Contacts of the helix formed by residues 220 - 231 (chain A) in PDB entry 2W5H
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 SER 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A THR* 5.9 2.9 - - - -
218A ALA* 3.3 2.7 + - - +
219A PHE* 1.3 82.8 - - - +
221A GLN* 1.3 59.1 + - - +
222A LYS* 3.3 15.9 + - - +
223A GLU* 3.1 31.3 + - - +
224A LEU* 2.9 29.3 + - - +
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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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176A PHE 5.2 5.3 + - - -
178A GLY 4.3 7.1 + - - -
179A THR* 5.0 3.4 - - + +
180A PRO* 3.5 40.0 - - + +
220A SER* 1.3 73.7 + - - +
222A LYS* 1.3 57.2 + - - +
224A LEU* 3.6 12.7 - - + +
225A ALA* 2.9 27.1 + - + +
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Residues in contact with LYS 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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220A SER* 3.1 9.1 + - - +
221A GLN* 1.3 78.5 - - - +
223A GLU* 1.3 62.5 + - + +
225A ALA* 3.5 7.0 + - - +
226A GLY* 3.2 21.1 + - - -
229A ARG* 4.5 4.5 + - - +
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Residues in contact with GLU 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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218A ALA* 3.9 11.2 - - + -
219A PHE* 4.1 11.1 - - - +
220A SER* 3.2 35.8 + - - +
222A LYS* 1.3 78.9 - - + +
224A LEU* 1.3 61.7 - - - +
226A GLY* 3.4 2.2 + - - -
227A LYS* 3.0 35.5 - - + -
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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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179A THR* 3.4 33.2 - - + -
180A PRO* 4.0 25.8 - - + +
181A TYR* 4.3 6.1 - - + +
216A PHE* 3.8 40.4 - - + +
217A THR* 4.1 4.5 - - - +
218A ALA* 3.4 14.3 - - + +
220A SER 2.9 16.5 + - - +
221A GLN* 3.6 9.2 - - + +
223A GLU* 1.3 75.1 + - - +
225A ALA* 1.3 64.5 + - - +
227A LYS* 3.2 3.8 + - + +
228A ILE* 2.9 38.6 + - + +
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Residues in contact with ALA 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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188A MET* 4.1 25.4 - - + +
221A GLN* 2.9 19.2 + - + +
222A LYS* 3.7 7.0 - - - +
223A GLU 3.4 0.2 - - - +
224A LEU* 1.3 77.1 - - - +
226A GLY* 1.3 61.7 + - - +
228A ILE* 3.4 2.4 + - - +
229A ARG* 3.0 45.4 + - - +
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Residues in contact with GLY 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 LYS 3.2 11.0 + - - -
223A GLU* 3.4 3.8 - - - -
224A LEU 3.3 0.4 - - - -
225A ALA* 1.3 76.7 - - - +
227A LYS* 1.3 62.3 + - - +
229A ARG* 3.2 22.0 + - - +
230A GLU* 3.2 25.6 + - - +
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Residues in contact with LYS 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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216A PHE* 3.7 25.8 - - + -
217A THR* 2.7 37.9 + - - +
218A ALA* 4.6 5.1 - - - +
223A GLU* 3.0 25.6 - - - +
224A LEU* 3.2 8.3 + - - +
226A GLY* 1.3 75.5 - - - +
228A ILE* 1.3 62.1 + - - +
230A GLU* 3.3 15.3 + - - +
231A GLY 3.3 8.5 + - - -
232A LYS* 4.3 3.5 + - - +
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Residues in contact with ILE 228 (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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180A PRO 4.4 11.7 - - - +
181A TYR 4.4 6.7 - - - +
183A MET* 3.4 30.3 - - + +
185A PRO* 4.1 11.3 - - + +
188A MET* 3.8 21.5 - - - -
200A TRP* 4.0 15.7 - - + -
216A PHE* 3.9 30.3 - - + -
224A LEU* 2.9 36.5 + - + +
225A ALA* 3.7 3.8 - - - +
227A LYS* 1.3 76.9 - - - +
229A ARG* 1.3 61.5 + - - +
231A GLY* 3.3 10.7 + - - -
254A LEU* 3.6 12.1 - - - +
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Residues in contact with ARG 229 (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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185A PRO* 5.4 6.7 - - + -
188A MET* 3.5 26.2 - - + +
189A ASN* 5.1 9.2 - - - +
222A LYS* 4.5 4.8 + - - +
225A ALA* 3.0 28.6 + - - +
226A GLY* 3.2 28.1 + - - +
228A ILE* 1.3 73.8 - - - +
230A GLU* 1.3 65.7 + - + +
254A LEU* 3.4 19.0 - - - +
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Residues in contact with GLU 230 (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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226A GLY 3.2 14.5 + - - +
227A LYS* 3.3 10.1 + - - +
229A ARG* 1.3 75.9 - - + +
231A GLY* 1.3 64.9 + - - +
232A LYS* 3.3 42.8 + - + +
254A LEU* 3.6 10.5 - - - +
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Residues in contact with GLY 231 (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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200A TRP* 5.1 0.9 - - - -
216A PHE* 4.0 13.0 - - - -
227A LYS 3.3 3.0 + - - -
228A ILE 3.3 10.5 + - - -
230A GLU* 1.3 79.4 - - - +
232A LYS* 1.3 60.3 + - - +
233A PHE* 3.7 16.7 - - - -
252A LEU 5.0 3.0 - - - +
254A LEU* 3.6 24.1 - - - +
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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