Contacts of the helix formed by residues 162 - 167 (chain A) in PDB entry 1Z9N
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 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A ASN* 4.9 0.5 + - - +
158A SER 3.4 7.4 - - - +
159A ASP 3.1 16.4 - - - +
160A HIS 3.3 0.5 - - - -
161A PRO* 1.3 83.8 - - + +
163A PRO* 1.3 74.6 - - + +
165A GLY* 3.6 3.2 + - - -
166A GLY* 3.7 25.1 + - - -
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Residues in contact with PRO 163 (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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159A ASP* 3.4 16.1 - - + +
161A PRO 4.5 2.9 - - - +
162A ALA* 1.3 89.7 - - + +
164A LEU* 1.3 78.4 + - + +
166A GLY* 3.1 9.7 + - - -
167A GLY 4.4 0.9 + - - -
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Residues in contact with LEU 164 (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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70A HIS* 4.3 7.4 + - - -
94A GLY* 6.2 2.0 - - - -
95A HIS* 3.7 36.6 - - + +
104A HIS* 3.5 15.3 + - - -
113A HIS* 3.6 31.9 - - + -
151A HIS* 6.4 1.1 - - + -
155A ASP* 4.8 0.3 - - - -
159A ASP* 2.8 25.3 + - - +
162A ALA 3.5 0.2 + - - -
163A PRO* 1.3 80.6 - - + +
165A GLY* 1.3 60.4 + - - +
166A GLY 3.2 1.4 + - - -
167A GLY* 3.5 9.0 + - - +
170A ARG* 5.8 5.8 - - - +
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Residues in contact with GLY 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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104A HIS* 3.4 1.7 - - - -
154A GLY 3.5 1.2 - - - +
155A ASP* 3.2 28.6 + - - -
156A ASN* 3.1 30.7 + - - +
158A SER 2.8 22.5 + - - -
162A ALA* 4.2 2.0 - - - -
163A PRO 3.1 0.4 + - - -
164A LEU* 1.3 75.8 - - - +
166A GLY* 1.3 59.5 + - - +
167A GLY 3.3 0.7 - - - -
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Residues in contact with GLY 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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153A GLY* 3.7 12.6 - - - -
154A GLY 3.6 4.9 + - - -
162A ALA* 3.7 26.0 + - - -
163A PRO 3.1 9.2 + - - -
165A GLY* 1.3 78.2 - - - +
167A GLY* 1.3 65.5 + - - +
168A GLY* 3.3 3.5 + - - -
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Residues in contact with GLY 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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68A GLY* 5.1 0.9 - - - -
70A HIS* 5.1 0.7 - - - -
151A HIS* 3.3 26.6 - - - +
153A GLY* 2.8 25.8 + - - -
154A GLY 3.3 14.5 + - - -
163A PRO 4.4 0.8 + - - -
164A LEU* 3.5 11.1 + - - +
165A GLY 3.3 3.6 - - - -
166A GLY* 1.3 78.0 - - - +
168A GLY* 1.3 67.1 + - - +
169A PRO* 3.5 1.0 - - - +
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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