Contacts of the helix formed by residues 167 - 179 (chain j) 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 ASN 167 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429I LYS* 6.0 2.1 - - - -
29j GLY 4.6 0.2 + - - -
163j CYS* 4.6 0.5 - - - -
165j GLY 3.5 0.4 + - - -
166j ASN* 1.3 100.8 + - - +
168j SER* 1.3 65.3 + - - +
169j ALA* 3.3 4.0 - - - +
170j ALA* 3.7 11.0 + - + +
171j ALA* 3.5 19.1 + - - +
200j THR* 3.0 38.1 + - - +
202j ASP* 4.9 4.9 - - - +
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Residues in contact with SER 168 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163j CYS* 2.9 39.3 + - - +
164j ILE* 3.4 4.6 + - - +
165j GLY 3.2 22.4 + - - -
166j ASN 3.2 1.2 - - - -
167j ASN* 1.3 79.0 - - - +
169j ALA* 1.3 57.5 + - - +
171j ALA* 3.2 5.0 + - - +
172j VAL* 2.9 35.4 + - - +
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Residues in contact with ALA 169 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387I LYS* 4.5 18.6 - - - +
428I TYR* 4.2 17.2 - - + +
167j ASN* 3.3 1.7 - - - -
168j SER* 1.3 75.6 - - - +
170j ALA* 1.3 66.1 + - - +
172j VAL* 3.1 12.5 + - - +
173j SER* 3.0 22.5 + - - -
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Residues in contact with ALA 170 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428I TYR* 3.7 20.0 - - + +
167j ASN* 3.7 17.0 + - + +
168j SER 3.4 0.4 - - - -
169j ALA* 1.3 77.0 - - - +
171j ALA* 1.3 63.0 + - - +
173j SER* 2.4 26.2 + - - -
174j MET* 2.9 18.9 + - + +
199j LYS* 6.0 4.7 - - + -
200j THR* 4.2 13.0 - - + -
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Residues in contact with ALA 171 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35j LEU* 5.3 0.2 - - + -
163j CYS* 3.5 30.1 - - + -
167j ASN 3.5 2.5 + - - +
168j SER 3.2 9.6 + - - +
169j ALA 3.2 0.2 - - - -
170j ALA* 1.3 78.9 - - - +
172j VAL* 1.3 57.4 + - - +
174j MET* 3.4 2.8 + - - +
175j LEU* 2.9 38.5 + - + +
196j VAL* 3.6 27.3 - - + +
200j THR* 3.8 9.8 - - + +
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Residues in contact with VAL 172 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159j TRP* 6.2 8.1 - - + -
162j THR* 5.3 5.8 - - - +
163j CYS* 5.0 11.2 - - + +
168j SER* 2.9 27.4 + - - +
169j ALA* 3.3 10.8 - - - +
171j ALA* 1.3 76.3 - - - +
173j SER* 1.3 57.5 + - - +
175j LEU* 3.3 10.0 + - - +
176j LYS* 2.9 52.5 + - + +
53k LEU* 4.4 4.2 - - + +
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Residues in contact with SER 173 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424I GLU* 4.0 9.5 + - - -
428I TYR* 3.0 44.4 - - - -
169j ALA 3.0 5.6 + - - -
170j ALA* 2.4 21.8 + - - -
172j VAL* 1.3 75.1 - - - +
174j MET* 1.3 68.8 + - - +
176j LYS* 3.1 13.1 + - - +
177j GLN* 3.0 25.7 + - - +
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Residues in contact with MET 174 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424I GLU* 5.6 3.6 - - - +
170j ALA* 2.9 20.9 + - + +
171j ALA 3.7 4.3 - - - +
173j SER* 1.3 82.0 + - - +
175j LEU* 1.3 58.1 + - - +
177j GLN* 3.2 7.9 + - + +
178j ASP* 2.9 46.1 + - - +
195j LYS* 4.1 20.2 - - - -
196j VAL* 3.9 37.7 - - + -
199j LYS* 3.5 54.7 - - + +
200j THR* 4.7 3.4 - - + -
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Residues in contact with LEU 175 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35j LEU* 5.1 10.8 - - + -
36j GLY 4.8 1.8 - - - +
37j ILE* 5.3 5.8 - - + -
161j ALA* 4.0 15.7 - - + -
162j THR* 3.8 41.1 - - - +
163j CYS* 4.8 2.7 - - + -
171j ALA* 2.9 27.3 + - + +
172j VAL* 3.6 7.4 - - - +
174j MET* 1.3 77.6 - - - +
176j LYS* 1.3 56.2 + - - +
178j ASP 4.5 0.4 - - - +
179j TYR* 2.9 37.3 + - + +
192j LEU* 3.6 34.8 - - + -
196j VAL* 4.1 9.0 - - + -
53k LEU* 4.0 13.7 - - + -
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Residues in contact with LYS 176 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385I MET* 4.9 18.8 + - + +
386I ALA 4.8 12.1 + - - -
172j VAL* 2.9 37.5 + - + +
173j SER* 3.1 13.2 + - - +
175j LEU* 1.3 76.6 - - - +
177j GLN* 1.3 61.7 + - - +
179j TYR* 4.5 3.0 + - - +
50k VAL 5.4 2.0 + - - -
51k ALA* 4.0 26.1 + - - +
52k LYS* 6.1 1.8 - - + -
53k LEU* 3.7 20.0 - - + -
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Residues in contact with GLN 177 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420I LYS* 4.2 26.3 - - - +
424I GLU* 5.7 4.3 - - - +
173j SER 3.0 14.3 + - - +
174j MET* 3.2 14.3 + - + +
176j LYS* 1.3 80.2 - - - +
178j ASP* 1.3 71.5 + - - +
179j TYR 3.6 3.5 + - - +
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Residues in contact with ASP 178 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174j MET* 2.9 26.8 + - - +
175j LEU 4.6 0.2 - - - +
177j GLN* 1.3 80.2 - - - +
179j TYR* 1.3 68.6 + - - +
180j LYS* 3.6 12.0 - - - +
192j LEU* 3.9 24.1 - - + +
195j LYS* 2.6 43.5 + - - +
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Residues in contact with TYR 179 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37j ILE* 4.9 4.5 - - + -
38j LEU* 2.7 35.1 + - - +
39j ALA* 4.6 0.2 - - - -
160j LYS* 2.9 52.4 + - + +
161j ALA* 3.7 15.9 - - + -
175j LEU* 2.9 19.1 + - + +
176j LYS 4.5 2.5 + - - +
177j GLN 3.5 5.0 - - - +
178j ASP* 1.3 83.3 - - - +
180j LYS* 1.3 88.7 + - - +
181j GLU* 4.0 19.9 + - + -
182j GLY 5.5 0.4 - - - -
184j MET* 4.3 7.9 - - + +
192j LEU* 4.4 9.6 - - + +
53k LEU* 3.9 24.0 - - + -
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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