Contacts of the helix formed by residues 164 - 172 (chain A) in PDB entry 3ASZ
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 GLN 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A LEU 5.4 1.2 - - - +
56A ARG* 2.9 28.7 + - - +
57A VAL 3.4 10.6 - - - +
58A ASN* 3.5 42.9 - - - +
59A TYR 4.4 1.2 + - - -
60A ASP* 4.7 2.2 - - - +
160A GLN* 2.8 38.2 + - + +
162A LEU 3.5 1.0 - - - -
163A GLU* 1.3 84.3 - - + +
165A VAL* 1.3 67.1 + - - +
166A LYS 3.4 1.6 - - - -
167A PRO* 3.2 4.0 - - - +
168A MET* 3.0 31.0 + - - +
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Residues in contact with VAL 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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15A THR* 3.8 27.6 - - + -
60A ASP* 3.5 33.4 + - - +
138A ARG* 5.7 0.7 - - - +
142A ARG* 3.7 24.5 - - - +
160A GLN* 3.1 18.2 + - + +
161A TYR* 3.8 28.9 - - + +
164A GLN* 1.3 74.1 - - - +
166A LYS* 1.3 59.0 + - - +
168A MET* 3.7 0.9 - - - +
169A HIS* 2.8 35.3 + - + +
212A C5P 3.8 0.7 - - - +
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Residues in contact with LYS 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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135A ALA* 6.4 2.0 - - + -
161A TYR* 2.8 53.2 + - + +
162A LEU* 4.7 15.9 - - + +
165A VAL* 1.3 73.8 - - - +
167A PRO* 1.3 70.4 - - + +
169A HIS* 3.1 7.4 + - - +
170A LEU* 3.1 43.3 + - + +
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Residues in contact with PRO 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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161A TYR 3.7 0.2 - - - +
162A LEU 3.5 22.2 - - - +
163A GLU 3.9 13.2 - - - +
164A GLN 3.2 15.0 - - - +
166A LYS* 1.3 98.0 - - + +
168A MET* 1.3 69.5 + - + +
170A LEU* 3.3 7.9 + - + +
171A HIS* 2.9 29.8 + - - +
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Residues in contact with MET 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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58A ASN* 3.5 35.0 - - - +
60A ASP* 3.4 26.0 - - + +
61A HIS* 3.9 14.8 - - - +
164A GLN* 3.0 21.6 + - - +
167A PRO* 1.3 87.2 - - + +
169A HIS* 1.3 61.0 + - - +
171A HIS* 4.6 6.7 - - + -
172A PHE* 2.8 58.8 + - + +
173A VAL* 3.4 6.9 + - - +
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Residues in contact with HIS 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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14A GLY* 3.5 29.3 - - - -
15A THR* 4.8 1.0 + - - +
60A ASP* 5.4 0.2 - - - +
130A PHE* 4.9 1.6 - + - -
138A ARG* 3.3 34.6 + - - +
165A VAL* 2.8 24.3 + - + +
166A LYS* 3.1 7.6 + - - +
168A MET* 1.3 77.5 - - - +
170A LEU* 1.3 68.6 + - + +
173A VAL* 3.1 33.4 + - + +
174A GLU* 2.7 63.1 + - + +
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Residues in contact with LEU 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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166A LYS* 3.1 45.6 + - + +
167A PRO* 3.7 5.8 - - + +
169A HIS* 1.3 90.2 - - + +
171A HIS* 1.3 59.8 + - - +
174A GLU* 4.3 11.9 - - + +
175A PRO* 3.4 18.5 - - - +
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Residues in contact with HIS 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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167A PRO 2.9 18.2 + - - +
168A MET* 4.5 5.8 - - + -
170A LEU* 1.3 78.3 - - - +
172A PHE* 1.3 98.2 + + + +
175A PRO* 3.5 14.4 - - - +
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Residues in contact with PHE 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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60A ASP 4.8 1.8 - - - +
61A HIS* 3.7 26.5 - + - -
62A PRO* 3.7 17.9 - - + -
114A LEU* 3.8 19.6 - - + +
117A TYR* 3.6 41.2 - + + -
168A MET* 2.8 51.4 + - + +
171A HIS* 1.3 107.6 - + + +
173A VAL* 1.3 62.6 + - - +
175A PRO* 3.7 6.1 - - - +
176A THR* 3.3 21.1 + - - +
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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