Contacts of the helix formed by residues 301 - 306 (chain Y) in PDB entry 1O1F
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 GLY 301 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154Y ASP* 4.0 5.4 + - - -
155Y SER 3.2 15.3 - - - -
156Y GLY* 4.8 1.1 - - - -
300Y SER* 1.3 75.7 - - - +
302Y GLY* 1.3 66.5 + - - +
304Y THR* 2.9 20.1 + - - -
305Y MET* 3.9 5.7 + - - +
335Y ARG* 3.1 13.5 + - - +
336Y LYS* 4.2 8.5 - - - -
339Y VAL* 6.0 1.3 - - - +
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Residues in contact with GLY 302 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155Y SER 3.3 2.8 + - - -
156Y GLY* 4.4 6.8 - - - -
301Y GLY* 1.3 68.6 - - - -
303Y THR* 1.3 61.7 + - - +
304Y THR 3.2 1.7 + - - -
305Y MET* 3.2 28.5 + - - +
306Y TYR* 4.9 0.9 + - - -
336Y LYS* 4.2 15.3 + - - +
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Residues in contact with THR 303 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155Y SER* 3.1 30.6 + - - +
156Y GLY 2.9 18.3 + - - -
181Y ALA 4.3 1.8 - - - -
182Y GLY* 3.1 21.6 - - - +
185Y LEU* 3.8 27.4 - - + -
213Y LYS* 5.1 1.0 + - - -
261Y LEU* 4.1 11.2 - - + +
302Y GLY* 1.3 76.1 - - - +
304Y THR* 1.3 56.5 + - - +
305Y MET 3.2 1.3 - - - -
306Y TYR* 3.0 37.9 + - + -
309Y ILE* 3.9 2.6 - - - +
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Residues in contact with THR 304 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153Y LEU* 4.0 20.2 - - + -
155Y SER* 3.6 21.3 - - - -
261Y LEU* 6.5 0.2 - - + -
299Y MET* 3.8 14.4 - - + -
300Y SER 3.3 27.8 + - - +
301Y GLY 2.9 14.1 + - - +
303Y THR* 1.3 75.7 - - - +
305Y MET* 1.3 54.0 + - - +
306Y TYR 3.5 1.6 - - - -
309Y ILE* 3.2 22.9 - - + +
335Y ARG* 2.7 46.3 + - - -
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Residues in contact with MET 305 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301Y GLY 3.9 7.0 - - - +
302Y GLY* 3.2 24.5 - - - +
303Y THR 3.2 1.8 - - - -
304Y THR* 1.3 78.1 - - - +
306Y TYR* 1.4 65.9 + - - +
307Y PRO* 3.1 10.8 - - - +
333Y PRO* 3.8 18.2 - - + +
335Y ARG* 3.3 44.5 + - + +
336Y LYS* 3.7 28.3 - - + -
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Residues in contact with TYR 306 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185Y LEU* 3.0 35.5 - - + +
213Y LYS* 3.7 43.3 + - + +
214Y GLU* 5.6 3.4 - - - -
217Y CYS* 4.0 15.9 - - + +
219Y VAL* 3.6 18.4 - - + +
257Y CYS* 5.5 0.4 - - - -
258Y PRO* 3.6 32.8 - - + -
261Y LEU* 4.0 9.6 - - + -
302Y GLY 4.9 0.4 + - - -
303Y THR* 3.0 38.8 + - + +
304Y THR 3.5 0.6 - - - -
305Y MET* 1.4 71.2 - - - +
307Y PRO* 1.3 71.0 - - + +
309Y ILE* 3.2 25.8 - - + +
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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
------------------------------------------------------------
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