Contacts of the helix formed by residues 262 - 276 (chain A) in PDB entry 5HVO
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 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A ASP 4.1 1.6 + - - -
259A GLY* 3.3 16.8 + - - -
260A LEU 3.2 2.0 - - - +
261A LYS* 1.3 79.6 - - - +
263A PRO* 1.3 69.5 - - - +
264A LYS* 3.2 13.0 + - - +
265A VAL* 3.2 25.1 + - - +
266A GLN* 3.1 21.7 + - - +
367A ASP* 5.0 4.6 + - - -
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Residues in contact with PRO 263 (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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261A LYS 3.2 6.9 - - - +
262A SER* 1.3 83.1 - - - +
264A LYS* 1.3 59.4 + - + +
266A GLN* 3.2 8.0 + - + +
267A ASN* 2.9 41.4 + - - +
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Residues in contact with LYS 264 (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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262A SER* 3.2 8.2 + - - +
263A PRO* 1.3 81.9 - - + +
265A VAL* 1.3 56.7 + - - +
267A ASN* 3.4 11.3 + - - +
268A ARG* 3.0 29.8 + - + +
365A SER* 5.0 5.3 + - - -
367A ASP* 3.8 33.6 + - + +
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Residues in contact with VAL 265 (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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259A GLY 3.6 14.4 - - - +
260A LEU* 4.0 19.3 - - + +
262A SER* 3.2 18.9 + - - +
264A LYS* 1.3 74.3 - - - +
266A GLN* 1.3 60.1 + - - +
268A ARG* 3.1 7.4 + - - +
269A ILE* 2.8 32.7 + - + +
367A ASP* 3.5 45.5 - - + +
370A ILE* 3.5 23.8 - - + -
371A ALA* 4.2 6.3 - - + -
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Residues in contact with GLN 266 (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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260A LEU* 2.6 40.2 + - - +
261A LYS* 4.5 5.8 - - - +
262A SER 3.1 12.2 + - - +
263A PRO* 3.7 9.4 - - + +
265A VAL* 1.3 74.8 - - - +
267A ASN* 1.3 63.4 + - - +
269A ILE* 3.5 21.2 + - - +
270A ALA* 3.1 22.9 + - - +
401A LYS* 5.3 7.1 + - - +
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Residues in contact with ASN 267 (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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263A PRO* 2.9 30.5 + - - +
264A LYS* 3.5 9.6 - - - +
266A GLN* 1.3 80.0 - - - +
268A ARG* 1.3 56.1 + - - +
270A ALA* 3.1 8.7 + - - +
271A SER* 2.9 28.9 + - - -
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Residues in contact with ARG 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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264A LYS* 3.0 16.7 + - + +
265A VAL* 3.1 10.1 + - - +
267A ASN* 1.3 74.5 - - - +
269A ILE* 1.3 65.0 + - - +
271A SER* 3.3 14.3 + - - -
272A LEU* 3.0 52.3 + - + +
275A LYS* 4.1 20.0 - - - +
367A ASP 5.2 0.9 - - - +
368A GLU* 2.8 41.1 + - - +
371A ALA* 3.5 21.8 - - + -
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Residues in contact with ILE 269 (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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260A LEU* 4.2 16.2 - - + -
265A VAL* 2.8 19.6 + - + +
266A GLN* 3.7 24.9 - - - +
268A ARG* 1.3 75.6 - - - +
270A ALA* 1.3 58.9 + - - +
272A LEU* 3.1 11.2 + - - +
273A GLU* 2.8 52.2 + - - +
371A ALA* 3.8 20.9 - - - +
374A ALA* 3.4 24.2 - - + +
375A ALA* 4.5 12.3 - - + +
401A LYS* 5.7 3.1 - - - +
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Residues in contact with ALA 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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266A GLN 3.1 12.4 + - - +
267A ASN* 3.1 12.1 + - - +
269A ILE* 1.3 81.4 - - - +
271A SER* 1.3 56.0 + - - +
273A GLU* 3.3 10.0 + - - +
274A ASN* 2.9 30.7 + - - +
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Residues in contact with SER 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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267A ASN 2.9 15.9 + - - -
268A ARG* 3.6 18.0 + - - -
270A ALA* 1.3 77.4 - - - +
272A LEU* 1.3 57.4 + - - +
274A ASN* 3.5 5.9 + - - +
275A LYS* 2.9 58.1 + - - +
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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 ARG* 3.0 50.1 + - + +
269A ILE 3.5 5.2 - - - +
271A SER* 1.3 71.7 - - - +
273A GLU* 1.3 62.1 + - - +
275A LYS* 3.1 8.7 + - + -
276A PHE* 2.9 56.8 + - + +
281A LEU* 5.1 1.8 - - + -
368A GLU* 5.6 2.0 - - - +
371A ALA* 3.7 35.4 - - + +
372A LEU* 4.0 17.5 - - + -
375A ALA* 3.8 16.8 - - + -
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Residues in contact with GLU 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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269A ILE* 2.8 43.8 + - + +
270A ALA* 3.3 8.0 + - - +
272A LEU* 1.3 77.0 - - - +
274A ASN* 1.3 60.7 + - - +
276A PHE* 3.7 2.5 - - - -
277A GLN* 3.3 22.9 + - - +
374A ALA 5.1 0.3 - - - +
375A ALA* 4.7 4.9 - - + +
401A LYS* 4.6 16.3 + - - +
402A ARG* 3.2 31.4 + - - +
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Residues in contact with ASN 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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270A ALA 2.9 16.2 + - - +
271A SER* 3.8 6.7 - - - +
273A GLU* 1.3 77.5 - - - +
275A LYS* 1.3 67.9 + - - +
276A PHE 3.3 0.3 + - - -
277A GLN* 2.9 41.7 + - - +
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Residues in contact with LYS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ARG* 4.1 14.4 - - - +
271A SER* 2.9 45.6 + - - +
272A LEU* 3.1 15.9 + - + +
274A ASN* 1.3 83.2 - - - +
276A PHE* 1.3 75.1 + - + +
277A GLN* 3.4 9.1 + - - +
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Residues in contact with PHE 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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272A LEU* 2.9 46.6 + - + +
273A GLU* 3.7 4.5 - - - -
275A LYS* 1.3 89.4 - - + +
277A GLN* 1.3 54.9 + - - +
278A GLY 3.5 2.0 - - - -
279A THR* 2.8 62.8 + - + +
281A LEU* 3.8 43.7 - - + -
316A VAL* 4.4 9.9 - - + -
318A VAL* 5.0 4.3 - - + -
358A HIS* 4.1 31.0 - + - -
372A LEU* 6.6 0.2 - - + -
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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