Contacts of the strand formed by residues 204 - 211 (chain A) in PDB entry 4I7C
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 GLN 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A GLU 3.6 1.4 - - - +
195A LYS* 3.5 2.5 - - - +
196A GLN* 2.9 37.5 + - + +
198A LYS* 5.2 19.0 - - + +
203A GLN* 1.3 78.9 - - - +
205A PHE* 1.3 62.2 + - - +
206A PHE* 3.5 24.4 - - + -
254A SER* 5.6 0.7 + - - -
258A VAL* 3.7 18.8 - - + +
259A PHE 3.6 8.2 - - - +
260A ASP* 4.7 8.2 - - + +
202C HIS* 6.0 2.8 - - - -
204C GLN* 5.7 4.8 - - - +
260C ASP* 3.5 25.3 + - - +
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Residues in contact with PHE 205 (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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170A ILE* 3.6 37.2 - - + -
171A ASN* 5.9 0.4 - - - -
178A TRP* 4.3 4.9 - + - -
193A LEU* 4.1 19.1 - - + -
194A GLU 3.4 2.5 - - - -
195A LYS* 3.6 43.7 - - + -
203A GLN 4.7 0.4 - - - -
204A GLN* 1.3 72.9 - - - +
206A PHE* 1.3 66.6 + - - +
207A ALA 4.4 0.2 - - - -
257A LEU 3.9 0.6 - - - +
258A VAL* 3.5 8.0 - - - +
259A PHE* 2.6 71.0 + + + +
260A ASP 4.0 4.3 - - - -
261A THR* 3.8 24.0 - - + -
264A ALA* 3.9 14.6 - - + -
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Residues in contact with PHE 206 (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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192A VAL 3.7 1.7 - - - +
193A LEU* 3.3 4.4 - - - -
194A GLU* 2.8 49.6 + - + +
196A GLN* 3.3 31.6 - - - -
204A GLN* 3.5 42.2 - - + -
205A PHE* 1.3 75.1 - - - +
207A ALA* 1.3 59.4 + - - +
208A ILE 4.3 0.2 - - - -
251A ILE* 3.4 52.0 - - + +
254A SER* 4.3 7.4 - - - -
256A CYS* 3.8 19.3 - - - -
257A LEU 3.4 4.5 - - - -
258A VAL* 3.9 19.7 - - + -
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Residues in contact with ALA 207 (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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165A PHE* 6.3 0.4 - - + -
192A VAL 3.3 8.7 - - - +
193A LEU* 4.1 15.9 - - + -
205A PHE 4.4 0.2 - - - -
206A PHE* 1.3 73.4 - - - +
208A ILE* 1.3 61.0 + - - +
223A TYR* 4.5 0.7 + - - -
225A LEU* 3.5 24.1 - - + +
256A CYS* 3.3 5.2 - - - +
257A LEU* 3.0 43.2 + - + -
259A PHE* 4.9 2.0 - - + -
275A ILE* 4.4 13.2 - - + -
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Residues in contact with ILE 208 (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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190A MET 3.9 0.9 - - - +
191A LEU* 3.9 0.2 - - - -
192A VAL* 3.0 37.5 + - + +
206A PHE 5.4 0.2 - - - +
207A ALA* 1.3 77.0 - - - +
209A VAL* 1.3 73.9 + - - +
223A TYR* 3.5 16.8 - - - +
225A LEU* 3.9 3.2 - - - +
241A ARG* 4.2 10.3 - - + -
247A ILE* 3.7 47.8 - - + +
250A ALA* 3.7 30.1 - - + -
251A ILE* 4.4 12.3 - - + -
255A ASP 4.1 9.0 - - - +
256A CYS* 4.0 9.9 - - + -
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Residues in contact with VAL 209 (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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189A PHE* 4.1 24.5 - - + -
190A MET 3.4 7.6 - - - +
191A LEU* 4.0 27.8 - - + -
208A ILE* 1.3 87.5 - - - +
210A GLN* 1.3 63.2 + - - +
223A TYR* 3.3 41.2 + - + -
225A LEU* 4.1 14.4 - - + -
240A PRO* 3.4 14.3 - - + +
241A ARG* 3.3 16.1 + - - +
277A VAL* 4.2 4.5 - - + -
279A ILE* 4.5 5.6 - - + -
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Residues in contact with GLN 210 (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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129A PRO* 3.6 24.8 + - - +
189A PHE* 3.4 2.5 - - - +
190A MET* 2.7 66.0 + - + +
192A VAL* 4.2 2.3 - - + +
209A VAL* 1.3 80.1 - - - +
211A LEU* 1.3 60.5 + - - +
241A ARG* 3.0 16.4 - - + +
243A ILE* 3.8 25.3 - - + +
246A GLY* 3.8 15.9 - - - -
247A ILE* 3.2 45.3 + - + +
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Residues in contact with LEU 211 (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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187A PHE* 3.7 26.7 - - + -
188A HIS 3.5 11.2 - - - +
189A PHE* 3.6 28.9 - - + -
210A GLN* 1.3 71.0 - - - +
212A ILE* 1.3 67.4 + - - +
213A GLY* 3.1 15.9 + - - +
214A THR 4.1 1.3 - - - +
217A GLN* 3.6 18.2 - - + -
218A ALA* 3.4 39.3 - - + +
221A PHE* 4.0 9.9 - - + -
240A PRO* 4.2 6.1 - - + +
241A ARG 2.7 13.0 + - - +
242A SER* 3.7 1.7 - - - -
243A ILE* 3.0 27.8 + - - +
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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