Contacts of the strand formed by residues 191 - 199 (chain A) in PDB entry 2F24
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 ILE 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A ALA 3.5 0.7 - - - +
181A TYR* 4.0 0.4 - - - -
182A ARG* 2.8 38.8 + - - +
184A LEU* 4.7 17.3 - - + -
188A GLN* 5.9 5.6 - - + -
189A ARG 3.7 10.1 - - - +
190A PRO* 1.3 75.5 - - - +
192A PRO* 1.3 72.2 - - + +
193A SER* 4.8 0.2 - - - +
214A GLN* 3.9 30.7 - - + +
215A ASP* 3.6 33.9 - - - +
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Residues in contact with PRO 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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179A TYR* 4.3 7.2 - - + -
180A ALA 3.1 10.8 - - - +
181A TYR* 3.6 35.6 - - + -
190A PRO 4.0 1.8 - - - +
191A ILE* 1.3 88.4 - - + +
193A SER* 1.3 55.7 + - - +
215A ASP* 2.7 45.6 + - - +
216A THR 3.0 13.2 + - - +
217A LEU* 3.7 29.2 - - + -
239A HIS* 4.7 3.1 - - - +
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Residues in contact with SER 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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179A TYR* 3.2 1.8 - - - -
180A ALA 2.9 28.0 + - - -
182A ARG* 4.0 13.8 + - - -
191A ILE* 4.4 1.7 + - - +
192A PRO* 1.3 76.9 + - - +
194A ALA* 1.3 62.6 + - - +
211A PHE* 3.5 36.2 - - - +
212A VAL 4.4 0.3 + - - -
213A ALA 4.0 5.6 - - - -
214A GLN* 3.3 25.6 + - - +
216A THR* 3.3 11.1 + - - -
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Residues in contact with ALA 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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178A ALA 3.2 13.7 - - - +
179A TYR* 3.8 1.8 - - - -
193A SER* 1.3 72.3 - - - +
195A PHE* 1.3 64.7 + - - +
211A PHE* 3.3 3.5 - - - -
212A VAL* 3.0 41.5 + - + +
216A THR* 2.8 16.7 + - - +
217A LEU 3.8 13.0 - - - +
219A CYS* 3.8 20.9 - - + -
234A LEU* 4.3 6.3 - - + -
236A ALA* 4.5 0.2 - - + -
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Residues in contact with PHE 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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154A TRP* 3.8 13.7 - + - -
157A PHE* 5.5 2.0 - + + -
177A PRO* 3.8 1.2 - - - +
178A ALA* 2.8 38.9 + - + +
179A TYR* 3.6 28.3 - - - -
180A ALA* 3.8 10.5 - - + -
193A SER 3.8 2.9 - - - -
194A ALA* 1.3 78.4 - - - +
196A CYS* 1.3 87.1 + - - +
197A PHE* 3.6 44.6 - + - -
208A ARG* 3.8 9.2 - - + -
209A GLY 3.8 13.2 - - - +
210A HIS 3.7 19.1 - - - +
211A PHE* 3.5 23.3 - + + -
212A VAL* 5.2 1.1 - - - -
219A CYS* 4.3 2.1 - - - -
234A LEU* 4.4 6.3 - - - +
255A PHE* 5.2 1.3 - - - -
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Residues in contact with CYS 196 (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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175A VAL* 3.8 24.0 - - + -
176A VAL 3.4 4.5 - - - +
177A PRO* 4.5 4.7 - - - -
195A PHE* 1.3 89.8 - - - +
197A PHE* 1.3 57.2 + - - +
198A LEU* 5.3 1.4 - - + +
209A GLY* 2.7 33.7 + - - -
210A HIS 5.0 0.2 + - - -
221A VAL* 3.6 31.2 - - - -
232A VAL* 5.0 0.4 - - - -
234A LEU* 3.9 3.1 - - - -
251A ASP 5.3 0.2 - - - +
252A GLY* 4.0 19.6 + - - +
253A LEU* 5.6 0.2 - - - +
255A PHE* 3.9 19.3 - - - -
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Residues in contact with PHE 197 (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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124A LEU* 3.9 20.6 - - + -
146A ALA* 3.5 40.2 - - + -
147A ILE* 3.7 24.0 - - + -
154A TRP* 5.1 0.2 - + - -
157A PHE* 5.2 4.5 - + - -
159A VAL* 4.0 13.7 - - + -
174A LEU 3.8 0.5 - - - +
175A VAL* 3.4 6.9 - - - +
176A VAL* 2.9 42.9 + - + +
178A ALA* 3.9 16.4 - - + -
195A PHE* 3.6 34.5 - + - -
196A CYS* 1.3 74.3 - - - +
198A LEU* 1.3 58.7 - - - +
206A TRP* 3.8 17.0 - + + -
207A ALA 3.3 9.0 - - - -
208A ARG* 4.2 6.3 - - + -
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Residues in contact with LEU 198 (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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173A SER* 3.9 19.1 - - - -
174A LEU 3.5 11.2 - - - +
175A VAL* 3.9 5.6 - - + -
196A CYS* 4.1 2.0 - - + +
197A PHE* 1.3 75.0 - - - +
199A SER* 1.3 66.7 + - - +
200A HIS* 3.8 23.3 - - + +
206A TRP* 3.5 5.3 - - - -
207A ALA* 2.8 45.1 + - + +
250A ASN 4.4 0.2 - - - +
251A ASP* 3.7 43.5 - - + +
252A GLY 5.7 0.9 - - - -
253A LEU* 3.7 39.9 - - + +
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Residues in contact with SER 199 (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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173A SER* 3.2 4.0 - - - -
174A LEU* 2.8 40.0 + - - +
198A LEU* 1.3 74.9 - - - +
200A HIS* 1.3 62.2 + - - +
201A ASP* 2.8 14.7 + - - -
203A GLY 2.9 18.3 + - - -
205A THR 2.8 25.1 + - - -
206A TRP* 3.5 24.5 - - - -
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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