Contacts of the helix formed by residues 267 - 280 (chain A) in PDB entry 5H15
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 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A ARG* 3.9 15.1 + - - +
265A ILE* 3.3 0.6 - - - +
266A ASN* 1.4 85.3 - - - +
268A LYS* 1.3 59.3 + - - +
269A ARG* 3.8 7.6 + - - +
270A MET* 3.1 28.6 + - - +
271A MET* 2.9 27.4 + - - +
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Residues in contact with LYS 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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266A ASN 4.8 1.6 - - - +
267A SER* 1.3 74.1 - - - +
269A ARG* 1.3 56.8 + - - +
271A MET* 3.5 5.8 + - - +
272A ASN* 3.0 32.7 + - - +
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Residues in contact with ARG 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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267A SER* 4.0 7.6 - - - +
268A LYS* 1.3 78.7 - - - +
270A MET* 1.4 56.9 + - - +
272A ASN* 3.4 4.4 + - - +
273A ALA* 3.0 27.9 + - - +
292A GLN* 2.9 31.6 + - - +
293A LYS 3.1 28.1 + - - +
294A ILE* 3.5 29.8 - - + +
295A HIS 5.5 1.0 - - - +
296A PHE* 6.1 2.4 - - - -
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Residues in contact with MET 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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217A LEU* 3.7 29.8 - - + -
226A VAL* 4.2 9.0 - - + -
227A ALA* 3.9 28.0 - - + -
229A PHE* 4.0 10.3 - - + -
264A ARG 3.8 13.7 - - - +
265A ILE* 3.4 25.4 - - + +
267A SER* 3.1 18.2 + - - +
269A ARG* 1.4 76.2 - - + +
271A MET* 1.3 59.4 + - - +
272A ASN 3.1 0.2 - - - -
273A ALA* 3.2 9.0 + - - +
274A ILE* 2.9 36.7 + - + +
292A GLN* 4.6 1.3 - - - -
294A ILE* 3.9 24.7 - - + -
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Residues in contact with MET 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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265A ILE 3.7 13.7 - - - +
266A ASN* 3.5 26.2 - - - +
267A SER 2.9 17.5 + - - +
268A LYS* 4.0 5.6 - - - +
270A MET* 1.3 74.7 - - - +
272A ASN* 1.4 57.6 + - - +
274A ILE* 3.6 9.3 + - + +
275A LYS* 3.1 26.6 + - - +
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Residues in contact with ASN 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 LYS 3.0 18.3 + - - +
269A ARG* 3.9 4.4 - - - +
270A MET 3.1 0.2 - - - -
271A MET* 1.4 75.1 - - - +
273A ALA* 1.4 59.1 + - - +
275A LYS* 3.2 17.1 + - - +
276A GLU* 2.9 57.1 + - - +
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Residues in contact with ALA 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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226A VAL* 3.8 17.0 - - + +
269A ARG 3.0 14.7 + - - +
270A MET* 3.2 9.2 + - - +
272A ASN* 1.4 76.4 + - - +
274A ILE* 1.3 55.8 + - - +
276A GLU* 3.4 12.1 + - - +
277A SER* 3.0 27.9 + - - -
289A PHE* 4.0 6.5 - - + -
292A GLN* 3.4 36.8 - - + +
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Residues in contact with ILE 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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199A HIS* 6.0 0.4 - - + +
202A ASP* 4.8 1.6 - - - +
205A LEU* 4.0 35.7 - - + -
217A LEU* 4.3 16.4 - - + -
226A VAL* 3.9 16.4 - - + -
265A ILE* 4.4 18.8 - - + +
270A MET* 2.9 27.0 + - + +
271A MET* 3.8 7.2 - - + +
273A ALA* 1.3 70.2 - - - +
275A LYS* 1.3 68.2 + - - +
277A SER* 2.7 25.5 + - - -
278A TYR* 3.5 22.6 - - + -
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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
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271A MET 3.1 15.8 + - - +
272A ASN* 3.2 20.4 + - - +
274A ILE* 1.3 77.3 - - - +
276A GLU* 1.3 61.5 + - + +
278A TYR* 3.2 25.2 + - + +
279A ASP* 3.4 22.4 + - - +
62D GLN* 4.6 16.6 + - - -
63D ARG* 6.2 0.2 - - - +
64D ARG* 6.3 0.6 - - - +
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Residues in contact with GLU 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 ASN* 2.9 48.9 + - - +
273A ALA* 3.7 10.3 - - - +
274A ILE 3.3 0.2 - - - -
275A LYS* 1.3 73.4 - - + +
277A SER* 1.4 55.1 + - - +
279A ASP* 2.9 34.1 + - + +
280A TYR* 3.1 10.0 + - - -
289A PHE* 3.7 19.5 - - + -
292A GLN* 5.1 6.9 + - - -
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Residues in contact with SER 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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205A LEU* 5.1 0.2 - - - +
219A ASN* 2.8 22.3 + - - +
222A THR* 2.7 28.1 + - - +
224A THR* 3.4 19.9 + - - -
226A VAL* 3.7 21.1 - - - +
273A ALA 3.0 11.4 + - - -
274A ILE* 2.7 21.3 + - - +
276A GLU* 1.4 73.6 - - - +
278A TYR* 1.3 55.4 + - - +
279A ASP 3.7 0.2 + - - -
280A TYR* 3.8 7.8 + - - +
289A PHE* 3.6 16.7 - - - -
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Residues in contact with TYR 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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202A ASP* 2.6 41.2 + - - -
204A ASN* 3.1 13.3 + - - +
205A LEU* 4.9 1.5 - - + +
219A ASN* 3.6 22.4 - - - -
221A GLN* 3.3 35.0 - - - -
222A THR* 4.0 12.4 - - + +
274A ILE* 3.5 31.4 + - + -
275A LYS* 3.2 12.7 + - + +
276A GLU 3.1 0.4 - - - -
277A SER* 1.3 79.1 + - - +
279A ASP* 1.4 60.7 + - - +
280A TYR 3.5 1.5 - - - +
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Residues in contact with ASP 279 (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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275A LYS* 3.6 30.0 + - - +
276A GLU* 2.9 21.5 + - - +
278A TYR* 1.4 77.5 - - - +
280A TYR* 1.4 63.5 + - - +
157B ASN 5.4 4.0 - - - +
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Residues in contact with TYR 280 (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 THR* 4.2 25.5 - - - +
223A ASP 5.6 1.3 - - - -
224A THR* 3.4 20.9 - - + -
276A GLU 3.1 5.0 + - - +
277A SER 3.8 11.0 - - - +
278A TYR 3.5 1.8 - - - +
279A ASP* 1.4 81.2 - - - +
288A PRO* 3.5 26.3 - - - +
289A PHE* 3.3 52.2 + + + -
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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