Contacts of the strand formed by residues 187 - 194 (chain A) in PDB entry 3I7O
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 GLY 187 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A GLN* 3.5 5.9 - - - +
184A ASP 3.0 30.8 + - - +
186A GLN* 1.3 82.0 - - - +
188A ARG* 1.3 62.2 + - - -
189A HIS* 3.3 7.7 - - - -
214A ALA* 6.0 4.3 - - - -
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Residues in contact with ARG 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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163A HIS* 5.1 0.8 - - - -
165A ILE* 3.4 28.0 - - - +
181A VAL* 4.3 3.8 - - + -
182A TYR 3.2 7.2 - - - +
183A GLN* 2.6 52.7 + - + -
187A GLY* 1.3 72.4 - - - -
189A HIS* 1.3 70.8 + - - +
211A ASN* 3.9 2.3 - - - +
212A VAL* 3.2 41.3 + - + +
213A GLU 3.4 20.9 - - - +
214A ALA* 2.8 29.4 + - - +
215A GLU* 4.7 7.3 + - - +
216A ALA* 2.9 25.9 + - - -
217A SER* 5.5 1.4 - - - -
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Residues in contact with HIS 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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180A PHE 3.3 1.9 - - - +
181A VAL* 3.1 2.1 - - - -
182A TYR* 2.7 67.2 + - + -
184A ASP* 3.1 31.9 - - - -
186A GLN* 3.9 16.6 + - + +
187A GLY* 3.3 22.8 + - - -
188A ARG* 1.3 78.0 + - - +
190A VAL* 1.3 60.0 + - - +
209A GLN* 3.1 29.6 - - - +
210A GLU 3.6 3.1 - - - +
211A ASN* 2.8 29.8 + - - -
212A VAL* 3.7 6.2 - - - +
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Residues in contact with VAL 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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179A CYS* 3.7 28.9 - - - -
180A PHE 3.4 7.9 - - - +
181A VAL* 4.3 5.2 - - + +
189A HIS* 1.3 71.8 - - - +
191A LYS* 1.3 67.9 + - - +
207A TRP* 5.0 11.9 - - + +
208A LYS 5.4 0.7 - - - +
209A GLN* 3.0 20.8 - - - +
210A GLU* 3.1 40.2 + - + +
211A ASN 4.0 0.9 - - - +
212A VAL* 3.7 25.1 - - + +
231A ILE* 5.0 11.2 - - + -
240A HIS* 4.0 15.9 - - + +
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Residues in contact with LYS 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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160A GLU* 4.9 2.2 - - - +
161A GLU* 2.5 30.4 + - - +
179A CYS* 3.3 4.2 - - - -
180A PHE* 2.9 42.5 + - + -
182A TYR* 3.6 31.9 - - + +
190A VAL* 1.3 79.8 - - - +
192A THR* 1.3 78.6 + - - +
193A TYR* 2.4 40.9 + - - -
204A LYS* 6.1 6.5 - - - +
207A TRP* 5.1 1.3 - - - -
208A LYS 5.5 0.2 - - - -
209A GLN* 4.2 20.2 - - + +
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Residues in contact with THR 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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170A LEU* 3.6 22.9 - - + -
177A THR* 4.1 2.9 - - + -
178A ILE 3.1 16.6 - - - +
179A CYS* 4.2 4.5 - - + -
180A PHE* 4.7 0.4 - - - -
191A LYS* 1.3 85.6 - - - +
193A TYR* 1.3 78.0 + - - +
204A LYS* 4.4 6.1 - - - +
205A GLY* 3.3 21.7 + - - -
206A PRO* 4.4 2.5 - - + -
207A TRP* 2.8 49.7 + - + +
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Residues in contact with TYR 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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159A LEU* 4.5 5.4 - - + +
160A GLU* 4.7 6.9 + - - +
161A GLU* 2.8 7.8 + - - -
177A THR* 3.2 6.9 - - - -
178A ILE* 2.9 45.3 + - + +
180A PHE* 3.4 35.7 - + - -
191A LYS* 2.4 38.8 + - - -
192A THR* 1.3 78.3 - - - +
194A GLU* 1.3 69.8 + - - +
202A PHE* 3.7 40.6 - + + -
203A ASN 3.0 22.4 - - - +
204A LYS* 4.4 5.6 - - + -
205A GLY* 3.4 5.6 - - - +
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Residues in contact with GLU 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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175A ALA* 3.1 32.4 - - + +
176A PRO 3.1 4.3 - - - -
177A THR* 3.3 12.1 - - - +
193A TYR* 1.3 76.4 - - - +
195A VAL* 1.3 62.7 + - - +
202A PHE 2.2 28.8 + - - +
203A ASN* 4.1 12.1 + - + +
204A LYS 3.6 25.5 + - - +
205A GLY* 3.7 0.8 - - - -
206A PRO* 4.5 15.0 - - + +
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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