Contacts of the helix formed by residues 214 - 229 (chain A) in PDB entry 2HOF
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 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A ASN* 2.8 21.3 + - - +
192A ARG* 4.2 1.1 - - - -
213A LEU* 1.3 71.0 - - - +
215A LEU* 1.3 55.8 + - - +
216A GLY* 3.8 2.2 + - - -
217A VAL* 3.3 22.3 + - - +
218A THR* 2.6 37.5 + - - -
336B VAL* 3.8 23.4 - - - +
339B LEU* 3.5 25.7 - - - +
340B GLU* 4.0 7.4 - - - -
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Residues in contact with LEU 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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190A GLY* 3.5 26.9 - - - +
191A GLY 4.6 2.9 - - - +
192A ARG* 3.4 49.8 - - + +
214A SER* 1.3 75.5 - - - +
216A GLY* 1.3 57.6 + - - +
218A THR* 3.5 4.5 + - - -
219A LYS* 3.0 31.8 + - - +
340B GLU* 4.2 9.8 + - - +
341B ASP 6.0 1.8 - - - +
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Residues in contact with GLY 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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146A ARG* 4.4 13.4 + - - -
214A SER* 3.4 3.5 + - - -
215A LEU* 1.3 80.0 - - - +
217A VAL* 1.3 60.7 + - - +
219A LYS* 3.5 12.5 - - - +
220A LEU* 3.3 26.7 + - - +
340B GLU* 4.8 3.0 + - - -
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PHE* 4.3 14.4 - - + -
146A ARG* 4.8 2.5 - - - +
162A ALA 5.1 0.2 - - - +
165A GLY* 3.6 41.5 - - - +
166A ILE 3.9 2.0 - - - +
169A ASN* 3.7 11.4 - - - +
213A LEU* 3.8 22.0 - - + -
214A SER* 3.3 19.3 + - - +
216A GLY* 1.3 72.0 - - - +
218A THR* 1.3 61.0 + - - +
219A LYS 3.1 1.6 - - - -
220A LEU* 3.1 9.5 + - + +
221A VAL* 2.9 40.9 + - + +
339B LEU* 4.2 9.9 - - + -
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Residues in contact with THR 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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187A ARG* 3.9 7.4 - - - +
191A GLY 3.3 25.6 - - - +
192A ARG* 3.7 1.3 - - - -
193A MET* 3.1 40.0 + - + +
213A LEU* 3.5 17.6 + - - +
214A SER 2.6 25.8 + - - -
215A LEU* 3.7 7.6 - - + -
217A VAL* 1.3 76.1 - - - +
219A LYS* 1.3 56.8 + - - +
221A VAL* 3.5 3.3 + - - +
222A GLU* 3.0 33.0 + - - +
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Residues in contact with LYS 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 LEU 3.0 18.6 + - - +
216A GLY* 3.5 11.9 - - - +
217A VAL 3.1 0.2 - - - -
218A THR* 1.3 74.1 - - - +
220A LEU* 1.3 65.9 + - + +
222A GLU* 3.2 16.7 + - + +
223A ARG* 3.1 23.0 + - - +
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Residues in contact with LEU 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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142A PHE* 4.1 14.4 - - + -
146A ARG* 4.0 24.9 - - - +
150A GLU* 5.5 4.7 - - + +
158A ILE* 4.6 2.8 - - - +
161A LEU* 4.0 43.3 - - + +
162A ALA* 3.7 20.4 - - - +
165A GLY* 4.9 1.3 - - - -
216A GLY 3.3 16.4 + - - +
217A VAL* 3.1 14.5 + - + +
219A LYS* 1.3 79.7 - - + +
221A VAL* 1.3 62.1 + - + +
223A ARG* 3.5 7.8 + - - +
224A TRP* 3.4 16.3 + - - +
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Residues in contact with VAL 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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162A ALA* 4.0 16.6 - - + +
166A ILE* 3.7 29.6 - - + -
185A ILE* 5.3 0.2 - - + -
193A MET* 4.0 20.4 - - - -
213A LEU* 4.0 10.5 - - + -
217A VAL* 2.9 24.6 + - + +
218A THR 3.9 4.0 - - - +
220A LEU* 1.3 73.1 - - - +
222A GLU* 1.3 63.7 + - - +
224A TRP* 3.7 4.0 + - + +
225A ILE* 3.2 24.7 + - + +
238A LEU* 3.8 33.7 - - + -
239A PHE* 5.5 0.2 - - + -
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Residues in contact with GLU 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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187A ARG* 2.9 37.3 + - - +
193A MET* 4.9 7.2 - - + +
218A THR* 3.0 20.0 + - - +
219A LYS* 3.3 20.7 - - + +
220A LEU 3.2 0.2 - - - -
221A VAL* 1.3 74.7 - - - +
223A ARG* 1.3 64.9 + - - +
225A ILE* 3.2 20.9 + - + +
226A SER* 3.2 13.4 + - - -
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Residues in contact with ARG 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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149A MET 5.6 0.2 + - - -
150A GLU* 3.2 24.9 + - - +
151A ASN 5.3 0.8 - - - -
152A SER 3.1 28.2 + - - +
153A ASP* 4.0 11.9 + - - +
158A ILE* 3.7 31.4 - - + +
219A LYS 3.1 12.5 + - - +
220A LEU* 3.8 10.1 - - - +
221A VAL 3.4 0.2 - - - -
222A GLU* 1.3 76.6 - - - +
224A TRP* 1.3 61.3 + - - +
226A SER* 2.7 27.1 + - - +
227A VAL* 3.2 13.2 + - + +
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Residues in contact with TRP 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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155A CYS* 4.1 13.9 - - - -
158A ILE* 3.6 16.7 - - + +
159A ARG* 3.5 50.0 - - + -
162A ALA* 4.0 11.0 - - + -
220A LEU 3.4 9.7 + - - +
221A VAL* 3.9 8.3 - - + +
222A GLU 3.3 0.4 - - - -
223A ARG* 1.3 77.7 - - - +
225A ILE* 1.3 54.6 + - - +
227A VAL* 3.4 8.4 + - + +
228A SER* 2.7 65.9 + - - -
230A VAL* 4.6 0.2 - - - +
238A LEU* 2.8 40.3 + - + +
239A PHE* 3.8 17.2 - + - -
240A CYS* 3.6 30.5 - - - -
242A VAL* 3.8 16.2 - - + -
248A ALA* 3.9 1.3 - - + -
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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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182A VAL* 5.6 4.5 - - + -
185A ILE* 4.6 5.6 - - + -
193A MET* 3.8 26.9 - - + -
221A VAL* 3.2 16.7 + - + +
222A GLU* 3.2 12.4 + - + +
224A TRP* 1.3 78.7 - - + +
226A SER* 1.3 58.1 + - - +
228A SER* 3.2 5.8 + - - -
229A GLY* 3.0 28.8 + - - -
230A VAL* 3.8 10.0 + - + -
231A ALA* 3.8 26.9 - - + +
238A LEU* 3.7 30.5 - - + -
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Residues in contact with SER 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 GLU 3.2 10.9 + - - -
223A ARG* 2.7 24.6 + - - +
225A ILE* 1.3 81.1 - - - +
227A VAL* 1.3 72.0 + - - +
228A SER 3.3 0.2 + - - -
229A GLY* 3.6 7.8 + - - -
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Residues in contact with VAL 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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155A CYS* 3.8 29.3 - - - -
158A ILE* 3.9 33.9 - - + -
223A ARG* 3.5 14.1 - - + +
224A TRP* 3.5 12.1 - - + +
226A SER* 1.3 89.8 + - - +
228A SER* 1.3 60.5 + - - +
248A ALA* 4.9 2.4 + - - +
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Residues in contact with SER 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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224A TRP* 2.7 56.6 + - - -
225A ILE* 3.2 1.2 + - - -
227A VAL* 1.3 79.8 - - - +
229A GLY* 1.3 63.1 + - - +
230A VAL* 3.2 28.5 + - - +
248A ALA* 4.0 15.2 - - - +
250A PRO* 3.6 17.5 - - - +
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Residues in contact with GLY 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 3.0 12.7 + - - -
226A SER 3.6 7.7 + - - -
228A SER* 1.3 76.9 - - - +
230A VAL* 1.3 63.5 + - - +
231A ALA 3.3 3.1 - - - -
232A ASP* 3.4 35.2 - - - +
236A ASN* 4.5 1.9 + - - -
250A PRO* 3.9 9.1 - - - +
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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