Contacts of the helix formed by residues 267 - 278 (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 THR 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A ASP* 3.7 7.2 - - - -
238A TYR* 3.1 36.3 - - - -
241A ASP* 3.2 35.9 - - + +
245A LEU* 5.7 3.2 - - - +
266A SER* 1.3 75.5 - - - +
268A LEU* 1.4 72.1 + - - +
269A THR* 3.6 14.6 + - + +
270A GLN* 3.0 29.1 + - + +
271A GLN* 3.0 22.7 + - - +
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Residues in contact with LEU 268 (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* 3.9 20.4 - - + -
230A LEU* 3.7 24.5 - - + -
233A GLU* 3.8 18.6 - - + -
234A ASP* 3.1 28.8 + - - +
236A HIS* 4.4 14.8 - - + +
267A THR* 1.4 75.6 + - - +
269A THR* 1.4 56.1 + - - +
271A GLN* 3.1 30.4 + - - +
272A LEU* 3.0 29.2 + - - +
306A ILE* 4.7 6.3 - - + -
307A LEU* 4.7 9.6 - - + -
310A TYR* 3.5 37.6 - - + +
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Residues in contact with THR 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A HIS* 5.2 3.7 - - + -
238A TYR* 4.8 3.4 - - + -
239A GLU* 5.1 0.2 - - + -
241A ASP* 5.1 0.7 - - + -
267A THR* 3.6 24.2 - - + +
268A LEU* 1.4 76.3 - - - +
270A GLN* 1.4 55.7 + - - +
272A LEU* 3.9 4.4 - - - +
273A VAL* 3.3 29.8 + - - +
294A ALA* 3.7 24.0 + - - +
297A MET* 3.7 26.3 - - - +
298A ASP* 3.9 24.2 + - + +
306A ILE* 4.0 20.1 - - - +
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Residues in contact with GLN 270 (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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241A ASP* 3.0 29.9 - - - +
246A TYR* 3.1 28.7 + - - +
265A ALA 3.2 21.5 + - - +
266A SER* 3.5 5.8 + - - +
267A THR* 3.0 34.6 + - + +
269A THR* 1.4 72.4 - - - +
271A GLN* 1.4 64.7 + - - +
272A LEU 3.3 0.2 - - - -
273A VAL* 3.3 6.4 - - - +
274A LYS* 3.2 23.4 + - - +
287A LYS* 4.4 5.9 - - - +
290A GLU* 2.9 39.7 + - + +
291A ALA* 4.5 1.1 - - - -
294A ALA* 3.8 7.2 - - + -
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Residues in contact with GLN 271 (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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233A GLU* 2.7 27.0 + - - +
266A SER* 3.7 22.2 + - - +
267A THR 3.0 20.9 + - - +
268A LEU* 3.1 28.8 + - - +
270A GLN* 1.4 72.9 - - - +
272A LEU* 1.4 60.4 + - - +
274A LYS* 3.5 6.6 - - - +
275A ASN* 2.7 34.2 + - - +
310A TYR* 3.7 20.2 + - + -
901A M0E 2.5 47.7 + - + +
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Residues in contact with LEU 272 (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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268A LEU 3.0 16.6 + - - +
269A THR* 3.9 6.3 - - - +
271A GLN* 1.4 71.3 - - - +
273A VAL* 1.4 66.0 + - - +
275A ASN* 3.0 7.6 + - - +
276A LEU* 3.0 50.5 + - + +
297A MET* 3.7 24.7 - - + -
306A ILE* 3.5 31.0 - - + +
309A LEU* 3.8 16.8 - - + +
310A TYR* 3.8 36.3 - - + +
313A GLU* 4.3 6.7 - - + -
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Residues in contact with VAL 273 (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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91A ILE* 5.5 1.3 - - + -
269A THR 3.3 16.7 + - - +
270A GLN* 3.3 17.5 - - - +
272A LEU* 1.4 77.1 - - - +
274A LYS* 1.3 54.8 + - - +
277A PHE* 2.8 50.4 + - + +
278A LEU* 3.5 3.9 + - - +
290A GLU* 3.4 34.1 - - + +
293A MET* 3.8 32.5 - - + +
294A ALA 4.3 0.7 - - - +
297A MET* 3.6 25.1 - - + +
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Residues in contact with LYS 274 (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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266A SER* 6.2 0.2 - - - -
270A GLN 3.2 19.6 + - - +
271A GLN* 3.5 6.3 - - - +
272A LEU 3.2 0.4 - - - -
273A VAL* 1.3 75.4 - - - +
275A ASN* 1.3 60.4 + - - +
278A LEU* 3.1 42.5 + - - +
279A SER 4.9 0.2 - - - +
286A ARG* 3.6 38.6 - - - +
290A GLU* 3.6 13.2 - - - +
901A M0E 2.7 91.5 + - - +
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Residues in contact with ASN 275 (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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271A GLN 2.7 24.4 + - - +
272A LEU* 3.0 6.0 + - - +
274A LYS* 1.3 82.8 - - - +
276A LEU* 1.3 59.8 + - - +
278A LEU 4.7 3.3 - - - +
313A GLU* 3.6 32.2 - - + +
314A VAL* 5.3 7.9 - - - +
315A TYR* 4.7 5.2 + - - +
325A ARG* 3.6 19.3 + - - +
901A M0E 2.8 40.0 + - - +
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Residues in contact with LEU 276 (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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94A ARG* 3.3 36.7 + - + +
95A ILE* 4.9 4.5 - - + -
99A VAL* 4.5 16.4 - - + -
100A TRP* 4.0 14.6 - - + +
272A LEU* 3.0 33.0 + - + +
275A ASN* 1.3 77.3 - - - +
277A PHE* 1.4 85.2 + - + +
297A MET* 4.5 10.3 - - + -
309A LEU* 4.7 11.0 - - + +
313A GLU* 3.4 38.8 - - + +
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Residues in contact with PHE 277 (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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90A LYS 4.3 4.5 - - - -
91A ILE* 3.8 35.9 - - + -
94A ARG* 3.6 42.6 - - + +
95A ILE* 4.9 2.0 - - + -
273A VAL* 2.8 33.6 + - + +
276A LEU* 1.4 97.8 - - + +
278A LEU* 1.3 61.4 + - + +
293A MET* 3.9 27.1 - - + +
297A MET* 4.3 13.5 - - + -
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Residues in contact with LEU 278 (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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273A VAL 3.5 7.2 - - - +
274A LYS* 3.1 35.6 + - - +
275A ASN 4.7 3.8 - - - +
277A PHE* 1.3 87.1 - - + +
279A SER* 1.3 64.0 + - - +
286A ARG* 3.4 42.4 - - + +
289A ASN* 5.5 7.4 - - - +
290A GLU* 3.6 20.2 - - + +
293A MET* 3.6 33.0 - - + -
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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