Contacts of the helix formed by residues 164 - 168 (chain D) in PDB entry 2Y3I
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D ARG* 3.0 16.3 + - - +
22D VAL 3.5 8.1 - - - +
23D ASP* 3.4 30.1 - - + +
162D ASN* 3.0 10.5 + - - +
163D ASP* 1.3 75.0 - - - +
165D PHE* 1.3 62.7 + - - +
166D GLY 3.2 1.7 + - - -
167D THR* 3.8 15.0 - - - +
168D ALA* 3.2 21.0 + - - +
175D MET* 4.1 7.8 - - - +
189D MET* 4.3 2.2 - - - +
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Residues in contact with PHE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ASP* 5.0 0.4 - - - +
163D ASP 2.9 12.3 + - - +
164D ALA* 1.3 71.9 - - - +
166D GLY* 1.3 62.5 + - - +
168D ALA* 3.2 18.4 + - + +
188D LEU* 4.5 5.2 - - + +
189D MET* 3.9 30.0 - - - -
192D GLU* 3.4 44.2 - - + -
193D LEU* 3.7 24.0 - - + -
196D PHE* 4.4 11.9 - + - -
392D SER* 3.9 15.9 - - - -
393D THR* 3.6 17.9 - - - +
394D GLY* 4.0 7.2 - - - -
397D ALA* 3.4 17.6 - - + +
398D SER* 4.0 16.4 - - - -
401D LEU* 4.6 6.5 - - + -
407D LEU* 4.4 9.6 - - + -
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Residues in contact with GLY 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ASP* 2.8 22.6 + - - +
38D ARG* 4.7 0.7 - - - -
164D ALA* 3.2 1.8 - - - +
165D PHE* 1.3 79.5 - - - +
167D THR* 1.3 55.1 + - - +
168D ALA 3.5 0.2 - - - -
169D HIS* 3.4 18.5 + - - -
393D THR* 4.1 9.2 + - - -
394D GLY* 3.8 23.4 - - - -
397D ALA* 4.0 3.9 + - - +
1420D 3PG 3.4 12.3 - - - +
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Residues in contact with THR 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ARG* 3.9 9.0 + - - +
23D ASP* 2.5 29.3 + - - +
62D HIS* 3.4 28.6 - - + +
122D ARG* 4.5 3.6 - - - +
164D ALA* 3.4 7.9 + - - +
165D PHE 3.2 0.4 - - - -
166D GLY* 1.3 74.2 - - - +
168D ALA* 1.3 52.0 + - - +
169D HIS* 2.8 10.2 + - - -
170D ARG* 2.7 51.0 + - + +
172D HIS* 5.2 1.3 - - - +
175D MET* 4.1 19.0 - - + +
1420D 3PG 4.1 9.0 - - - +
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Residues in contact with ALA 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ALA 3.2 13.1 + - - +
165D PHE* 3.2 22.2 + - + +
167D THR* 1.3 76.4 - - - +
169D HIS* 1.3 58.2 + - - +
170D ARG 3.2 2.1 + - - +
175D MET* 3.9 10.5 - - + -
189D MET* 4.2 17.9 - - + -
407D LEU* 3.9 24.7 - - + +
408D PRO* 3.7 3.6 - - - +
409D GLY* 2.9 29.1 + - - -
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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