Contacts of the strand formed by residues 176 - 183 (chain D) in PDB entry 6QCG
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 176 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154D ILE* 4.0 1.1 - - - +
173D GLY* 2.9 30.1 + - - +
174D GLU 3.4 2.3 - - - -
175D LEU* 1.3 90.7 - - - +
177D ASN* 1.3 65.1 + - - +
78E ILE* 5.3 0.9 - - - -
115E GLU 3.3 13.7 - - - -
116E MET* 4.2 3.6 - - - -
117E LYS* 4.6 10.3 - - - -
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Residues in contact with ASN 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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154D ILE* 3.9 8.3 - - - +
171D ALA 3.2 16.4 - - - +
172D SER* 3.7 17.8 + - - +
175D LEU* 4.9 0.4 - - - +
176D GLY* 1.3 74.1 - - - +
178D GLY* 1.3 60.0 + - - +
179D ASN* 5.4 3.8 - - - +
78E ILE* 5.8 1.0 - - - +
113E ASP 4.6 0.2 - - - +
114E TYR* 3.5 3.8 - - - +
115E GLU* 2.9 57.0 + - - +
117E LYS* 3.6 10.9 + - - -
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Residues in contact with GLY 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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151D LEU* 4.6 4.6 - - - +
154D ILE* 4.3 3.6 - - - +
169D PHE 4.6 0.4 - - - -
170D SER* 3.4 0.7 - - - -
171D ALA* 3.0 29.7 + - - +
177D ASN* 1.3 74.4 - - - +
179D ASN* 1.3 71.9 + - - +
113E ASP 3.6 5.2 - - - -
114E TYR* 3.4 28.3 - - - -
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Residues in contact with ASN 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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168D LYS* 3.7 26.4 + - + +
169D PHE 3.4 4.5 - - - -
170D SER* 3.4 22.6 + - - -
171D ALA 4.5 0.8 + - - +
177D ASN* 5.4 3.8 - - - +
178D GLY* 1.3 97.0 + - - +
180D ILE* 1.3 62.5 + - - +
181D LYS* 4.2 5.2 - - - -
111E VAL 3.7 1.1 - - - +
112E SER* 3.4 1.6 - - - -
113E ASP* 2.8 56.9 + - + +
114E TYR* 4.7 1.6 - - - -
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Residues in contact with ILE 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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147D ILE* 4.0 33.7 - - + +
150D ASP* 4.8 5.4 - - + +
151D LEU* 4.0 24.2 - - + -
168D LYS* 3.2 3.3 - - - -
169D PHE* 2.8 51.2 + - + +
179D ASN* 1.3 75.6 - - - +
181D LYS* 1.3 65.0 + - - +
182D LEU* 4.0 0.7 - - + -
81E CYS 5.6 0.2 - - - +
110E LYS* 3.6 26.0 - - + +
111E VAL 3.7 2.9 - - - -
112E SER* 3.5 23.1 - - - +
114E TYR* 3.3 25.6 - - - +
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Residues in contact with LYS 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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167D VAL 3.4 5.4 - - - +
168D LYS* 3.7 39.0 - - + +
179D ASN* 4.6 7.0 - - + +
180D ILE* 1.3 71.7 - - - +
182D LEU* 1.3 63.0 - - - +
183D SER* 4.2 2.7 + - - +
110E LYS* 3.2 4.3 - - - +
111E VAL* 2.8 56.0 + - + +
113E ASP* 3.9 24.2 + - + +
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Residues in contact with LEU 182 (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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139D MET* 3.7 37.9 - - + -
143D GLU* 4.5 11.9 - - + -
147D ILE* 4.1 23.1 - - + -
166D GLY* 3.2 2.6 - - - -
167D VAL* 2.9 47.1 + - + +
169D PHE* 4.3 4.9 - - + -
180D ILE* 4.0 1.7 + - + -
181D LYS* 1.3 75.0 - - - +
183D SER* 1.3 60.3 + - - +
195D VAL* 4.2 24.2 - - + -
109E GLU 4.0 5.8 - - - +
110E LYS* 3.6 35.9 - - + -
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Residues in contact with SER 183 (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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165D ASP 4.0 9.0 - - - -
166D GLY* 4.1 2.0 - - - -
181D LYS* 4.1 2.3 + - - +
182D LEU* 1.3 74.3 - - - +
184D GLN* 1.3 68.6 + - - +
185D THR* 3.7 6.8 - - - +
195D VAL* 3.5 18.9 - - - +
197D ILE* 5.7 0.2 - - - -
109E GLU* 3.5 28.8 + - - +
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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