Contacts of the strand formed by residues 175 - 181 (chain A) in PDB entry 1C7G
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 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A GLN* 4.7 2.7 + - - -
116A TYR* 3.3 14.8 - - + +
118A ALA* 4.9 4.5 - - + +
163A LEU* 5.6 1.3 - - + -
166A LEU* 4.1 27.6 - - + +
167A ILE* 3.8 40.6 - - + +
170A LYS* 5.1 2.5 - - + -
171A GLY 4.0 11.2 - - - +
172A ALA* 3.1 13.5 + - - +
173A GLU 3.4 0.5 - - - +
174A ASN* 1.3 80.6 - - - +
176A ALA* 1.3 64.9 + - - +
177A TYR 3.9 15.5 - - - +
178A ILE* 4.8 6.3 - - + -
209A ILE* 3.8 33.2 - - + +
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Residues in contact with ALA 176 (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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110A ALA* 3.4 24.8 - - - +
111A ILE* 4.0 7.0 - - + -
115A GLN* 3.6 25.6 - - + +
116A TYR 2.7 17.2 + - - +
117A VAL* 3.9 9.6 - - + -
174A ASN 3.8 2.8 + - - -
175A ILE* 1.3 74.3 - - - +
177A TYR* 1.3 73.6 + - + +
210A LYS* 3.9 11.1 + - - +
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Residues in contact with TYR 177 (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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106A LEU* 3.9 25.5 - - + +
107A SER* 3.8 12.3 + - - -
110A ALA* 3.7 25.6 - - + -
111A ILE* 3.6 23.4 - - + +
117A VAL* 3.4 18.4 - - + +
118A ALA 3.4 19.4 + - - -
130A GLN* 3.8 20.7 + - - +
175A ILE* 3.3 8.5 - - - +
176A ALA* 1.3 89.1 - - + +
178A ILE* 1.3 71.0 + - - +
179A CYS* 4.0 21.7 - - + -
209A ILE* 4.3 1.1 - - - -
210A LYS* 3.1 26.5 - - + +
212A PHE* 3.6 18.6 - + + -
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Residues in contact with ILE 178 (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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118A ALA* 3.1 18.2 - - + +
140A ILE* 4.7 1.6 - - + -
158A ILE* 4.2 24.9 - - + -
163A LEU* 3.6 38.6 - - + -
175A ILE* 4.8 3.1 - - + -
177A TYR* 1.3 76.4 - - - +
179A CYS* 1.3 59.4 + - - +
180A LEU* 3.5 9.5 + - + +
200A VAL* 4.2 11.7 - - + -
204A ALA* 4.0 27.4 - - + -
209A ILE* 4.3 14.1 - - + -
210A LYS 2.7 11.9 + - - +
211A ILE* 3.4 8.5 - - + +
212A PHE 2.9 25.6 + - - +
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Residues in contact with CYS 179 (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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106A LEU* 6.5 0.4 - - - -
117A VAL* 4.2 4.3 - - + -
118A ALA 2.7 11.9 + - - +
119A GLY* 3.1 23.0 - - - -
120A ASN* 3.4 5.2 + - - +
121A MET 5.2 1.3 - - - +
126A THR* 4.6 9.4 - - - -
130A GLN* 4.0 19.3 - - - +
137A PHE* 6.0 1.8 - - + -
177A TYR* 3.9 19.6 + - + -
178A ILE* 1.3 70.4 - - - +
180A LEU* 1.3 57.5 + - - +
181A ALA* 3.7 2.3 + - - +
212A PHE* 3.2 12.1 - - - -
213A TYR 5.3 0.4 - - - -
214A ASP* 4.3 22.0 - - - -
252A THR* 6.1 0.2 - - - -
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Residues in contact with LEU 180 (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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120A ASN* 3.5 7.4 - - - +
158A ILE* 4.0 26.9 - - + -
178A ILE* 3.5 6.0 + - + -
179A CYS* 1.3 72.5 - - - +
181A ALA* 1.3 65.0 + - - +
182A VAL* 3.6 26.9 - - + -
192A VAL* 4.0 18.4 - - + -
196A ASN* 5.0 0.7 - - - +
197A MET* 4.1 27.1 - - + -
200A VAL* 4.5 15.7 - - + -
211A ILE* 4.8 2.9 - - + -
212A PHE 3.2 5.7 + - - -
213A TYR* 3.0 35.2 - - + +
214A ASP* 2.9 21.6 + - - -
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Residues in contact with ALA 181 (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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120A ASN* 2.8 40.0 + - - +
121A MET 5.8 1.1 - - - +
122A TYR* 6.5 0.7 - - - -
179A CYS* 3.7 3.8 + - - +
180A LEU* 1.3 72.3 - - - +
182A VAL* 1.3 70.9 + - - +
183A THR 3.7 12.1 - - - +
184A VAL* 3.8 6.0 - - + +
185A ASN 5.8 0.2 - - - +
192A VAL* 3.4 5.4 - - - +
214A ASP* 3.6 25.1 - - + +
1000A PLP 5.3 4.3 - - + -
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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