Contacts of the helix formed by residues 222 - 234 (chain A) in PDB entry 5HLB
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 PRO 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A SER 5.6 0.2 - - - +
220A GLY 3.7 8.3 - - - +
221A PHE* 1.4 85.5 - - + +
223A ASP* 1.4 64.8 + - - +
224A LEU* 3.1 8.8 + - + +
225A LEU* 3.3 26.6 + - + +
226A VAL* 3.3 11.1 + - - +
339A VAL 4.3 9.4 - - - +
340A GLU* 4.2 23.1 - - + +
347A GLN* 3.9 24.0 - - - +
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Residues in contact with ASP 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 ARG* 4.2 22.3 + - - -
221A PHE 3.7 2.2 + - - +
222A PRO* 1.4 70.9 - - - +
224A LEU* 1.4 57.7 + - + +
226A VAL* 3.4 10.6 - - + +
227A ASP* 3.0 39.3 + - - +
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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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222A PRO* 3.1 4.6 - - + +
223A ASP* 1.4 75.1 - - + +
225A LEU* 1.4 53.9 + - - +
226A VAL 3.2 1.3 - - - -
227A ASP* 3.0 19.7 + - + +
228A THR* 2.8 35.9 + - - -
344A LEU* 4.3 21.5 - - + -
347A GLN* 3.6 17.3 - - - +
385A ILE* 5.5 10.1 - - + -
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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 PHE* 3.6 21.5 - - + -
222A PRO* 3.3 14.9 + - + +
224A LEU* 1.4 75.0 - - - +
226A VAL* 1.4 56.1 + - - +
228A THR* 3.8 4.9 - - - -
229A LEU* 2.9 30.8 + - - +
311A MET* 3.6 24.2 - - + -
327A PHE* 4.4 16.4 - - + -
339A VAL* 3.6 21.3 - - + -
342A LEU* 4.9 2.2 - - + -
347A GLN* 3.2 52.1 + - + +
351A VAL* 4.2 13.6 - - + +
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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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218A ARG* 4.3 28.5 - - - +
221A PHE* 4.5 5.6 - - + -
222A PRO 3.3 12.0 + - - +
223A ASP* 3.4 17.3 - - + +
224A LEU 3.2 0.2 - - - -
225A LEU* 1.4 77.4 - - - +
227A ASP* 1.4 63.2 + - - +
229A LEU* 3.5 4.7 + - - +
230A LEU* 3.1 40.4 + - + +
307A LEU* 3.8 28.3 - - + -
311A MET* 4.0 20.0 - - + -
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Residues in contact with ASP 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 ASP* 3.0 26.3 + - - +
224A LEU* 3.0 20.9 + - + +
226A VAL* 1.4 79.3 - - - +
228A THR* 1.4 55.6 + - - +
229A LEU 3.1 1.1 - - - -
230A LEU* 3.0 12.2 + - - +
231A ALA* 2.7 37.0 + - - +
380A LEU* 4.9 1.1 - - + -
385A ILE* 4.7 25.9 - - + +
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Residues in contact with THR 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 LEU 2.8 22.2 + - - -
225A LEU* 3.8 9.0 - - - -
227A ASP* 1.4 70.8 - - - +
229A LEU* 1.4 61.1 + - - +
231A ALA* 3.6 3.1 + - - +
232A THR* 3.4 25.8 + - - +
344A LEU* 3.6 19.0 - - + +
347A GLN* 3.8 2.8 + - + -
348A ALA* 3.8 35.0 - - + +
351A VAL* 3.8 9.3 - - + +
376A VAL* 4.2 7.0 - - + -
380A LEU* 3.5 29.7 - - + +
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Residues in contact with LEU 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 LEU 2.9 18.1 + - - +
226A VAL 3.5 5.4 - - - +
228A THR* 1.4 73.9 - - - +
230A LEU* 1.4 59.4 + - + +
232A THR* 2.6 20.8 + - - -
233A GLU* 3.0 17.6 + - + +
268A LEU* 3.9 28.0 - - + -
307A LEU* 4.5 10.1 - - + -
310A TYR* 3.7 37.2 - - + +
311A MET* 4.2 25.4 - - + -
327A PHE* 4.4 11.0 - - + -
351A VAL* 3.7 23.3 - - + +
354A VAL* 5.4 3.4 - - + -
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Residues in contact with LEU 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* 3.1 30.3 + - + +
227A ASP* 3.0 12.8 + - - +
229A LEU* 1.4 71.6 - - + +
231A ALA* 1.3 58.5 + - - +
232A THR 3.1 4.7 - - - -
234A ASP* 2.8 54.1 + - + +
235A ARG* 5.5 4.0 - - - +
236A HIS* 4.0 25.6 - - + -
268A LEU* 3.7 28.9 - - + -
307A LEU* 5.0 5.6 - - + -
383A GLN* 5.9 1.6 - - - -
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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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227A ASP 2.7 19.0 + - - +
228A THR 3.6 7.9 - - - +
229A LEU 3.3 0.2 - - - -
230A LEU* 1.3 71.1 - - - +
232A THR* 1.4 60.5 + - + +
379A LEU* 4.7 15.2 - - + +
380A LEU* 4.1 28.5 - - + -
383A GLN* 4.8 24.7 - - + +
385A ILE* 4.8 5.4 - - + -
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Residues in contact with THR 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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228A THR 3.4 14.4 - - - +
229A LEU 2.6 17.8 + - - -
231A ALA* 1.4 83.0 - - + +
233A GLU* 1.4 74.0 + - - +
234A ASP 3.9 0.7 - - - -
351A VAL* 3.2 19.4 - - + +
352A GLY* 5.8 0.7 - - - -
355A LYS* 4.2 15.4 + - - -
372A ARG* 6.5 0.2 - - - -
376A VAL* 3.6 32.1 - - + -
379A LEU* 4.7 16.6 - - + +
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Residues in contact with GLU 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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229A LEU* 3.0 13.7 + - + +
232A THR* 1.4 92.6 + - - +
234A ASP* 1.4 73.0 + - - +
266A SER 4.1 11.4 - - - +
268A LEU* 3.8 22.4 - - + -
271A GLN* 2.7 32.0 + - - +
310A TYR* 4.4 4.3 - - - +
351A VAL 4.9 0.2 - - - +
354A VAL* 3.3 25.1 - - + +
355A LYS* 3.7 26.2 + - - +
901A M0E 3.4 8.6 + - - +
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Residues in contact with ASP 234 (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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230A LEU* 2.8 51.7 + - + +
232A THR 3.9 0.4 - - - -
233A GLU* 1.4 85.7 - - - +
235A ARG* 1.4 67.8 + - - +
236A HIS* 3.5 11.5 + - - +
238A TYR* 3.0 34.4 + - + -
267A THR* 3.7 4.5 - - - -
268A LEU* 3.1 39.8 + - + +
383A GLN* 5.9 0.7 + - - -
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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