Contacts of the strand formed by residues 175 - 181 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D GLN* 4.7 3.8 + - - -
116D TYR* 3.4 16.8 - - + +
118D ALA* 5.0 4.7 - - + +
163D LEU* 5.6 1.6 - - + -
166D LEU* 4.0 28.3 - - + +
167D ILE* 3.8 40.4 - - + +
170D LYS* 5.1 2.5 - - + -
171D GLY 4.1 10.8 - - - +
172D ALA* 3.0 14.1 + - - +
173D GLU 3.3 2.0 - - - +
174D ASN* 1.3 81.6 - - - +
176D ALA* 1.3 65.4 + - - +
177D TYR 3.9 13.9 - - - +
178D ILE* 4.8 5.8 - - + -
209D ILE* 3.9 31.3 - - + +
210D LYS 5.4 0.2 + - - -
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Residues in contact with ALA 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ALA* 3.6 23.9 - - - +
111D ILE* 4.2 6.3 - - + -
115D GLN* 3.6 25.6 - - + +
116D TYR 2.7 16.4 + - - +
117D VAL* 3.9 12.3 - - + -
174D ASN 3.9 2.6 + - - -
175D ILE* 1.3 73.5 - - - +
177D TYR* 1.3 74.4 + - + +
210D LYS* 3.9 11.3 + - - +
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Residues in contact with TYR 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LEU* 4.2 17.4 - - + +
107D SER* 3.8 18.9 + - - -
110D ALA* 3.8 23.6 - - + -
111D ILE* 3.6 28.8 - - + +
117D VAL* 3.7 14.8 - - + -
118D ALA 3.5 18.7 + - - -
130D GLN* 3.9 9.8 + - - +
175D ILE* 3.4 8.5 - - - +
176D ALA* 1.3 90.2 - - + +
178D ILE* 1.3 74.0 + - - +
179D CYS* 3.8 21.0 + - + -
209D ILE* 4.4 1.8 - - - -
210D LYS* 3.0 27.1 - - + +
212D PHE* 3.6 25.6 - + + -
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Residues in contact with ILE 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D ALA* 3.2 15.3 - - + +
140D ILE* 4.9 2.7 - - + -
158D ILE* 4.2 24.5 - - + -
163D LEU* 3.9 34.3 - - + -
175D ILE* 4.8 4.9 - - + -
177D TYR* 1.3 76.5 - - - +
179D CYS* 1.3 61.5 + - - +
180D LEU* 3.5 5.6 + - + +
200D VAL* 4.3 12.8 - - + -
204D ALA* 3.7 30.1 - - + -
209D ILE* 4.1 14.8 - - + -
210D LYS 2.5 12.7 + - - +
211D ILE* 3.5 8.2 - - + +
212D PHE 2.9 25.8 + - - +
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Residues in contact with CYS 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LEU* 6.4 0.9 - - - -
117D VAL* 4.4 4.5 - - + -
118D ALA 2.7 12.3 + - - +
119D GLY* 3.0 24.8 - - - -
120D ASN* 3.3 5.4 + - - +
121D MET 5.3 0.3 - - - +
126D THR* 4.9 7.4 - - - -
130D GLN* 4.1 18.8 - - - +
137D PHE* 6.0 1.8 - - + -
177D TYR* 3.8 20.2 + - + -
178D ILE* 1.3 70.7 - - - +
180D LEU* 1.3 62.1 + - - +
181D ALA* 3.7 2.5 + - - +
212D PHE* 3.4 11.2 - - - -
213D TYR 5.4 0.2 - - - -
214D ASP* 4.4 21.1 - - - -
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Residues in contact with LEU 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ASN* 3.5 7.6 - - - +
158D ILE* 3.7 27.6 - - + -
178D ILE* 3.5 6.3 + - + +
179D CYS* 1.3 72.9 - - - +
181D ALA* 1.3 60.6 + - - +
182D VAL* 3.7 26.2 - - + -
192D VAL* 4.1 12.1 - - + -
196D ASN* 4.9 0.2 - - - +
197D MET* 4.0 25.4 - - + -
200D VAL* 4.3 23.1 - - + -
211D ILE* 4.9 2.2 - - + -
212D PHE 3.2 6.1 + - - -
213D TYR* 3.2 35.7 - - + +
214D ASP* 2.9 21.8 + - - -
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Residues in contact with ALA 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ASN* 2.8 42.0 + - - +
121D MET 5.9 0.4 - - - +
122D TYR* 6.6 0.4 - - - -
179D CYS* 3.7 2.9 + - - +
180D LEU* 1.3 73.2 - - - +
182D VAL* 1.3 66.7 + - - +
183D THR 3.3 16.0 - - - +
184D VAL* 4.7 4.0 - - - -
185D ASN 5.6 0.2 - - - +
192D VAL* 3.5 4.7 - - - +
214D ASP* 3.7 24.2 - - + +
1000D PLP 5.3 5.2 - - + -
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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