Contacts of the strand formed by residues 192 - 199 (chain A) in PDB entry 6H25
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 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A SER* 3.5 14.6 - - - +
151A ILE* 3.7 25.6 - - + +
154A ILE* 5.4 2.5 - - + -
190A MET* 4.7 2.5 - - + +
191A PRO* 1.3 75.2 - - - +
193A CYS* 1.3 74.5 + - - +
194A VAL* 4.7 5.8 - - + +
223A ILE 3.9 0.3 - - - +
224A ALA* 3.0 4.8 - - - -
225A MET 2.9 31.1 + - - +
258A VAL* 3.6 35.4 - - + -
261A ILE* 3.7 36.3 - - + -
262A THR* 5.6 2.2 - - - +
265A ILE* 4.2 14.6 - - + -
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Residues in contact with CYS 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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32A TYR* 3.9 2.3 + - - -
105A LEU* 5.3 2.2 - - - -
106A MET* 6.4 1.1 - - - -
109A CYS* 3.9 30.5 - - - -
146A ILE* 3.7 30.1 - - + -
147A ASP* 2.9 19.4 - - - +
150A SER* 3.4 24.2 + - - -
151A ILE* 5.9 0.3 - - - +
192A ILE* 1.3 88.4 - - - +
194A VAL* 1.3 65.9 + - - +
222A VAL* 4.2 8.5 - - + -
223A ILE 3.6 3.6 - - - -
224A ALA* 4.1 6.1 - - - +
261A ILE* 5.5 1.4 - - - +
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Residues in contact with VAL 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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32A TYR* 3.3 23.6 - - + +
147A ASP* 3.6 0.9 - - - -
192A ILE* 4.7 12.1 - - + +
193A CYS* 1.3 79.6 - - - +
195A SER* 1.3 63.8 + - - +
196A PHE* 3.6 34.5 + - + -
207A VAL* 4.8 2.2 - - + -
221A LEU 3.8 0.3 - - - +
222A VAL* 3.5 3.9 - - - -
223A ILE* 2.9 38.7 + - + +
225A MET* 6.1 1.3 - - + +
254A ALA* 4.4 19.7 - - + +
257A LYS* 4.2 23.1 - - + -
258A VAL* 4.9 1.3 - - + +
261A ILE* 5.4 0.9 - - + -
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Residues in contact with SER 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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32A TYR* 3.8 0.6 + - - -
144A ASN* 3.4 32.2 + - - +
146A ILE* 4.0 13.0 - - - +
147A ASP* 3.2 27.0 + - - +
194A VAL* 1.3 74.5 - - - +
196A PHE* 1.3 72.3 + - - +
207A VAL* 3.9 3.1 - - - +
208A ASP 3.5 19.2 + - - -
209A PRO* 4.8 2.2 - - - -
220A LEU* 5.2 4.9 - - - -
221A LEU 3.4 6.7 - - - -
222A VAL* 4.2 8.0 - - - +
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Residues in contact with PHE 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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194A VAL* 3.6 27.8 - - + -
195A SER* 1.3 82.0 - - - +
197A ALA* 1.3 60.4 + - - +
198A PHE* 4.1 5.0 + - + -
205A LEU* 4.1 14.6 - - + -
206A LEU 3.4 11.9 - - - +
207A VAL* 3.6 21.8 - - + -
209A PRO* 5.3 1.6 - - - -
219A GLY 3.8 0.2 - - - +
220A LEU* 3.4 7.6 - - - +
221A LEU* 2.8 46.9 + - + +
223A ILE* 3.8 18.4 - - + -
250A CYS* 3.5 53.2 - - + -
253A ILE* 4.5 11.7 - - + -
254A ALA* 4.3 10.5 - - + -
257A LYS* 6.1 0.7 - - + -
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Residues in contact with ALA 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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195A SER 4.4 0.2 + - - -
196A PHE* 1.3 73.0 - - - +
198A PHE* 1.3 64.5 + - - +
199A PHE* 3.7 21.6 - - + -
204A TYR 3.6 3.5 - - - +
206A LEU* 2.9 40.6 + - + +
209A PRO* 4.0 27.5 - - + +
217A MET* 4.1 9.6 - - + -
219A GLY 3.4 7.6 - - - +
220A LEU* 5.9 0.2 - - - -
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Residues in contact with PHE 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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196A PHE* 4.1 5.6 + - + -
197A ALA* 1.3 79.8 - - - +
199A PHE* 1.3 57.6 + - - +
202A GLY* 4.5 17.9 - - - +
204A TYR 3.8 9.2 - - - -
205A LEU* 3.6 28.7 - - + -
217A MET* 4.1 1.2 - - - +
218A ASP* 2.8 24.3 + - - +
219A GLY 2.9 19.7 + - - +
221A LEU* 4.6 17.9 - - + -
240A ILE* 3.6 32.8 - - + -
242A LEU* 3.7 21.3 - - + -
246A GLN* 3.6 33.0 - - + -
247A VAL* 5.6 0.9 - - + -
250A CYS* 4.3 16.2 - - - -
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Residues in contact with PHE 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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14A LEU* 5.4 0.2 - - + -
15A LEU* 4.4 18.4 - - + -
18A ILE* 4.4 16.6 - - + -
197A ALA* 3.7 20.6 - - + -
198A PHE* 1.3 76.9 - - - +
200A GLN* 1.3 78.7 + - + +
201A GLN 3.4 2.6 + - - -
202A GLY 3.5 0.5 + - - +
203A THR* 3.3 17.5 + - - -
204A TYR* 3.4 17.7 + - + +
206A LEU* 3.6 45.8 - - + -
213A GLU* 3.7 23.3 - - + -
216A VAL* 3.7 18.4 - - + -
217A MET* 3.6 29.8 - - + -
218A ASP* 3.7 1.6 - - - -
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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