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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12A TYR* 5.7 0.2 - - + -
176A TYR* 3.3 6.7 - - - -
177A PHE* 2.8 44.0 + - + +
179A LEU* 4.0 5.0 - - + +
193A ALA* 1.3 72.7 - - - +
195A CYS* 1.3 66.1 + - - +
196A ILE* 3.5 15.8 + - + -
199A GLY* 3.6 28.5 - - - +
200A THR 3.6 8.7 - - - +
201A ILE* 4.0 13.2 - - + -
453A LEU* 4.0 24.9 - - + -
513A ILE* 4.1 22.7 - - + +
519A LEU* 4.8 7.4 - - + -
520A VAL* 4.7 13.7 - - + -
523A LEU* 5.1 5.4 - - + -
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Residues in contact with CYS 195 (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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174A VAL 5.7 0.2 - - - -
175A GLU 4.8 0.2 - - - -
176A TYR* 3.6 38.1 - - + -
193A ALA 4.1 0.6 + - - -
194A LEU* 1.3 70.1 - - - +
196A ILE* 1.3 60.6 + - - +
197A GLU* 3.7 20.4 - - - -
198A ASP* 3.0 33.9 - - - +
199A GLY* 2.9 28.8 + - - -
200A THR* 2.9 10.5 + - - +
202A HIS* 3.6 21.6 - - - +
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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