Contacts of the helix formed by residues 178 - 182 (chain K) in PDB entry 2AAZ
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 178 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125K PRO* 3.8 19.4 - - + +
129K PHE* 4.2 7.3 - - - -
130K GLN* 2.9 31.5 + - - +
135K GLY* 5.4 1.0 + - - -
136K ALA 4.5 7.6 - - - +
138K TYR* 5.3 1.5 - - - +
175K ASN* 3.0 19.3 + - - +
177K LYS* 1.3 88.5 - - - +
179K LEU* 1.3 66.5 + - - +
180K PRO* 3.3 2.5 - - - -
181K LEU* 2.8 34.2 + - - +
182K MET* 3.4 11.5 + - + +
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Residues in contact with LEU 179 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174K TRP* 3.8 35.7 - - + -
175K ASN 3.0 24.8 + - - +
176K PRO* 3.7 18.2 - - + +
178K ASP* 1.3 75.6 - - - +
180K PRO* 1.3 66.1 - - + +
182K MET* 2.8 45.8 + - + +
185K PRO* 4.2 17.0 - - + +
186K PRO* 4.0 18.8 - - + -
168L ARG* 6.0 3.1 - - + +
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Residues in contact with PRO 180 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K VAL 5.4 1.7 - - - +
115K LEU* 3.8 15.2 - - - +
176K PRO 4.0 5.6 - - - +
177K LYS 3.5 15.9 - - - +
178K ASP 3.4 2.0 - - - -
179K LEU* 1.3 94.5 - - + +
181K LEU* 1.3 65.6 + - + +
182K MET 3.2 5.3 + - - +
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Residues in contact with LEU 181 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115K LEU* 4.4 7.0 - - + -
117K HIS* 5.9 4.5 - - + +
118K ARG* 2.7 43.2 + - - +
125K PRO* 3.6 26.2 - - + +
138K TYR* 4.7 19.7 - - + +
177K LYS 5.2 1.1 - - - +
178K ASP* 2.8 31.7 + - - +
180K PRO* 1.3 80.3 - - + +
182K MET* 1.3 55.2 + - - +
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Residues in contact with MET 182 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K VAL* 5.3 1.2 - - - +
115K LEU* 4.0 6.1 - - - +
123K LEU 3.6 4.5 - - - -
125K PRO* 3.7 30.7 - - + +
126K VAL* 3.8 13.0 - - + -
130K GLN* 4.3 4.5 - - - +
173K ALA 4.5 4.7 - - - +
175K ASN* 3.9 8.3 - - + +
178K ASP* 3.6 14.6 - - + +
179K LEU* 2.8 52.0 + - + +
180K PRO 4.2 2.6 - - - +
181K LEU* 1.3 80.9 - - - +
183K ALA* 1.3 66.1 + - - +
184K LEU* 3.2 17.6 + - - +
185K PRO* 4.3 2.6 - - - +
186K PRO* 3.6 31.2 - - + -
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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