Contacts of the helix formed by residues 164 - 176 (chain C) in PDB entry 1A6Z
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 164 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A HIS* 5.4 4.7 + - - -
159C ALA 3.5 0.2 + - - -
160C TYR* 3.2 40.7 + - + +
163C ARG* 1.3 117.8 + - - +
165C CYS* 1.3 64.5 + - - +
167C ALA* 3.3 6.5 + - - +
168C GLN* 3.0 22.6 + - - +
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Residues in contact with CYS 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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8C LEU* 3.5 23.0 - - - +
10C TYR* 5.7 0.2 - - - -
101C GLY* 3.8 8.3 - - - -
102C CYS* 2.1 53.0 - - - -
160C TYR* 2.8 45.5 + - + +
161C LEU* 3.8 5.4 - - - +
164C ASP* 1.3 72.9 - - - +
166C PRO* 1.3 67.6 - - + +
168C GLN* 3.0 8.0 + - - +
169C LEU 2.9 17.8 + - - -
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Residues in contact with PRO 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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102C CYS* 4.0 7.2 - - - -
104C MET* 3.7 27.0 - - + +
110C THR* 3.6 27.8 - - + +
161C LEU 3.4 8.7 - - - +
162C GLU 3.4 18.6 - - - +
163C ARG* 3.0 19.3 - - - +
165C CYS* 1.3 90.9 - - + +
167C ALA* 1.3 54.9 + - - +
169C LEU* 3.1 7.5 + - + +
170C GLN* 2.9 34.3 + - - +
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Residues in contact with ALA 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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163C ARG* 3.2 19.9 + - + +
164C ASP* 3.6 7.0 - - - +
166C PRO* 1.3 76.8 - - - +
168C GLN* 1.3 62.7 + - - +
170C GLN* 3.5 8.4 + - - +
171C GLN* 3.1 39.3 + - - +
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Residues in contact with GLN 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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8C LEU* 3.7 8.6 - - + +
10C TYR* 2.8 30.5 + - - -
61C MET* 4.3 13.8 - - + -
64C GLN* 5.2 7.9 - - + +
65C LEU* 3.0 31.3 - - - +
68C SER* 5.0 9.3 + - - -
72C TRP* 4.8 2.8 - - - -
160C TYR* 3.7 20.8 + - - -
164C ASP 3.0 11.7 + - - +
165C CYS 3.0 8.4 + - - +
167C ALA* 1.3 75.0 - - - +
169C LEU* 1.3 64.9 + - - +
171C GLN* 3.6 10.8 + - - +
172C LEU* 3.1 25.9 + - + +
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Residues in contact with LEU 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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6C HIS* 3.7 31.2 - - + +
7C SER* 3.5 27.4 - - - +
8C LEU* 3.7 18.4 - - + +
31C VAL* 4.0 11.7 - - + -
102C CYS* 4.7 6.7 - - - +
104C MET* 3.8 25.4 - - + +
165C CYS 2.9 12.5 + - - +
166C PRO* 3.1 10.5 + - + +
168C GLN* 1.3 75.1 - - - +
170C GLN* 1.3 55.9 + - - +
172C LEU* 2.9 6.0 + - + +
173C LEU* 2.7 57.4 + - + +
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Residues in contact with GLN 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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104C MET* 3.5 33.8 - - + +
108C ASN* 3.5 19.2 + - - +
166C PRO 2.9 22.2 + - - +
167C ALA* 3.7 7.9 - - - +
169C LEU* 1.3 76.2 - - - +
171C GLN* 1.3 63.4 + - + +
173C LEU* 3.1 22.1 + - - +
174C GLU* 3.1 22.2 + - - +
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Residues in contact with GLN 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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61C MET* 2.9 33.0 - - + +
64C GLN* 3.9 7.1 + - - -
167C ALA* 3.1 28.5 + - - +
168C GLN* 3.8 9.4 - - - +
170C GLN* 1.3 79.4 - - + +
172C LEU* 1.3 52.6 + - - +
174C GLU* 3.1 11.2 - - - +
175C LEU* 2.8 35.9 - - + +
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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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8C LEU* 4.1 13.7 - - + -
31C VAL* 4.6 14.4 - - + -
36C PHE* 3.5 48.7 - - + -
52C TRP* 4.1 10.0 + - - +
53C VAL* 5.0 6.7 - - + -
61C MET* 4.0 22.0 - - + -
65C LEU* 4.8 1.6 - - + -
168C GLN* 3.1 26.0 + - + +
169C LEU* 2.9 7.2 + - - +
171C GLN* 1.3 73.4 - - - +
173C LEU* 1.3 63.6 + - - +
174C GLU 2.8 6.3 + - - -
175C LEU* 2.9 29.2 - - + +
176C GLY* 3.0 12.0 + - - -
180C LEU* 4.9 2.4 - - - +
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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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6C HIS* 3.5 53.2 - - + +
31C VAL* 4.0 9.2 - - + -
32C ASP* 3.8 2.9 - - - +
104C MET* 6.1 0.4 - - - -
169C LEU* 2.7 31.4 + - + +
170C GLN* 3.1 23.5 + - - +
172C LEU* 1.3 72.2 - - - +
174C GLU* 1.3 62.1 + - - +
176C GLY* 3.8 1.2 - - - -
177C ARG* 3.3 18.4 + - - +
180C LEU* 3.7 26.5 - - + -
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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 GLN 3.1 10.9 + - - +
171C GLN* 3.1 17.6 - - - +
172C LEU 2.8 0.8 - - - -
173C LEU* 1.3 74.0 - - - +
175C LEU* 1.3 63.2 + - + +
176C GLY 2.6 14.7 + - - -
177C ARG* 3.0 20.4 + - - +
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Residues in contact with LEU 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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52C TRP* 3.0 43.9 - - + +
53C VAL* 5.5 1.8 - - + -
58C SER* 5.0 18.8 - - - +
60C GLN* 6.1 0.7 - - - +
61C MET* 5.6 10.5 - - + -
171C GLN* 2.8 26.0 - - + +
172C LEU* 2.9 49.1 - - + +
174C GLU* 1.3 77.9 - - + +
176C GLY* 1.3 57.0 + - - +
177C ARG 4.7 2.9 - - - +
179C VAL* 5.3 0.3 - - - +
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Residues in contact with GLY 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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52C TRP* 3.6 18.8 - - - -
172C LEU 3.0 14.7 + - - -
173C LEU 4.0 1.8 - - - -
174C GLU 2.6 8.9 + - - -
175C LEU* 1.3 76.2 - - - +
177C ARG* 1.3 65.7 + - - +
179C VAL* 3.0 6.8 + - - +
180C LEU* 2.9 34.2 + - - -
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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