Contacts of the helix formed by residues 207 - 212 (chain X) in PDB entry 2QW0
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 HIS 207 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159X PHE* 4.0 2.2 - - - -
160X TYR 6.1 0.7 - - - -
203X MET* 4.0 12.9 - - + +
204X PRO* 3.3 23.5 + - + +
205X LEU 3.2 0.6 - - - -
206X TYR* 1.3 89.3 - + + +
208X VAL* 1.3 65.7 + - + +
209X VAL* 3.1 47.5 + - + +
210X GLY* 2.9 6.6 + - - +
211X PHE* 2.8 26.0 + - - +
307X THR* 4.6 9.3 + - - -
505X 34Z 2.8 38.5 + + - -
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Residues in contact with VAL 208 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159X PHE* 3.5 46.4 - - + -
173X ILE* 5.1 0.4 - - + -
181X ARG* 3.5 22.7 - - - +
207X HIS* 1.3 78.9 + - + +
209X VAL* 1.3 59.3 + - - +
211X PHE 4.4 0.2 - - - +
212X PHE* 2.8 37.7 + - + +
307X THR* 4.0 24.8 + - + +
310X MET* 3.5 20.2 - - - +
505X 34Z 3.9 16.6 - - + -
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Residues in contact with VAL 209 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203X MET* 4.0 11.4 - - + -
207X HIS* 3.1 28.3 + - + +
208X VAL* 1.3 72.1 - - - +
210X GLY* 1.3 68.3 + - - +
211X PHE 3.1 0.7 + - - -
213X ALA* 3.1 10.1 + - + -
214X VAL* 2.9 32.4 + - + +
249X PHE* 3.6 50.0 - - + -
310X MET* 3.9 1.6 - - + -
505X 34Z 3.5 37.0 - - + -
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Residues in contact with GLY 210 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203X MET* 3.6 23.3 - - - +
204X PRO 3.1 25.7 + - - -
205X LEU* 3.7 13.9 - - - +
207X HIS* 2.9 5.5 + - - +
209X VAL* 1.3 80.0 - - - +
211X PHE* 1.3 54.9 + - - +
214X VAL* 3.5 5.3 - - - +
215X LEU* 3.2 20.1 + - - +
225X TYR* 5.0 0.5 - - - -
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Residues in contact with PHE 211 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X VAL* 4.5 1.3 - - + -
71X ILE* 3.7 23.8 - - + -
72X LEU* 4.2 10.1 - - + -
83X LEU* 4.5 5.6 - - + -
157X PHE* 3.7 38.1 - + - -
159X PHE* 3.7 27.1 - + + -
205X LEU* 3.6 24.4 + - + +
207X HIS 2.8 11.4 + - - +
208X VAL 4.1 1.1 - - - +
209X VAL 3.1 0.2 - - - -
210X GLY* 1.3 73.9 - - - +
212X PHE* 1.3 77.1 + + - +
215X LEU* 3.4 28.6 + - + +
216X VAL* 2.8 53.1 + - + +
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Residues in contact with PHE 212 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X VAL* 4.0 19.3 - - + -
157X PHE* 4.1 9.2 - + - -
159X PHE* 3.6 26.7 - + - -
173X ILE* 3.9 21.8 - - + -
178X ALA* 4.0 19.7 - - + -
181X ARG* 3.7 47.1 - - + +
182X VAL* 3.6 9.5 - - + +
208X VAL* 2.8 36.6 + - + +
211X PHE* 1.3 94.6 - + - +
213X ALA* 1.3 58.4 + - - +
214X VAL 3.3 0.2 - - - -
216X VAL* 4.1 5.4 - - + -
217X ALA* 3.0 28.9 + - - +
310X MET* 4.0 2.2 - - + -
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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