Contacts of the helix formed by residues 218 - 233 (chain A) in PDB entry 1H41
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 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A ARG* 2.9 19.8 + - - +
217A LEU* 1.3 80.5 - - - +
219A ASP* 1.3 59.9 + - - +
220A GLN* 3.7 11.7 + - - +
221A PHE* 3.5 14.7 + - - -
222A LEU* 2.8 27.1 + - - +
251A PHE* 3.7 24.2 - - - -
271A ARG* 4.2 1.6 - - - +
711B LEU* 4.1 14.2 - - - +
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Residues in contact with ASP 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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217A LEU 4.0 0.8 + - - -
218A SER* 1.3 72.4 - - - +
220A GLN* 1.3 63.6 + - - +
222A LEU* 4.4 4.9 - - - +
223A GLN* 3.0 35.6 + - - +
271A ARG* 4.9 1.1 + - - +
274A LYS* 2.8 38.1 + - - +
278A TYR* 2.8 31.4 + - - +
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Residues in contact with GLN 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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215A ARG* 5.9 1.2 - - - +
218A SER* 3.2 10.1 + - - +
219A ASP* 1.3 80.7 - - - +
221A PHE* 1.3 78.0 + - + +
223A GLN* 3.8 12.2 - - - +
224A LYS* 3.4 34.1 + - - +
695B THR* 2.8 28.2 + - - -
696B THR* 3.7 9.3 - - - +
697B TYR* 2.9 29.9 + - - +
711B LEU* 6.3 0.4 - - - +
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Residues in contact with PHE 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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163A LEU* 4.0 24.0 - - + -
179A TRP* 3.8 46.7 - + + -
215A ARG* 3.3 48.2 - - + +
216A VAL* 3.9 9.2 - - - -
218A SER* 3.2 7.8 + - - -
220A GLN* 1.3 100.9 - - + +
222A LEU* 1.3 59.5 + - - +
223A GLN 3.2 1.8 - - - -
224A LYS* 3.0 8.7 + - + +
225A ILE* 2.8 33.8 + - + +
697B TYR* 3.7 34.1 - + + -
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Residues in contact with LEU 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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216A VAL 3.4 17.5 - - - +
217A LEU* 3.5 22.7 - - - +
218A SER 2.8 20.0 + - - +
219A ASP 3.3 0.9 + - - +
221A PHE* 1.3 71.1 - - - +
223A GLN* 1.3 57.2 + - - +
225A ILE* 3.8 6.8 - - + +
226A ALA* 2.8 31.5 + - - +
241A LEU* 4.2 15.5 - - + -
271A ARG* 5.0 0.2 - - - -
274A LYS* 3.9 28.0 - - + -
275A ILE* 4.0 34.3 - - + -
278A TYR* 3.7 25.6 - - + +
279A ILE* 4.9 6.1 - - + +
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Residues in contact with GLN 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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183A PRO* 3.6 33.3 - - + +
219A ASP* 3.0 28.2 + - - +
220A GLN* 3.8 10.7 + - - +
222A LEU* 1.3 78.2 - - - +
224A LYS* 1.3 60.4 + - - +
226A ALA* 3.6 3.4 + - - +
227A ALA* 3.4 14.2 + - - +
278A TYR* 3.7 28.3 + - + +
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Residues in contact with LYS 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 TRP* 3.0 50.1 + - + +
180A GLY* 5.0 1.8 + - - -
182A LEU* 2.9 48.0 + - + +
183A PRO* 4.1 8.0 - - + +
220A GLN* 3.4 40.4 + - - +
221A PHE* 3.0 22.3 + - + +
223A GLN* 1.3 73.0 - - - +
225A ILE* 1.3 65.3 + - - +
227A ALA* 3.1 14.7 + - - +
228A LEU* 3.4 14.2 + - - +
654B ARG* 4.8 10.5 - - - +
697B TYR* 5.0 4.9 - - - +
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Residues in contact with ILE 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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179A TRP* 3.8 25.1 - - + -
207A ILE* 4.2 2.5 - - + -
216A VAL* 3.5 33.7 - - + +
221A PHE* 2.8 26.0 + - + +
222A LEU* 3.9 5.6 - - + +
224A LYS* 1.3 73.0 - - - +
226A ALA* 1.3 60.8 + - - +
228A LEU* 3.2 8.6 + - - +
229A ALA* 2.9 25.8 + - - +
239A MET* 3.9 26.2 - - + -
241A LEU* 4.0 27.4 - - + -
279A ILE* 3.8 17.7 - - + -
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Residues in contact with ALA 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 LEU 2.8 18.6 + - - +
223A GLN* 3.8 6.5 - - - +
225A ILE* 1.3 78.4 - - - +
227A ALA* 1.3 55.6 + - - +
229A ALA* 3.2 1.7 + - - +
230A ASP* 2.8 38.3 + - - +
278A TYR* 3.7 31.4 - - + +
279A ILE* 3.9 15.7 - - + +
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Residues in contact with ALA 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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182A LEU* 4.1 5.2 - - + -
183A PRO* 3.8 30.7 - - + -
186A LEU* 3.9 25.3 - - + +
190A TYR* 6.0 0.6 - - - -
223A GLN 3.4 2.6 + - - +
224A LYS 3.1 11.9 + - - +
226A ALA* 1.3 79.6 - - - +
228A LEU* 1.3 62.1 + - - +
230A ASP* 3.3 12.3 + - - +
231A ALA* 3.2 20.8 + - - +
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Residues in contact with LEU 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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177A TRP* 4.0 25.4 - - + -
179A TRP* 4.0 20.2 - - + -
182A LEU* 4.1 6.7 - - + -
190A TYR* 3.7 52.0 - - + -
207A ILE* 4.0 25.6 - - + -
224A LYS 3.4 8.7 + - - +
225A ILE* 3.2 7.7 + - - +
227A ALA* 1.3 76.7 - - - +
229A ALA* 1.3 64.0 + - - +
231A ALA* 3.0 5.3 + - - +
232A PHE* 3.0 34.6 + - + -
239A MET* 3.8 10.3 - - + -
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Residues in contact with ALA 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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225A ILE 2.9 13.9 + - - +
226A ALA* 3.2 9.8 + - - +
228A LEU* 1.3 75.6 - - - +
230A ASP* 1.3 57.8 + - - +
232A PHE* 3.2 5.7 + - - +
233A ARG* 2.9 39.9 + - - +
237A ILE 4.9 1.9 - - - +
239A MET* 3.6 22.8 - - + +
279A ILE* 3.9 28.9 - - + -
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Residues in contact with ASP 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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186A LEU* 6.4 2.2 - - + -
226A ALA* 2.8 24.3 + - - +
227A ALA* 3.5 13.0 - - - +
228A LEU 3.1 0.2 - - - -
229A ALA* 1.3 77.9 - - - +
231A ALA* 1.3 59.4 + - - +
233A ARG* 2.8 29.2 + - - +
234A PRO* 3.3 19.1 - - - +
278A TYR 5.1 4.9 - - - +
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Residues in contact with ALA 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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186A LEU* 6.1 5.8 - - + -
190A TYR* 4.2 23.3 - - + -
191A THR* 4.6 14.0 + - - +
194A ALA* 4.3 2.4 - - - +
227A ALA 3.2 10.4 + - - +
228A LEU* 3.0 10.4 + - - +
230A ASP* 1.3 76.1 - - - +
232A PHE* 1.3 69.9 + - + +
234A PRO* 3.5 13.1 - - - +
235A TYR* 3.9 12.3 - - - -
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Residues in contact with PHE 232 (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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177A TRP* 3.8 17.7 - + - -
190A TYR* 3.6 33.9 - - + -
193A TYR* 3.6 22.7 - + - -
194A ALA* 4.1 11.9 - - + -
205A THR* 3.7 31.9 - - + -
207A ILE* 4.4 4.5 - - + -
228A LEU* 3.0 27.4 + - + +
229A ALA* 3.2 4.2 + - - +
231A ALA* 1.3 82.1 - - - +
233A ARG* 1.3 63.1 + - - +
234A PRO 3.4 0.4 - - - -
235A TYR* 3.0 16.8 + - - +
237A ILE* 3.4 38.4 + - + +
239A MET* 3.8 24.2 - - + -
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Residues in contact with ARG 233 (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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41A THR* 4.2 3.6 + - - -
229A ALA* 2.9 22.6 + - - +
230A ASP* 2.8 40.3 + - - +
232A PHE* 1.3 75.9 - - - +
234A PRO* 1.3 69.5 - - + +
236A GLY* 2.9 15.8 + - - -
237A ILE 4.3 8.3 - - - +
278A TYR 5.3 0.6 + - - -
279A ILE* 3.9 16.8 - - - +
280A PRO* 4.2 13.9 - - - +
281A ASP* 2.8 43.8 + - - +
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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