Contacts of the helix formed by residues 168 - 177 (chain X) 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 ALA 168 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35X THR* 3.0 15.6 + - - +
167X LYS* 1.3 75.5 - - + +
169X ARG* 1.3 63.1 + - - +
170X GLN 3.5 1.3 - - - +
171X ALA* 4.3 7.9 - - + +
172X ALA* 3.2 22.6 + - - +
200X VAL* 3.4 42.6 - - + +
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Residues in contact with ARG 169 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X GLU* 3.1 32.8 + - - +
35X THR* 4.8 1.3 - - - -
164X ALA* 3.2 36.4 - - + +
165X ILE* 4.4 3.8 - - + -
166X GLY 3.5 14.0 + - - +
167X LYS 3.0 5.9 + - - +
168X ALA* 1.3 75.3 - - - +
170X GLN* 1.3 79.2 + - - +
172X ALA* 3.2 5.2 + - - +
173X LYS* 2.9 54.5 + - + +
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Residues in contact with GLN 170 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167X LYS 5.0 0.2 + - - -
168X ALA 3.5 0.2 - - - -
169X ARG* 1.3 94.1 - - + +
171X ALA* 1.3 66.2 + - - +
173X LYS* 3.2 34.3 + - - +
174X THR* 3.0 33.7 + - + +
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Residues in contact with ALA 171 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168X ALA* 4.3 10.0 - - + +
170X GLN* 1.3 75.8 - - - +
172X ALA* 1.3 66.3 + - - +
174X THR* 2.4 26.8 + - - -
175X GLU* 3.0 14.5 + - + +
199X ILE* 6.5 0.2 - - + -
200X VAL* 3.8 19.5 - - + -
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Residues in contact with ALA 172 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X THR* 4.8 1.1 - - + -
37X ILE* 4.1 14.4 - - + -
164X ALA* 3.8 17.0 - - + -
168X ALA 3.2 19.9 + - - +
169X ARG 3.2 5.1 + - - +
171X ALA* 1.3 78.6 - - - +
173X LYS* 1.3 57.8 + - - +
175X GLU* 3.2 4.7 + - - +
176X ILE* 2.9 33.8 + - + +
196X ILE* 4.1 12.1 - - + +
200X VAL* 3.6 14.5 - - + +
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Residues in contact with LYS 173 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ASP* 3.3 25.0 + - - +
60B LEU* 3.7 19.2 - - + +
160X TYR* 5.8 8.4 - - + -
163X CYS* 5.5 2.7 - - - -
164X ALA* 4.7 15.9 - - + +
169X ARG* 2.9 45.3 + - + +
170X GLN* 3.2 34.6 + - - +
172X ALA* 1.3 74.2 - - - +
174X THR* 1.3 64.1 + - + +
176X ILE* 3.1 6.1 + - + +
177X GLU* 2.9 32.8 + - - +
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Residues in contact with THR 174 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170X GLN* 3.0 23.3 + - + +
171X ALA* 2.4 32.5 + - - -
173X LYS* 1.3 77.2 - - - +
175X GLU* 1.3 62.2 + - - +
177X GLU* 3.6 18.8 + - - +
178X LYS* 3.6 20.4 - - - +
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Residues in contact with GLU 175 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171X ALA* 3.0 18.7 + - + +
172X ALA 3.2 8.0 + - - +
174X THR* 1.3 77.6 + - - +
176X ILE* 1.3 61.2 + - - +
178X LYS* 3.5 45.2 + - - +
179X LEU* 4.3 3.6 + - - +
195X LYS* 5.1 4.7 + - - -
196X ILE* 3.8 29.7 - - + +
199X ILE* 3.3 47.0 - - + +
200X VAL* 5.5 0.9 - - + -
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Residues in contact with ILE 176 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LEU* 3.5 24.2 - - + +
37X ILE* 4.4 17.9 - - + -
38X GLY 5.1 2.2 - - - +
39X ILE* 5.2 15.5 - - + -
162X GLY* 4.7 11.4 - - - -
163X CYS* 4.1 29.2 - - - +
164X ALA* 4.6 1.6 - - + -
172X ALA 2.9 25.5 + - - +
173X LYS* 3.1 10.1 + - - +
175X GLU* 1.3 74.8 - - - +
177X GLU* 1.3 56.8 + - - +
178X LYS 3.0 4.3 - - - -
179X LEU* 2.9 29.7 + - + +
181X MET* 4.7 6.7 - - + +
196X ILE* 3.5 22.0 - - + -
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Residues in contact with GLU 177 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ASP* 2.7 29.8 - - - +
59B LYS* 4.5 8.7 + - + -
60B LEU* 3.6 22.7 - - + +
173X LYS* 2.9 24.0 + - - +
174X THR* 3.9 12.6 - - - +
175X GLU 3.5 0.6 - - - -
176X ILE* 1.3 73.0 - - - +
178X LYS* 1.3 59.8 + - + +
179X LEU 3.2 7.8 + - - +
180X GLN* 4.6 6.2 + - - -
181X MET* 5.7 0.2 - - - -
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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