Contacts of the helix formed by residues 213 - 227 (chain A) in PDB entry 5WWW
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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214A HIS* 1.3 65.4 + - - -
215A HIS* 3.1 5.2 - - - -
216A HIS* 3.1 37.6 + - - +
217A HIS* 3.3 11.1 + - - +
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Residues in contact with HIS 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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213A GLY* 1.3 71.9 - - - -
215A HIS* 1.3 101.0 + + - +
217A HIS* 3.3 8.6 + - + +
218A HIS* 2.9 36.5 + - + +
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Residues in contact with HIS 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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213A GLY* 3.1 2.6 - - - -
214A HIS* 1.3 116.7 + + - +
216A HIS* 1.3 65.7 + + + +
218A HIS* 3.5 5.6 + - - +
219A HIS* 2.9 31.9 + - - +
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Residues in contact with HIS 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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213A GLY* 3.1 30.5 + - - +
215A HIS* 1.3 83.0 - + + +
217A HIS* 1.3 58.2 + - - +
219A HIS* 3.4 4.5 + - - +
220A MET* 2.8 30.9 + - - +
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Residues in contact with HIS 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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213A GLY 3.3 9.3 + - - +
214A HIS* 3.8 10.3 - - - +
216A HIS* 1.3 78.5 - - - +
218A HIS* 1.3 65.3 + - + +
220A MET* 3.2 13.1 + - + +
221A GLN* 2.9 65.5 + - + +
265A TYR* 6.1 3.4 - - - -
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Residues in contact with HIS 218 (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 HIS* 2.9 22.8 + - + +
215A HIS* 3.9 6.2 + - - +
217A HIS* 1.3 82.2 - - + +
219A HIS* 1.3 62.0 + - - +
221A GLN* 3.2 9.1 + - + +
222A ALA* 2.9 37.2 + - + +
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Residues in contact with HIS 219 (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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215A HIS 2.9 19.6 + - - +
216A HIS* 3.9 4.5 - - - +
218A HIS* 1.3 78.2 - - - +
220A MET* 1.3 61.1 + - - +
222A ALA* 3.2 11.2 + - + +
223A ALA* 2.9 33.1 + - + +
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Residues in contact with MET 220 (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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216A HIS 2.8 18.3 + - - +
217A HIS* 3.5 12.6 - - + +
219A HIS* 1.3 77.0 + - - +
221A GLN* 1.3 80.5 + - + +
223A ALA* 3.1 7.8 + - + +
224A LEU* 3.0 53.4 + - + +
230A VAL* 6.5 0.7 - - + -
265A TYR* 3.4 51.1 - - + -
280A THR* 5.9 0.7 - - - -
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Residues in contact with GLN 221 (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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217A HIS* 2.9 51.0 + - - +
218A HIS* 3.2 8.9 + - + +
220A MET* 1.3 91.1 - - + +
222A ALA* 1.3 62.6 + - - +
224A LEU* 3.2 10.0 + - + +
225A LEU* 3.0 31.6 + - + +
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Residues in contact with ALA 222 (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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218A HIS* 2.9 25.0 + - + +
219A HIS* 3.5 18.4 - - + +
221A GLN* 1.3 74.4 - - - +
223A ALA* 1.3 62.8 + - - +
225A LEU* 3.2 14.0 + - + +
226A ARG* 3.1 31.0 + - + +
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Residues in contact with ALA 223 (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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219A HIS* 2.9 19.4 + - + +
220A MET* 3.5 11.2 - - + +
222A ALA* 1.3 74.7 - - - +
224A LEU* 1.3 65.8 + - + +
226A ARG* 3.3 15.4 + - - +
227A ARG* 3.2 15.6 + - - -
228A LYS 4.5 1.6 + - - -
229A SER* 5.4 5.2 + - - +
230A VAL* 4.1 28.8 + - + +
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Residues in contact with LEU 224 (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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220A MET* 3.0 45.9 + - + +
221A GLN* 3.5 12.1 - - + +
223A ALA* 1.3 77.7 - - + +
225A LEU* 1.3 59.7 + - + +
227A ARG* 3.0 24.8 + - - +
230A VAL* 3.4 33.1 - - + +
280A THR* 4.1 19.5 - - + -
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Residues in contact with LEU 225 (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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221A GLN* 3.0 21.4 + - + +
222A ALA* 3.2 15.2 + - + +
224A LEU* 1.3 78.3 - - + +
226A ARG* 1.3 61.8 + - + +
227A ARG* 4.6 2.3 - - - +
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Residues in contact with ARG 226 (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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222A ALA* 3.1 18.2 + - + +
223A ALA* 3.7 12.9 + - - +
224A LEU 3.2 0.4 - - - -
225A LEU* 1.3 77.1 - - - +
227A ARG* 1.3 68.9 + - - +
228A LYS* 3.2 55.4 + - + +
229A SER* 4.4 9.9 + - - -
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Residues in contact with ARG 227 (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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223A ALA 3.2 4.0 + - - -
224A LEU 3.0 14.3 + - - +
225A LEU 4.6 2.2 - - - +
226A ARG* 1.3 79.0 - - - +
228A LYS* 1.3 64.7 + - - +
230A VAL 3.3 19.3 - - - +
231A ASN* 3.6 37.8 + - + +
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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
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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