Contacts of the helix formed by residues 311 - 324 (chain A) in PDB entry 1O62
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 HIS 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A ILE* 4.2 8.1 - - + -
288A ASN* 3.3 20.0 + - + +
309A THR 3.7 1.2 + - - -
310A LEU* 1.3 73.3 - - - +
312A PRO* 1.3 71.4 - - + +
313A LYS* 3.0 57.4 + - + +
314A ILE* 2.8 34.1 + - + +
315A SER* 3.2 7.6 + - - -
357A GLN* 2.8 33.3 + - + +
358A LYS* 4.2 29.6 - - + -
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Residues in contact with PRO 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A THR* 6.2 0.4 - - + -
310A LEU 3.3 5.8 - - - +
311A HIS* 1.3 99.3 - - + +
313A LYS* 1.3 63.2 - - + +
315A SER* 3.1 19.5 + - - +
316A LYS* 3.1 16.3 + - - +
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Residues in contact with LYS 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A TYR* 6.0 3.2 - - - -
287A ILE* 3.4 33.6 - - + +
288A ASN* 3.5 24.5 + - - +
311A HIS* 3.0 23.6 + - + +
312A PRO* 1.3 79.5 - - + +
314A ILE* 1.3 59.7 + - - +
316A LYS* 3.9 6.7 - - + +
317A LEU* 2.9 29.9 + - - +
383A SER* 4.9 0.7 + - - +
384A ILE* 3.9 35.0 + - + +
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Residues in contact with ILE 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A PHE* 4.5 2.7 - - + -
287A ILE* 3.5 36.3 - - + -
310A LEU* 3.9 19.1 - - + -
311A HIS* 2.8 12.2 + - + +
313A LYS* 1.3 77.2 - - - +
315A SER* 1.3 60.4 + - - +
317A LEU* 3.1 11.7 + - + +
318A ILE* 2.9 46.1 + - + +
330A PRO* 5.5 0.7 - - + -
357A GLN 3.9 14.8 - - - +
358A LYS 3.5 16.2 - - - +
359A GLY 3.5 20.0 - - - +
360A ILE* 4.2 17.5 - - + -
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Residues in contact with SER 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 4.2 27.7 + - - +
311A HIS 3.2 3.7 + - - -
312A PRO* 3.1 17.8 + - - +
314A ILE* 1.3 79.7 - - - +
316A LYS* 1.3 63.3 + - - +
318A ILE* 3.4 5.2 + - - +
319A GLU* 3.1 22.9 + - - +
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Residues in contact with LYS 316 (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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312A PRO 3.1 16.0 + - - +
313A LYS* 4.0 7.2 - - + +
315A SER* 1.3 80.3 + - - +
317A LEU* 1.3 56.8 + - - +
319A GLU* 3.1 6.8 + - + +
320A ASP* 2.7 70.4 + - - +
382A LYS 5.2 0.8 + - - -
383A SER* 3.3 28.3 + - - +
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Residues in contact with LEU 317 (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 PHE* 4.0 18.2 - - + -
313A LYS 2.9 20.1 + - - +
314A ILE* 3.3 11.7 - - + +
316A LYS* 1.3 75.7 - - - +
318A ILE* 1.3 62.5 + - - +
320A ASP* 4.0 0.5 - - - +
321A LEU* 3.0 35.9 + - + +
328A THR* 4.6 0.2 - - - -
360A ILE* 3.8 31.4 - - + -
380A ILE* 3.5 59.7 - - + +
383A SER* 3.6 14.5 + - - +
384A ILE* 5.0 2.9 - - + -
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Residues in contact with ILE 318 (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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310A LEU* 4.2 11.7 - - + -
314A ILE* 2.9 33.8 + - + +
315A SER* 3.7 5.6 - - - +
317A LEU* 1.3 76.1 - - - +
319A GLU* 1.3 61.8 + - - +
321A LEU 4.1 0.2 - - - -
322A LYS* 3.1 24.3 + - + +
326A ILE 5.1 0.5 - - - +
328A THR* 3.4 26.0 + - - +
329A ARG 4.2 0.4 - - - -
330A PRO* 3.8 31.0 - - + -
360A ILE* 3.6 19.1 - - + -
217B LEU* 3.7 26.9 - - + -
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Residues in contact with GLU 319 (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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315A SER 3.1 14.4 + - - +
316A LYS* 3.5 10.8 - - + +
318A ILE* 1.3 74.9 - - - +
320A ASP* 1.3 69.9 + - - +
322A LYS* 3.1 22.4 + - - +
323A ASN* 3.1 32.1 + - - +
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Residues in contact with ASP 320 (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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316A LYS* 2.7 45.8 + - - +
317A LEU 4.0 1.1 - - - +
319A GLU* 1.3 76.5 - - - +
321A LEU* 1.3 60.1 + - + +
323A ASN* 2.8 31.2 + - - +
324A LYS* 3.2 14.8 + - + +
379A LEU 5.6 1.1 - - - +
383A SER* 2.5 33.8 + - - +
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Residues in contact with LEU 321 (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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317A LEU* 3.0 28.9 + - + +
320A ASP* 1.3 77.9 - - + +
322A LYS* 1.3 52.1 + - - +
324A LYS* 3.0 13.4 + - - +
326A ILE* 2.7 51.4 + - + +
328A THR* 3.2 34.1 - - + +
376A ILE* 4.3 6.7 - - + +
379A LEU* 3.5 44.2 - - + +
380A ILE* 3.4 29.4 - - + -
383A SER* 6.1 0.2 - - - -
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Residues in contact with LYS 322 (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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318A ILE* 3.1 18.3 + - + +
319A GLU* 3.1 23.1 + - - +
320A ASP 3.0 0.4 - - - -
321A LEU* 1.3 74.4 - - - +
323A ASN* 1.3 56.4 + - - +
324A LYS 3.0 5.4 - - - -
325A GLN* 3.1 21.8 + - - +
326A ILE 3.6 9.2 + - - +
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Residues in contact with ASN 323 (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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319A GLU* 3.1 39.3 + - - +
320A ASP* 2.8 15.4 + - - +
322A LYS* 1.3 78.6 - - - +
324A LYS* 1.3 70.4 + - - +
325A GLN* 3.0 18.9 + - - +
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Residues in contact with LYS 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ASP 3.2 9.7 + - - +
321A LEU* 3.0 12.1 + - + +
322A LYS 3.0 0.8 - - - -
323A ASN* 1.3 96.6 + - - +
325A GLN* 1.3 79.6 + - - +
326A ILE* 3.2 11.2 + - + +
379A LEU* 3.7 45.0 - - + +
382A LYS* 6.3 1.6 - - - +
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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