Contacts of the helix formed by residues 200 - 210 (chain F) in PDB entry 1Z6Z
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 THR 200 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15F GLY* 3.7 22.2 - - - -
16F PHE 4.0 2.0 - - - +
198F LEU* 2.8 24.8 + - + -
199F ASP* 1.3 80.0 - - - +
201F ASP* 1.3 65.7 + - - +
202F MET 3.4 4.7 + - - -
203F GLN* 3.2 2.6 + - - +
204F GLN* 3.1 22.3 + - - +
207F ARG* 5.4 0.2 + - - -
231F CYS* 3.8 11.2 - - - -
806F NAP 2.4 50.8 + - - +
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Residues in contact with ASP 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ARG* 2.9 46.3 + - - +
15F GLY* 5.7 0.2 - - - -
200F THR* 1.3 74.7 - - - +
202F MET* 1.3 57.3 + - - +
204F GLN* 3.5 18.9 + - - +
205F LEU* 2.9 28.3 + - - +
806F NAP 3.8 4.7 + - - +
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Residues in contact with MET 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F GLY 3.5 29.2 - - - +
100F SER* 3.7 17.0 - - - -
101F LEU* 3.7 24.1 - - + +
167F TYR* 4.1 16.6 - - - -
200F THR* 3.2 2.0 + - - -
201F ASP* 1.3 75.3 - - - +
203F GLN* 1.3 66.2 + - - +
205F LEU* 3.2 9.5 + - + +
206F ALA* 3.0 22.9 + - - +
806F NAP 3.6 76.2 + - - +
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Residues in contact with GLN 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F TRP* 5.9 3.0 - - - -
197F PRO* 4.0 11.4 - - - +
198F LEU 2.9 25.1 - - - +
199F ASP* 4.9 0.2 - - - -
200F THR* 3.2 9.0 + - - +
202F MET* 1.3 79.2 - - - +
204F GLN* 1.3 51.2 + - - +
206F ALA* 3.3 9.2 + - - +
207F ARG* 2.8 50.5 + - - +
219F LEU* 3.4 34.8 - - - +
222F LEU* 4.4 1.4 - - - +
228F LEU* 3.8 25.5 - - + +
806F NAP 2.7 29.4 + - - +
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Residues in contact with GLN 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200F THR 3.1 13.8 + - - +
201F ASP* 3.6 23.9 - - - +
203F GLN* 1.3 74.0 - - - +
205F LEU* 1.3 58.8 + - - +
207F ARG* 3.2 29.8 + - - +
208F GLU* 2.9 61.7 + - - +
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Residues in contact with LEU 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F LEU* 4.1 26.7 - - + +
102F GLY 4.6 8.1 - - - +
104F VAL* 5.3 0.7 - - + -
201F ASP 2.9 14.2 + - - +
202F MET* 3.2 13.0 + - + +
204F GLN* 1.3 75.4 - - - +
206F ALA* 1.3 55.6 + - - +
208F GLU* 3.3 4.1 + - - +
209F THR* 2.6 60.0 + - + +
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Residues in contact with ALA 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F LEU* 3.6 18.6 - - + +
104F VAL* 4.5 1.1 - - - -
164F TRP* 3.7 29.4 - - + -
202F MET 3.0 12.1 + - - +
203F GLN* 3.5 13.7 - - - +
205F LEU* 1.3 75.2 - - - +
207F ARG* 1.3 63.2 + - - +
208F GLU 3.3 0.5 + - - -
210F SER* 2.7 33.1 + - - -
216F ARG* 4.5 0.2 - - - +
219F LEU* 3.6 10.2 - - + +
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Residues in contact with ARG 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199F ASP* 4.7 6.7 + - - -
203F GLN* 2.8 45.2 + - - +
204F GLN* 3.2 40.3 + - - +
206F ALA* 1.3 72.8 - - - +
208F GLU* 1.3 66.2 + - + +
216F ARG* 3.7 23.0 - - - +
219F LEU* 3.6 31.3 + - + +
220F GLN* 3.9 27.8 - - + +
223F LYS* 3.9 32.3 - - - +
228F LEU* 4.2 13.3 - - - +
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Residues in contact with GLU 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204F GLN* 2.9 52.1 + - + +
205F LEU* 4.2 3.3 - - - +
207F ARG* 1.3 89.9 + - + +
209F THR* 1.3 67.9 + - + +
210F SER 3.8 0.7 - - - -
216F ARG* 3.7 12.6 - - - +
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Residues in contact with THR 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F ASP* 5.9 0.4 - - - -
104F VAL* 3.3 17.2 + - - +
105F SER* 3.2 33.1 - - - -
205F LEU* 2.6 43.9 + - + +
208F GLU* 1.3 87.3 - - + +
210F SER* 1.3 67.7 + - - +
211F VAL* 4.4 0.3 - - - -
216F ARG* 4.6 0.2 - - - -
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Residues in contact with SER 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F VAL* 3.5 10.3 - - - +
162F LYS 5.7 1.3 - - - -
164F TRP* 3.1 30.4 + - - -
206F ALA* 2.7 27.7 + - - -
208F GLU 3.8 0.8 - - - -
209F THR* 1.3 79.0 + - - +
211F VAL* 1.3 54.1 + - - +
212F ASP 4.3 7.9 - - - -
215F MET* 4.5 9.9 - - - -
216F ARG* 2.6 44.6 + - - +
219F LEU* 4.6 0.3 - - - +
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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