Contacts of the helix formed by residues 164 - 176 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A ALA 3.5 0.2 + - - -
160A TYR* 3.3 40.1 + - + +
163A ARG* 1.3 118.4 + - - +
165A CYS* 1.3 63.5 + - - +
167A ALA* 3.3 6.1 + - - +
168A GLN* 3.0 22.8 + - - +
74C HIS* 5.5 4.3 + - - -
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Residues in contact with CYS 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 3.6 17.7 - - - +
10A TYR* 5.8 0.2 - - - -
101A GLY* 3.8 8.3 - - - -
102A CYS* 2.0 52.0 - - - -
160A TYR* 2.8 46.0 + - + +
161A LEU* 3.8 5.8 - - - +
164A ASP* 1.3 72.2 - - - +
166A PRO* 1.3 68.4 - - + +
168A GLN* 2.9 8.2 + - - +
169A LEU* 2.9 18.4 + - - +
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Residues in contact with PRO 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A CYS* 4.0 7.2 - - - -
104A MET* 3.7 27.3 - - + +
110A THR* 3.6 27.4 - - + +
161A LEU 3.4 9.0 - - - +
162A GLU 3.4 18.2 - - - +
163A ARG 3.0 21.5 - - - +
165A CYS* 1.3 90.5 - - + +
167A ALA* 1.3 56.7 + - - +
169A LEU* 3.1 6.3 + - + +
170A GLN* 2.9 35.1 + - - +
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Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ARG* 3.1 14.8 + - + +
164A ASP* 3.5 10.1 - - - +
166A PRO* 1.3 76.8 - - - +
168A GLN* 1.3 63.9 + - - +
170A GLN* 3.5 8.0 + - - +
171A GLN* 3.1 39.3 + - - +
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Residues in contact with GLN 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 3.8 8.0 - - + +
10A TYR* 2.8 30.2 + - - -
61A MET* 4.3 14.5 - - + -
64A GLN* 5.2 7.3 - - + +
65A LEU* 3.1 32.3 - - - +
68A SER* 5.0 8.6 + - - -
72A TRP* 4.8 2.4 - - - -
160A TYR* 3.7 21.0 + - - -
164A ASP 3.0 11.6 + - - +
165A CYS 2.9 9.0 + - - +
167A ALA* 1.3 74.7 - - - +
169A LEU* 1.3 65.5 + - - +
171A GLN* 3.6 10.5 + - - +
172A LEU* 3.1 26.5 + - + +
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Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A HIS* 3.7 30.5 - - + +
7A SER* 3.5 26.7 - - - +
8A LEU* 3.7 19.7 - - + +
31A VAL* 3.9 11.0 - - + -
102A CYS* 4.7 6.1 - - - +
104A MET* 3.8 25.8 - - + +
165A CYS 2.9 10.9 + - - +
166A PRO* 3.1 10.7 + - + +
168A GLN* 1.3 75.7 - - - +
170A GLN* 1.3 55.1 + - - +
172A LEU* 3.0 6.1 + - + +
173A LEU* 2.7 56.6 + - + +
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Residues in contact with GLN 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A MET* 3.5 28.3 - - + +
108A ASN* 3.5 24.0 + - - +
166A PRO 2.9 22.8 + - - +
167A ALA* 3.7 7.9 - - - +
168A GLN 3.4 0.2 - - - -
169A LEU* 1.3 75.2 - - - +
171A GLN* 1.3 64.3 + - + +
173A LEU* 3.1 21.3 + - - +
174A GLU* 3.1 21.5 + - - +
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Residues in contact with GLN 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A MET* 2.9 34.7 - - + +
64A GLN* 3.8 7.6 + - - +
167A ALA* 3.1 28.8 + - - +
168A GLN* 3.8 8.5 - - - +
169A LEU 3.3 0.2 - - - -
170A GLN* 1.3 80.1 - - + +
172A LEU* 1.3 57.0 + - - +
174A GLU* 3.1 11.2 - - - +
175A LEU* 2.8 31.2 - - + +
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.1 13.2 - - + -
10A TYR* 4.8 0.2 - - - +
31A VAL* 4.6 14.8 - - + -
36A PHE* 3.5 48.5 - - + -
52A TRP* 4.1 10.7 + - - +
53A VAL* 4.9 6.7 - - + -
61A MET* 4.0 21.1 - - + -
65A LEU* 4.8 1.6 - - + -
168A GLN* 3.1 27.0 + - + +
169A LEU* 3.0 7.0 + - - +
171A GLN* 1.3 72.1 - - - +
173A LEU* 1.3 60.4 + - - +
174A GLU 2.8 10.5 + - - -
175A LEU* 2.9 29.6 - - + +
176A GLY* 3.0 11.4 + - - -
180A LEU* 5.0 1.8 - - - +
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A HIS* 3.5 52.3 - - + +
31A VAL* 4.0 9.9 - - + -
32A ASP* 3.8 2.9 - - - +
104A MET* 6.1 0.9 - - - -
169A LEU* 2.7 30.0 + - + +
170A GLN* 3.1 24.2 + - - +
172A LEU* 1.3 71.3 - - - +
174A GLU* 1.3 62.8 + - - +
176A GLY* 3.8 1.5 - - - +
177A ARG* 3.3 17.3 + - - +
180A LEU* 3.7 26.7 - - + -
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Residues in contact with GLU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A GLN 3.1 10.7 + - - +
171A GLN* 3.1 17.3 - - - +
172A LEU 2.8 0.6 - - - -
173A LEU* 1.3 74.8 - - - +
175A LEU* 1.3 63.9 + - + +
176A GLY 2.6 14.2 + - - -
177A ARG* 3.0 19.3 + - - +
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TRP* 3.0 45.2 - - + +
53A VAL* 5.5 1.8 - - + -
58A SER* 5.0 19.3 - - - +
60A GLN* 6.1 0.7 - - - +
61A MET* 5.5 10.8 - - + -
171A GLN* 2.8 22.2 - - + +
172A LEU* 2.9 50.0 - - + +
174A GLU* 1.3 78.3 - - + +
176A GLY* 1.3 57.3 + - - +
177A ARG 3.7 2.6 - - - +
179A VAL* 5.2 0.3 - - - +
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Residues in contact with GLY 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TRP* 3.6 18.4 - - - -
172A LEU 3.0 15.1 + - - -
173A LEU 4.0 2.0 - - - -
174A GLU 2.6 9.5 + - - -
175A LEU* 1.3 74.9 - - - +
177A ARG* 1.3 66.8 + - - -
179A VAL* 3.0 6.2 + - - +
180A LEU* 2.9 34.9 + - - -
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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