Contacts of the helix formed by residues 165 - 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 ASN 165 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163C GLY 3.5 1.0 + - - -
164C LYS* 1.3 87.0 - - - +
166C TYR* 1.3 66.1 + - - +
167C VAL* 3.2 8.2 + - - -
168C ASN* 3.4 19.2 + - + +
169C GLY* 3.2 18.4 + - - -
197C SER* 3.6 32.3 + - - +
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Residues in contact with TYR 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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29C ALA* 4.7 16.8 - - + -
33C PRO* 6.3 0.2 - - - -
161C ALA* 3.6 29.0 - - - +
162C MET* 3.7 12.1 - - - -
163C GLY 3.2 24.7 - - - +
164C LYS 3.1 2.0 + - - -
165C ASN* 1.3 81.2 - - - +
167C VAL* 1.3 81.8 + - + +
169C GLY 3.9 0.8 - - - -
170C LYS* 3.0 48.0 + - - +
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Residues in contact with VAL 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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165C ASN* 4.4 7.9 - - - -
166C TYR* 1.3 106.6 - - + +
168C ASN* 1.3 80.7 + - - +
170C LYS* 3.1 11.7 + - + +
171C THR* 3.0 31.4 + - + +
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Residues in contact with ASN 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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165C ASN* 3.4 18.6 + - + +
167C VAL* 1.3 86.8 - - - +
169C GLY* 1.3 60.6 + - - +
171C THR* 2.6 24.4 + - - +
172C PHE* 3.0 18.0 + - - +
196C GLU* 5.6 9.3 - - + +
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Residues in contact with GLY 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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161C ALA* 4.5 7.4 - - - -
165C ASN 3.2 10.9 + - - -
166C TYR 3.9 3.4 - - - -
168C ASN* 1.3 81.2 - - - +
170C LYS* 1.3 55.0 + - - +
172C PHE* 3.4 4.1 + - - +
173C LEU* 2.9 38.0 + - - +
193C THR* 3.7 19.0 + - - -
196C GLU* 5.9 2.9 - - - +
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Residues in contact with LYS 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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157C TRP* 4.4 15.2 - - + -
160C THR* 2.7 31.1 + - - -
161C ALA* 3.6 11.5 + - - +
166C TYR* 3.0 40.1 + - - +
167C VAL* 3.2 10.1 - - + +
169C GLY* 1.3 77.0 - - - +
171C THR* 1.3 57.8 + - + +
173C LEU* 3.3 13.1 + - + +
174C GLU* 2.9 27.4 + - - +
53D HIS* 4.4 30.3 - - + +
55D LEU* 4.6 7.7 - - + +
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Residues in contact with THR 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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167C VAL 3.0 14.6 + - - +
168C ASN* 2.6 32.4 + - - +
170C LYS* 1.3 73.4 - - + +
172C PHE* 1.3 59.3 + - - -
174C GLU* 2.9 24.3 + - - +
175C LYS* 3.0 14.9 + - - +
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Residues in contact with PHE 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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168C ASN 3.0 13.9 + - - +
169C GLY* 3.5 7.2 - - - +
171C THR* 1.3 81.5 + - - +
173C LEU* 1.3 60.4 + - + +
175C LYS* 3.9 2.9 - - - +
176C ARG* 2.8 48.6 + - + +
189C THR* 4.3 7.2 - - - -
192C LEU* 4.0 19.7 - - + -
193C THR* 3.6 36.8 - - - +
196C GLU* 3.3 41.5 - - + -
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Residues in contact with LEU 173 (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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35C VAL* 5.3 0.9 - - + -
36C GLY 5.0 0.7 - - - +
37C ILE* 4.1 20.6 - - + -
159C ALA* 4.1 9.6 - - + +
160C THR* 3.6 45.3 - - - +
161C ALA* 4.1 6.7 - - + +
169C GLY 2.9 22.4 + - - +
170C LYS* 3.4 11.2 - - - +
171C THR 3.1 0.2 - - - -
172C PHE* 1.3 75.2 - - - +
174C GLU* 1.3 64.7 + - - +
175C LYS 3.3 0.3 + - - -
177C TYR* 3.2 34.3 + - + +
189C THR* 4.5 6.7 - - - +
193C THR* 3.7 32.1 - - + +
55D LEU* 4.5 11.3 - - + +
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Residues in contact with GLU 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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170C LYS* 2.9 12.3 + - - +
171C THR* 2.9 14.4 + - - +
173C LEU* 1.3 76.5 - - - +
175C LYS* 1.3 61.6 + - - +
177C TYR 3.8 7.2 - - - +
178C ASN* 4.0 7.8 + - - -
53D HIS* 3.5 26.9 + - - -
54D LYS* 2.9 29.5 - - - +
55D LEU* 4.8 12.8 - - + +
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Residues in contact with LYS 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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171C THR 3.0 13.2 + - - +
172C PHE* 3.9 4.3 - - - +
174C GLU* 1.3 78.2 - - - +
176C ARG* 1.3 60.1 + - + +
177C TYR 2.8 13.3 + - - +
178C ASN* 4.8 2.3 + - - -
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Residues in contact with ARG 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 PHE* 2.8 43.5 + - + +
175C LYS* 1.3 73.3 - - + +
177C TYR* 1.3 61.7 + - - +
181C LEU* 5.6 0.7 - - - +
189C THR* 3.8 13.0 + - - +
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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