Contacts of the helix formed by residues 213 - 217 (chain A) in PDB entry 1W1J
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 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A GLY* 5.4 1.8 - - - -
212A THR* 1.3 73.7 - - - +
214A MET* 1.3 64.9 + - - -
216A ALA* 3.0 17.5 + - - +
243A PRO* 3.2 23.3 - - - -
244A TYR 4.3 2.9 - - - -
245A GLY* 3.7 15.9 - - - -
246A PHE 5.3 0.2 + - - -
249A TYR* 5.7 0.2 - - - -
251A ASP* 4.1 5.9 + - - -
517B TYR* 4.2 3.5 - - - -
524B PHE* 4.5 13.1 - - - -
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Residues in contact with MET 214 (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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199A GLY* 5.6 0.6 - - - +
212A THR 3.5 0.2 + - - -
213A GLY* 1.3 66.1 - - - -
215A GLY* 1.3 51.9 + - - +
216A ALA 2.6 5.7 + - - -
217A LEU* 2.6 41.1 + - - +
236A SER* 3.8 3.9 + - - +
238A ILE* 3.2 47.8 - - + +
239A ALA* 3.8 6.3 + - - -
242A PHE* 3.5 44.8 + - + +
243A PRO* 5.5 0.2 - - - +
245A GLY* 3.7 10.7 - - - +
428B ILE* 3.8 10.1 - - + -
501B GLY* 3.7 24.5 - - - +
502B GLU 4.3 2.0 - - - +
517B TYR* 3.0 37.7 - - - +
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Residues in contact with GLY 215 (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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211A ARG* 3.0 26.4 + - - +
212A THR 2.8 17.2 + - - -
214A MET* 1.3 73.4 - - - +
216A ALA* 1.3 57.4 + - - +
217A LEU 3.5 4.4 - - - +
235A TRP* 3.8 26.4 - - - -
236A SER* 5.2 0.7 - - - -
239A ALA* 3.9 12.3 + - - +
519B TRP* 4.1 9.9 - - - -
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Residues in contact with ALA 216 (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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211A ARG 3.6 15.5 - - - +
212A THR 3.7 0.2 + - - -
213A GLY 3.0 12.6 + - - +
214A MET 2.6 6.5 + - - -
215A GLY* 1.3 75.1 - - - +
217A LEU* 1.3 58.2 + - - +
218A PRO 3.4 0.2 - - - -
517B TYR* 3.1 32.5 - - + +
519B TRP* 3.0 35.7 + - + +
524B PHE* 4.0 20.0 - - + -
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Residues in contact with LEU 217 (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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214A MET* 2.6 22.6 + - - +
215A GLY 4.3 3.6 - - - +
216A ALA* 1.3 69.4 - - - +
218A PRO* 1.3 92.8 - - + +
236A SER* 2.9 31.4 + - - +
496B ALA* 4.2 12.6 - - + +
499B GLY* 3.9 26.9 - - - -
500B TRP 4.2 4.0 - - - +
501B GLY* 3.8 24.7 - - - +
516B THR* 3.0 41.7 - - + +
517B TYR* 3.4 17.7 - - + +
519B TRP* 4.7 0.2 - - - -
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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