Contacts of the helix formed by residues 221 - 231 (chain A) in PDB entry 1HLG
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 PHE 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A LEU* 3.7 25.1 - - + -
194A LYS* 3.4 56.1 - - + -
197A PHE* 5.5 7.2 - + - -
217A PHE* 3.2 33.9 - + - -
218A PHE* 3.2 25.5 + + + +
219A ASP 3.1 3.9 - - - +
220A GLN* 1.3 97.0 - - + +
222A LEU* 1.3 57.6 + - - +
223A ALA 4.6 0.4 - - - +
224A THR* 2.6 36.8 + - - +
225A GLU* 3.2 4.6 + - - +
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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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220A GLN 4.0 1.4 + - - -
221A PHE* 1.3 70.6 - - - +
223A ALA* 1.3 53.2 + - - +
225A GLU* 2.7 42.1 + - + +
226A VAL* 2.9 36.6 + - + +
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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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191A LEU* 4.2 28.0 - - + -
221A PHE* 3.3 1.0 - - - +
222A LEU* 1.3 77.8 - - - +
224A THR* 1.3 56.4 + - - +
226A VAL* 3.7 10.2 + - - +
227A CYS* 3.1 26.5 + - - +
246A PHE* 3.7 13.4 - - + -
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Residues in contact with THR 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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191A LEU* 3.9 17.2 - - - +
218A PHE* 2.8 29.5 + - + +
219A ASP* 4.0 22.2 - - - +
221A PHE* 2.6 21.2 + - - +
223A ALA* 1.3 71.1 - - - +
225A GLU* 1.3 60.9 + - - -
227A CYS* 3.7 4.1 - - - +
228A SER* 3.1 23.2 + - - -
236A CYS* 4.5 21.9 - - + +
242A ILE* 5.9 0.2 - - - +
246A PHE* 4.4 5.5 - - + -
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Residues in contact with GLU 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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219A ASP 5.0 3.7 + - - +
221A PHE 3.2 6.0 + - - +
222A LEU* 2.7 31.6 + - + +
224A THR* 1.3 72.0 - - - +
226A VAL* 1.3 59.8 + - + +
228A SER* 3.4 7.1 + - - -
229A ARG* 3.0 44.6 + - + +
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Residues in contact with VAL 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* 3.1 37.7 - - + +
223A ALA* 3.7 8.7 - - - +
225A GLU* 1.3 74.5 - - + +
227A CYS* 1.3 65.5 + - - +
229A ARG* 3.3 9.6 + - + +
230A GLU* 3.2 49.5 + - - +
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Residues in contact with CYS 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 3.1 19.1 + - - +
224A THR 3.7 4.3 - - - +
225A GLU 3.3 0.2 - - - -
226A VAL* 1.3 76.8 - - - +
228A SER* 1.3 63.2 + - - +
230A GLU* 2.9 8.8 + - - -
231A MET* 2.8 39.0 + - - +
235A LEU* 4.7 1.1 - - - -
236A CYS* 2.1 46.7 - - + -
246A PHE* 3.3 40.2 - - + -
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Residues in contact with SER 228 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A THR* 3.1 16.2 + - - -
225A GLU* 3.5 9.0 - - - -
227A CYS* 1.3 78.5 - - - +
229A ARG* 1.3 62.7 + - - +
231A MET 3.4 12.5 - - - +
233A ASN* 3.2 23.8 + - - +
236A CYS* 3.3 13.2 - - - -
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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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225A GLU* 3.0 37.0 + - + +
226A VAL* 3.3 12.8 - - + +
228A SER* 1.3 79.1 + - - +
230A GLU* 1.3 62.5 + - + +
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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 VAL* 3.2 37.0 + - - +
227A CYS* 2.9 4.8 + - - +
228A SER 4.5 0.2 - - - -
229A ARG* 1.3 82.2 - - + +
231A MET* 1.3 88.8 + - + +
249A LYS* 5.3 4.9 + - - +
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Residues in contact with MET 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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227A CYS* 2.8 21.1 + - - +
228A SER 3.4 18.9 - - - +
230A GLU* 1.3 106.4 - - + +
232A LEU* 1.3 70.5 + - - +
233A ASN 3.7 0.5 + - - -
235A LEU* 3.5 22.2 - - + -
246A PHE* 3.1 42.0 - - + +
247A ASP* 4.5 5.8 - - - +
248A SER* 3.5 21.3 - - - +
249A LYS* 5.2 9.6 - - - +
256A LEU* 6.0 2.2 - - + -
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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