Contacts of the helix formed by residues 169 - 174 (chain I) in PDB entry 2ZHX
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 GLY 169 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67I GLN* 6.2 1.3 - - - -
167I LEU 4.4 1.2 - - - +
168I TRP* 1.3 76.6 + - - +
170I ARG* 1.3 66.6 + - - -
171I ASP* 3.6 2.5 - - - -
172I ALA* 3.7 1.0 + - - +
173I SER* 3.5 19.1 + - - -
189I SER 3.0 15.5 + - - +
190I PRO* 4.3 0.7 - - - -
191I HIS* 3.5 23.8 - - - +
23J LEU 6.0 1.1 - - - -
24J MET* 5.1 0.2 - - - -
28J GLU* 3.9 10.1 - - - -
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Residues in contact with ARG 170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169I GLY* 1.3 71.2 - - - -
171I ASP* 1.3 68.2 + - - +
172I ALA 3.0 2.0 - - - -
173I SER* 2.8 31.8 + - - +
174I THR* 3.3 12.8 + - - +
188I GLU* 5.9 0.2 + - - -
23J LEU 5.6 0.4 + - - -
25J LEU* 3.6 30.4 - - + +
27J GLU* 5.0 14.5 - - + +
28J GLU* 3.4 36.7 + - + +
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Residues in contact with ASP 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I VAL* 5.8 0.3 - - - +
66I GLY 5.1 0.7 - - - +
67I GLN* 3.6 39.5 - - - +
128I ARG* 4.2 25.7 + - - +
141I ARG* 4.9 4.4 + - - -
168I TRP 5.9 0.2 - - - +
169I GLY* 5.4 0.4 - - - -
170I ARG* 1.3 74.3 - - - +
172I ALA* 1.3 59.7 + - - +
174I THR* 2.5 32.5 + - - -
175I LEU* 4.1 3.3 - - - +
23J LEU* 3.8 30.1 + - + +
24J MET* 5.9 0.4 - - - +
25J LEU* 4.9 10.9 - - + +
28J GLU* 4.8 1.6 + - - -
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Residues in contact with ALA 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I VAL* 4.1 26.5 - - + +
67I GLN* 5.7 0.2 - - - +
128I ARG* 5.8 0.2 - - - +
167I LEU* 3.4 15.0 - - + +
168I TRP 3.5 34.9 + - - +
169I GLY 3.7 4.1 + - - +
170I ARG 3.0 0.6 - - - -
171I ASP* 1.3 84.1 + - - +
173I SER* 1.3 61.9 + - - +
175I LEU* 3.0 25.4 + - - +
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Residues in contact with SER 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167I LEU* 3.8 9.2 - - - +
169I GLY 3.5 10.8 + - - -
170I ARG* 2.8 35.3 + - - -
172I ALA* 1.3 69.1 - - - +
174I THR* 1.3 50.9 + - - -
175I LEU 2.8 6.1 - - - -
176I LYS* 2.7 33.0 + - - +
177I PRO* 3.9 2.1 - - - +
188I GLU* 3.1 37.7 + - - +
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Residues in contact with THR 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128I ARG* 3.7 8.5 + - - -
170I ARG 3.3 8.8 + - - +
171I ASP* 2.5 27.2 + - - +
173I SER* 1.3 75.3 - - - +
175I LEU* 1.3 67.1 - - - +
176I LYS 3.2 0.2 - - - -
177I PRO* 3.2 20.9 - - - +
178I MET* 4.6 4.9 - - - +
25J LEU* 5.9 6.5 - - + -
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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