Contacts of the helix formed by residues 162 - 179 (chain D) in PDB entry 6GR2
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 THR 162 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161D GLY* 1.3 74.7 - - - -
163D ILE* 1.3 76.0 + - + +
164D ALA* 3.2 16.2 - - + +
165D ALA* 3.1 22.6 + - - +
166D ARG* 3.1 20.9 + - - +
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Residues in contact with ILE 163 (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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162D THR* 1.3 78.7 - - + +
164D ALA* 1.3 62.9 + - - +
166D ARG* 3.2 28.9 + - - +
167D ALA* 3.1 18.0 + - - +
188D PHE* 5.4 1.3 - - + -
191D LEU* 3.7 24.0 - - + +
192D MET* 3.4 41.3 - - + -
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Residues in contact with ALA 164 (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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162D THR* 3.2 12.0 - - + +
163D ILE* 1.3 79.0 - - - +
165D ALA* 1.3 57.0 + - - +
167D ALA* 3.1 3.3 + - - +
168D GLN* 2.9 49.1 + - - +
188D PHE* 4.0 29.4 - - + -
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Residues in contact with ALA 165 (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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150D TYR* 5.1 1.1 - - - +
161D GLY* 4.6 4.9 - - - -
162D THR* 3.1 29.3 + - - +
164D ALA* 1.3 79.0 - - - +
166D ARG* 1.3 58.0 + - + +
168D GLN* 3.3 11.6 + - - +
169D VAL* 2.9 35.3 + - + +
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Residues in contact with ARG 166 (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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150D TYR* 3.3 39.7 - - + +
154D GLN* 3.3 24.7 + - - +
159D ASP* 3.3 31.3 + - - +
160D SER 5.6 0.4 + - - -
161D GLY 4.2 11.2 + - - -
162D THR 3.1 16.5 + - - +
163D ILE* 3.5 30.7 - - - +
164D ALA 3.2 0.2 - - - -
165D ALA* 1.3 76.6 - - + +
167D ALA* 1.3 63.2 + - - +
169D VAL* 3.2 2.9 + - - +
170D CYS* 3.1 27.4 + - - -
191D LEU* 3.7 21.6 - - + +
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Residues in contact with ALA 167 (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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163D ILE 3.1 7.2 + - - +
164D ALA 3.1 8.0 + - - +
166D ARG* 1.3 79.4 - - - +
168D GLN* 1.3 57.0 + - + +
170D CYS* 3.2 3.8 + - - +
171D GLN* 2.9 28.9 + - - +
184D ILE* 4.9 5.8 - - + +
187D GLN* 3.7 19.6 - - + +
188D PHE* 4.0 28.0 - - + +
191D LEU* 3.2 20.7 - - + +
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Residues in contact with GLN 168 (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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164D ALA* 2.9 35.8 + - - +
165D ALA* 3.7 8.5 - - - +
167D ALA* 1.3 73.5 - - + +
169D VAL* 1.3 61.1 + - - +
171D GLN* 3.7 13.1 - - - +
172D GLN* 2.9 28.8 + - - +
184D ILE* 4.5 17.3 - - + +
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Residues in contact with VAL 169 (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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113D VAL* 4.5 7.9 - - + +
116D TYR* 3.7 38.5 - - + +
117D TYR 4.5 1.1 - - - +
118D PRO* 4.4 11.7 - - + -
150D TYR* 3.5 31.4 - - + +
165D ALA* 2.9 18.7 + - + +
166D ARG 3.6 7.2 - - - +
168D GLN* 1.3 77.5 - - + +
170D CYS* 1.3 64.0 + - - +
172D GLN* 3.2 8.8 + - - +
173D ALA* 3.1 20.6 + - - +
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Residues in contact with CYS 170 (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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113D VAL* 4.5 4.9 - - - -
146D GLU* 3.2 49.4 - - + +
147D VAL* 4.0 11.2 - - + -
150D TYR* 3.8 21.3 - - - -
166D ARG 3.1 18.8 + - - +
167D ALA* 3.7 2.9 - - - +
169D VAL* 1.3 77.7 - - - +
171D GLN* 1.3 61.5 + - - +
173D ALA* 3.4 9.1 + - - +
174D GLU* 3.2 16.5 + - - +
187D GLN* 3.5 20.6 - - + -
191D LEU* 5.3 1.3 - - - -
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Residues in contact with GLN 171 (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 ALA 2.9 15.5 + - - +
168D GLN* 3.7 11.1 - - - +
170D CYS* 1.3 75.0 - - - +
172D GLN* 1.3 67.1 + - - +
174D GLU* 3.2 2.6 + - - +
175D HIS* 3.0 43.0 + - + +
182D CYS* 2.7 33.8 + - - -
183D GLY* 3.2 16.9 - - - +
184D ILE* 3.0 27.6 - - + +
187D GLN* 3.9 15.0 - - - +
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Residues in contact with GLN 172 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D TYR* 3.8 32.6 + - + -
168D GLN 2.9 13.8 + - - +
169D VAL* 3.2 11.2 + - - +
171D GLN* 1.3 75.9 - - - +
173D ALA* 1.3 61.5 + - - +
175D HIS* 3.2 14.2 + - - +
176D SER* 2.9 47.3 + - - -
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Residues in contact with ALA 173 (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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108D ASN 5.7 0.2 - - - -
109D TYR* 4.2 6.4 - - - +
112D GLY* 3.4 32.5 - - - +
113D VAL* 3.4 15.3 - - + +
116D TYR* 4.1 10.5 - - - -
146D GLU* 5.3 2.0 - - + -
169D VAL 3.1 12.4 + - - +
170D CYS 3.5 9.6 - - - +
171D GLN 3.2 0.4 - - - -
172D GLN* 1.3 76.6 - - - +
174D GLU* 1.3 58.4 + - - +
177D PHE* 2.8 34.4 + - - +
178D ALA* 3.5 0.7 + - - +
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Residues in contact with GLU 174 (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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109D TYR* 4.2 6.0 + - - -
142D SER* 3.5 20.8 + - - -
146D GLU* 2.6 31.9 + - - +
170D CYS 3.2 4.7 + - - +
171D GLN 3.2 8.8 + - - +
173D ALA* 1.3 78.2 - - - +
175D HIS* 1.3 62.9 + - - +
178D ALA* 3.2 17.3 - - + +
179D GLY 3.2 7.8 + - - -
180D MET* 3.1 53.5 + - + +
182D CYS* 3.7 18.8 - - - +
187D GLN* 3.2 15.8 + - - -
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Residues in contact with HIS 175 (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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171D GLN* 3.0 35.4 + - + +
172D GLN* 3.5 21.5 + - - +
173D ALA 3.2 0.2 - - - -
174D GLU* 1.3 76.8 - - - +
176D SER* 1.3 60.3 + - - +
179D GLY* 3.2 24.4 + - - -
180D MET 3.2 22.6 + - - -
181D PRO* 3.4 14.9 - - + +
182D CYS* 2.8 33.9 + - - -
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Residues in contact with SER 176 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101D PRO* 4.2 11.3 - - - +
116D TYR* 3.3 26.7 + - - -
172D GLN* 2.9 34.9 + - - -
175D HIS* 1.3 77.5 - - - +
177D PHE* 1.3 64.6 + - - +
179D GLY* 4.4 2.0 + - - -
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Residues in contact with PHE 177 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99D LEU* 3.5 24.7 - - + -
100D GLU 3.8 3.1 - - - -
101D PRO* 3.4 49.5 - - + +
108D ASN* 3.3 38.5 + - - +
111D LYS* 4.0 15.0 - - + -
112D GLY* 3.4 26.9 - - - -
115D GLN* 3.9 23.6 - - + -
116D TYR* 3.8 26.5 - + - -
173D ALA 2.8 11.9 + - - +
176D SER* 1.3 81.7 - - - +
178D ALA* 1.3 60.5 + - - +
179D GLY 3.6 0.9 - - - -
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Residues in contact with ALA 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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108D ASN* 4.9 2.9 - - + +
109D TYR* 3.5 46.5 + - + +
173D ALA 3.5 1.2 + - - +
174D GLU* 3.2 22.3 + - + +
177D PHE* 1.3 77.9 - - + +
179D GLY* 1.3 64.4 + - - +
180D MET* 3.3 5.0 + - + +
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Residues in contact with GLY 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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174D GLU 3.2 3.2 + - - -
175D HIS 3.2 15.4 + - - -
176D SER 4.4 1.8 + - - -
177D PHE 3.6 1.6 - - - -
178D ALA* 1.3 78.1 - - - +
180D MET* 1.3 58.7 + - - +
181D PRO* 3.8 8.5 - - - +
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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