Contacts of the helix formed by residues 174 - 190 (chain D) in PDB entry 3GHG
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 ASP 174 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172D GLU 4.3 0.6 + - - -
173D VAL* 1.3 75.8 - - - +
175D LEU* 1.3 65.1 + - - +
176D LYS* 3.4 20.0 - - - +
177D ASP* 3.8 21.4 + - + +
178D TYR* 3.7 16.3 - - - -
178E LYS* 4.5 11.7 + - - -
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Residues in contact with LEU 175 (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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148D LYS* 4.5 13.2 - - - +
173D VAL* 3.3 19.5 + - + +
174D ASP* 1.3 72.9 - - - +
176D LYS* 1.3 73.7 + - + +
177D ASP 3.1 0.2 - - - -
178D TYR* 2.8 23.4 + - - +
179D GLU* 3.0 20.9 + - + +
426E MET* 3.8 29.4 - - + -
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Residues in contact with LYS 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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174D ASP* 3.9 12.8 - - - +
175D LEU* 1.3 85.8 - - + +
177D ASP* 1.3 62.8 + - - +
179D GLU* 3.3 5.4 + - + +
180D ASP* 3.0 45.9 + - - +
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Residues in contact with ASP 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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174D ASP* 3.8 22.4 + - + +
175D LEU 3.1 0.6 - - - -
176D LYS* 1.3 79.0 - - - +
178D TYR* 1.3 62.8 + - - +
180D ASP* 3.0 11.3 + - - +
181D GLN* 3.0 38.0 + - - +
174E ASN* 3.5 15.7 + - - +
178E LYS* 3.0 25.0 + - - +
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Residues in contact with TYR 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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144D LEU* 3.8 26.7 - - + +
147D MET* 3.3 36.2 + - + +
148D LYS* 3.5 52.3 - - + -
151D GLU* 3.2 36.8 + - + -
173D VAL* 5.7 0.4 - - + -
174D ASP 3.7 17.5 - - - -
175D LEU* 2.8 17.3 + - - +
177D ASP* 1.3 75.3 - - - +
179D GLU* 1.3 52.4 + - - +
181D GLN* 4.1 4.2 - - - +
182D GLN* 2.8 39.5 + - - +
174E ASN* 6.1 0.2 - - - -
175E LEU* 4.8 8.6 - - + +
178E LYS* 4.0 21.7 - - + +
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Residues in contact with GLU 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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148D LYS* 3.6 18.3 + - - +
175D LEU* 3.0 20.0 + - + +
176D LYS* 3.8 8.5 - - + +
178D TYR* 1.3 75.4 - - - +
180D ASP* 1.3 61.8 + - - +
182D GLN* 3.7 15.3 + - - +
183D LYS* 3.1 27.2 + - - +
423E THR* 5.4 1.2 + - - +
425E ASP* 3.5 25.6 - - - +
426E MET* 5.8 3.4 - - + +
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Residues in contact with ASP 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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176D LYS* 3.0 43.1 - - - +
177D ASP* 3.0 9.9 + - - +
179D GLU* 1.3 81.9 - - - +
181D GLN* 1.3 62.6 + - + +
182D GLN 3.3 0.2 - - - -
183D LYS* 3.3 16.5 + - - +
184D GLN* 3.0 27.3 + - - +
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Residues in contact with GLN 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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144D LEU* 5.5 2.9 - - + -
177D ASP* 3.0 34.8 + - - +
178D TYR* 4.1 3.8 - - - +
180D ASP* 1.3 76.5 - - + +
182D GLN* 1.3 60.6 + - - +
184D GLN* 4.3 13.9 + - - +
185D LEU* 3.0 29.3 + - - +
167E VAL* 5.0 9.1 - - - +
170E SER* 4.2 13.8 + - - +
171E ILE* 3.2 47.5 + - + +
174E ASN* 4.5 12.9 - - - +
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Residues in contact with GLN 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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144D LEU* 3.5 29.1 - - + +
145D VAL* 4.0 22.4 - - - +
148D LYS* 3.7 21.3 - - - +
178D TYR* 2.8 23.3 + - - +
179D GLU* 3.7 28.5 + - - -
181D GLN* 1.3 71.4 - - - +
183D LYS* 1.3 64.1 + - - +
185D LEU* 3.3 4.8 + - + +
186D GLU* 3.0 28.6 + - + +
425E ASP* 4.0 9.4 + - - -
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Residues in contact with LYS 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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179D GLU 3.1 20.5 + - - +
180D ASP* 3.3 14.4 + - - +
182D GLN* 1.3 79.9 - - - +
184D GLN* 1.3 88.1 + - - +
186D GLU* 3.3 7.2 + - - +
187D GLN* 2.9 37.0 + - + +
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Residues in contact with GLN 184 (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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180D ASP 3.0 13.8 + - - +
181D GLN* 4.3 12.7 + - - +
183D LYS* 1.3 88.0 - - - +
185D LEU* 1.3 66.6 + - - +
187D GLN* 3.4 26.5 + - - +
188D VAL* 3.4 20.7 - - + +
167E VAL* 4.2 26.8 - - + +
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Residues in contact with LEU 185 (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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137D GLN* 5.7 1.1 - - + -
140D VAL* 4.2 16.6 - - + -
141D ARG* 4.5 11.9 - - + -
144D LEU* 3.9 24.0 - - + -
181D GLN 3.0 20.8 + - - +
182D GLN* 3.3 6.3 + - + +
184D GLN* 1.3 77.8 - - - +
186D GLU* 1.3 74.1 + - - +
188D VAL* 3.5 1.7 + - - +
189D ILE* 3.2 53.8 + - + +
167E VAL* 5.5 8.2 - - + +
168E LEU* 6.3 6.7 - - + -
171E ILE* 4.2 12.5 - - + +
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Residues in contact with GLU 186 (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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141D ARG* 2.5 54.2 + - - +
182D GLN* 3.0 18.8 + - + +
183D LYS* 3.8 5.4 - - - +
185D LEU* 1.3 87.1 - - - +
187D GLN* 1.3 65.4 + - - +
188D VAL 3.1 3.5 + - - -
189D ILE* 3.6 17.8 + - - +
190D ALA 4.5 4.3 + - - +
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Residues in contact with GLN 187 (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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183D LYS* 2.9 25.8 + - + +
184D GLN* 3.5 33.1 + - - +
185D LEU 3.3 0.4 - - - -
186D GLU* 1.3 77.4 - - - +
188D VAL* 1.3 62.1 + - + +
190D ALA 4.6 2.8 - - - +
191D LYS* 3.9 17.5 - - - +
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Residues in contact with VAL 188 (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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137D GLN* 4.7 3.5 - - - +
184D GLN* 3.4 20.6 - - + +
185D LEU* 3.5 4.5 + - - +
186D GLU 3.1 0.6 - - - -
187D GLN* 1.3 91.2 - - + +
189D ILE* 1.3 65.0 + - - +
190D ALA 3.4 4.0 - - - -
191D LYS* 4.2 17.4 + - + +
193D LEU* 5.5 1.0 - - - +
163E THR* 5.1 15.7 - - + -
167E VAL* 5.6 10.3 - - + -
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Residues in contact with ILE 189 (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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137D GLN* 2.7 66.9 + - + +
138D LYS* 4.3 9.4 - - - +
141D ARG* 4.1 27.1 - - + +
185D LEU* 3.2 56.5 + - + +
186D GLU* 3.6 16.2 + - - +
188D VAL* 1.3 78.3 - - - +
190D ALA* 1.3 63.1 - - + +
193D LEU* 3.6 12.8 - - - +
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Residues in contact with ALA 190 (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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141D ARG* 6.1 1.1 - - - +
186D GLU 4.5 4.4 + - - +
187D GLN 4.6 4.2 - - - +
188D VAL 4.4 1.1 - - - -
189D ILE* 1.3 83.0 - - + +
191D LYS* 1.3 65.2 + - - +
193D LEU* 4.3 15.3 - - + -
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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