Contacts of the helix formed by residues 159 - 176 (chain c) in PDB entry 5GJQ
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 159 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17c LYS* 5.2 2.0 - - - -
19c CYS* 4.7 0.2 - - - -
157c ASN 4.0 1.1 + - - +
158c MET* 1.3 74.6 - - - +
160c PRO* 1.3 76.6 - - + +
161c ASP* 3.6 25.5 + - - +
162c HIS* 2.9 45.9 + - - -
163c LEU* 2.9 11.3 + - - -
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Residues in contact with PRO 160 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17c LYS* 5.9 1.6 - - + -
19c CYS* 4.0 18.6 - - - -
158c MET 4.4 0.2 - - - +
159c ASP* 1.3 85.6 - - + +
161c ASP* 1.3 63.2 + - - +
163c LEU* 3.5 8.0 + - + +
164c PHE* 2.9 29.1 + - - +
189c ILE* 4.7 11.7 - - + +
191c GLU* 3.3 39.0 - - - +
198c ARG* 5.5 0.7 + - - -
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Residues in contact with ASP 161 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206b LYS* 4.3 22.5 - - + +
159c ASP* 3.0 14.8 + - - +
160c PRO* 1.3 80.9 - - - +
162c HIS* 1.3 62.8 + - + +
164c PHE* 3.3 7.7 + - - +
165c GLU* 2.9 33.3 + - + +
198c ARG* 5.1 9.5 + - - -
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Residues in contact with HIS 162 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203b ARG* 3.8 40.5 + - + -
204b CYS 5.0 9.1 + - - -
205b GLU* 5.6 4.6 + - - -
206b LYS* 5.4 10.1 + - + +
155c GLU* 5.0 1.0 + - - -
158c MET* 3.6 22.8 - - + +
159c ASP* 2.9 34.1 + - - +
161c ASP* 1.3 79.4 - - + +
163c LEU* 1.3 63.6 + - - +
165c GLU* 3.4 5.3 + - + +
166c THR* 2.6 35.6 + - - -
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Residues in contact with LEU 163 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14c MET* 3.7 29.6 - - + -
15c LYS 3.5 19.5 - - - +
16c GLY* 3.9 7.0 - - - +
19c CYS* 3.7 17.0 - - - -
20c VAL* 3.8 19.7 - - - -
21c ALA* 3.8 10.1 - - + +
158c MET* 4.1 15.1 - - + +
159c ASP 2.9 12.9 + - - +
160c PRO* 3.6 10.3 - - + +
162c HIS* 1.3 75.8 - - - +
164c PHE* 1.3 64.5 + - - +
166c THR* 3.6 0.5 - - - -
167c ILE* 3.0 26.4 + - - +
189c ILE* 3.5 26.5 - - + -
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Residues in contact with PHE 164 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209b THR* 3.7 23.6 - - - -
211b VAL* 3.6 18.4 - - + -
160c PRO 2.9 18.7 + - - +
161c ASP* 3.4 7.0 - - - +
163c LEU* 1.3 78.7 - - - +
165c GLU* 1.3 78.3 + - + +
167c ILE* 3.4 5.2 - - - +
168c SER* 2.7 46.7 + - - -
187c VAL* 4.7 12.6 - - + -
189c ILE* 4.7 10.1 - - + -
198c ARG* 3.2 61.0 - - + +
200c LEU* 4.0 9.6 - - + -
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Residues in contact with GLU 165 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204b CYS* 4.0 18.8 - - + +
205b GLU 4.1 0.9 - - - +
206b LYS* 4.0 16.6 - - + -
207b GLY* 3.0 21.2 + - - -
208b THR* 2.6 31.8 - - + +
209b THR* 2.1 41.5 + - - +
161c ASP 2.9 20.6 + - - +
162c HIS* 4.0 4.5 - - + +
164c PHE* 1.3 87.1 - - + +
166c THR* 1.3 58.3 + - - +
168c SER* 3.8 0.3 - - - -
169c GLN* 3.0 36.0 + - - +
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Residues in contact with THR 166 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203b ARG* 5.9 1.7 - - - +
14c MET* 3.7 20.9 - - + -
150c CYS* 6.1 0.4 - - - -
153c LEU* 3.8 42.8 + - + +
154c TRP* 4.1 7.4 - - - -
158c MET* 3.1 19.9 - - - +
162c HIS 2.6 21.4 + - - -
163c LEU 3.6 4.0 - - - -
165c GLU* 1.3 79.6 - - - +
167c ILE* 1.3 63.6 + - - +
169c GLN* 3.9 1.6 - - - +
170c ALA* 3.0 25.6 + - + +
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Residues in contact with ILE 167 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12c MET* 3.7 21.3 - - - +
14c MET* 3.7 23.8 - - + -
21c ALA* 3.6 39.7 - - + +
22c ILE* 3.8 4.0 - - - +
23c ALA* 4.0 22.0 - - + +
163c LEU 3.0 21.4 + - - +
164c PHE* 3.4 9.4 - - - +
166c THR* 1.3 76.6 - - - +
168c SER* 1.3 61.1 + - - +
170c ALA* 3.8 1.0 - - - +
171c MET* 2.9 29.9 + - - +
187c VAL* 3.6 21.8 - - + -
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Residues in contact with SER 168 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209b THR* 3.6 21.8 - - - -
164c PHE* 2.7 43.5 + - - -
167c ILE* 1.3 75.9 - - - +
169c GLN* 1.3 60.2 + - - +
171c MET* 3.4 1.8 + - - +
172c LEU* 2.9 36.8 + - - +
187c VAL* 4.0 5.8 - - - +
200c LEU* 3.6 24.6 - - - +
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Residues in contact with GLN 169 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204b CYS* 4.9 10.1 - - + -
208b THR* 4.4 14.1 + - + -
209b THR* 4.1 17.0 + - - +
149c MET* 4.4 0.4 - - - -
153c LEU* 3.9 17.9 - - + -
165c GLU 3.0 22.0 + - - +
166c THR* 5.0 0.2 - - - -
168c SER* 1.3 73.8 - - - +
170c ALA* 1.3 60.7 + - - +
172c LEU* 4.2 10.3 - - - +
173c ASN* 2.5 45.5 + - - +
151t ASN* 3.0 28.8 + - - +
156t LYS 3.6 3.5 - - - +
157t ASN* 2.6 38.4 + - - +
158t MET* 3.9 4.2 - - - +
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Residues in contact with ALA 170 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12c MET* 3.8 17.0 - - + -
14c MET* 4.8 1.1 - - + -
149c MET* 3.7 30.4 - - + +
150c CYS* 4.0 12.3 - - - +
153c LEU* 4.2 5.5 - - + +
166c THR 3.0 17.9 + - - +
167c ILE* 3.8 4.0 - - - +
169c GLN* 1.3 76.8 - - - +
171c MET* 1.3 59.6 + - - +
174c ALA* 2.9 33.6 + - - +
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Residues in contact with MET 171 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10c ALA* 4.2 6.3 - - + -
12c MET* 3.5 37.0 - - + -
23c ALA* 3.6 22.2 - - + +
24c ALA* 3.9 9.0 - - - -
25c ASP 3.9 24.9 - - - +
146c MET* 4.0 11.4 - - - +
167c ILE 2.9 21.1 + - - +
168c SER* 3.9 3.6 - - - +
170c ALA* 1.3 76.7 - - - +
172c LEU* 1.3 63.4 + - - +
174c ALA* 4.8 0.4 - - - -
175c VAL* 2.9 51.3 + - + +
185c VAL* 4.0 21.3 - - + -
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Residues in contact with LEU 172 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209b THR* 4.1 16.4 - - + -
168c SER 2.9 24.4 + - - +
169c GLN* 4.0 13.5 - - - +
171c MET* 1.3 74.1 - - - +
173c ASN* 1.3 57.3 + - - +
175c VAL* 4.7 1.1 - - - -
176c ASP* 2.9 43.5 + - - +
185c VAL* 3.7 17.0 - - + -
200c LEU* 3.8 20.2 - - + -
201c LYS 4.1 15.3 - - - +
202c ALA* 3.6 31.4 - - + -
157t ASN* 4.0 21.3 - - + +
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Residues in contact with ASN 173 (chain c).
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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149c MET* 3.6 25.3 - - + +
169c GLN* 2.5 52.9 + - - +
172c LEU* 1.3 72.8 - - - +
174c ALA* 1.3 62.7 + - - +
176c ASP* 3.7 8.0 + - - +
177c ARG* 3.8 17.3 + - - +
147t PRO* 4.0 11.4 - - - +
150t ASP* 4.8 4.2 - - + +
151t ASN* 3.6 22.1 + - - +
156t LYS* 3.6 15.6 - - - +
157t ASN* 3.2 19.7 + - - +
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Residues in contact with ALA 174 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142c CYS* 4.6 2.9 - - - +
145c GLN* 3.5 34.6 - - + +
146c MET* 3.4 36.1 - - + +
149c MET* 4.1 3.7 - - + +
170c ALA 2.9 19.9 + - - +
171c MET* 4.0 2.0 - - - +
173c ASN* 1.3 72.2 - - - +
175c VAL* 1.3 66.3 - - + +
177c ARG 3.2 10.2 + - - -
178c ASP* 3.6 8.5 + - - +
147t PRO* 4.8 0.7 - - - -
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Residues in contact with VAL 175 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10c ALA* 4.1 9.6 - - + -
25c ASP* 4.6 2.7 - - + -
142c CYS* 4.1 4.0 - - - -
171c MET* 2.9 40.6 + - + +
172c LEU* 4.2 0.7 - - + +
174c ALA* 1.3 79.2 - - + +
176c ASP* 1.3 70.2 + - - +
177c ARG 3.1 0.2 - - - -
178c ASP* 2.9 32.5 + - - +
181c SER* 3.5 24.5 - - - +
182c GLY* 3.5 28.5 - - - +
185c VAL* 4.7 10.3 - - + -
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Residues in contact with ASP 176 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172c LEU* 2.9 32.2 + - - +
173c ASN* 3.7 5.1 + - - +
174c ALA 3.3 0.6 - - - -
175c VAL* 1.3 87.5 - - - +
177c ARG* 1.3 64.2 + - + +
178c ASP 3.4 1.3 - - - -
202c ALA* 5.5 1.2 - - - +
203c ARG* 3.3 38.9 + - - +
19s ARG* 5.3 0.2 + - - -
26s ILE* 3.8 8.0 - - - +
29s GLN* 3.6 22.1 + - - +
157t ASN* 3.2 24.6 + - - +
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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