Contacts of the helix formed by residues 164 - 168 (chain A) in PDB entry 3C3C
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 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG* 3.3 22.4 + - - +
22A VAL 3.6 22.2 - - - -
23A ASP 3.8 10.1 - - - +
162A ASN* 2.7 15.7 + - - +
163A ASP* 1.3 72.7 - - - +
165A PHE* 1.3 63.7 + - - +
166A GLY 3.4 1.6 - - - -
167A THR* 3.5 4.8 + - - -
168A ALA 3.3 15.4 + - - -
175A MET* 3.7 10.3 - - - +
189A MET* 3.6 10.6 - - - +
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Residues in contact with PHE 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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23A ASP* 4.9 0.6 - - - +
163A ASP 3.2 4.9 + - - -
164A ALA* 1.3 70.9 - - - +
166A GLY* 1.3 60.2 + - - +
167A THR 2.9 10.9 + - - -
168A ALA* 3.0 17.9 + - + +
188A LEU* 4.6 6.4 - - + +
189A MET* 4.0 31.2 - - - -
192A GLU* 3.4 55.9 - - + -
193A LEU* 4.2 21.8 - - + -
196A PHE* 4.5 10.1 - + - -
392A SER* 3.9 2.7 - - - -
393A THR* 3.9 8.5 - - - +
394A GLY* 3.7 22.0 - - - -
397A ALA* 3.4 10.7 - - + +
398A SER* 3.9 18.8 - - - -
401A LEU* 4.5 8.1 - - + -
407A LEU* 4.4 11.0 - - + -
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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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23A ASP* 3.2 22.1 + - - +
38A ARG* 4.1 1.6 + - - -
164A ALA 3.4 0.4 - - - -
165A PHE* 1.3 80.3 - - - +
167A THR* 1.3 53.7 + - - +
168A ALA 3.7 0.2 - - - -
169A HIS* 3.4 10.7 - - - -
188A LEU* 5.7 0.2 - - - +
393A THR* 3.7 26.5 + - - -
394A GLY* 4.2 9.2 - - - +
397A ALA* 3.9 3.6 - - - +
418A 3PG 3.1 22.5 - - - +
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Residues in contact with THR 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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21A ARG* 3.6 21.4 + - - +
23A ASP* 2.6 24.0 + - - -
62A HIS* 3.2 21.0 - - + +
122A ARG* 4.9 2.0 - - - +
164A ALA* 3.5 5.6 + - - -
165A PHE 3.0 1.0 - - - -
166A GLY* 1.3 74.4 - - - +
168A ALA* 1.3 51.7 + - - +
169A HIS* 3.1 11.0 - - - -
170A ARG* 2.8 42.8 + - + +
172A HIS* 5.2 0.9 - - - +
175A MET* 3.7 30.1 - - + +
418A 3PG 3.6 1.6 + - - -
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Residues in contact with ALA 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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164A ALA 3.3 9.1 + - - +
165A PHE* 3.0 23.1 + - + +
166A GLY 3.7 0.2 - - - -
167A THR* 1.3 74.0 - - - +
169A HIS* 1.3 56.6 + - - +
170A ARG 3.2 0.9 - - - -
175A MET* 3.7 12.3 - - - -
189A MET* 4.3 12.1 - - + -
397A ALA* 4.8 0.4 - - + -
407A LEU* 3.4 28.5 - - + +
408A PRO* 3.2 8.8 - - - +
409A GLY* 3.0 26.2 + - - -
410A VAL* 4.8 1.1 - - + -
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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