Contacts of the helix formed by residues 315 - 328 (chain F) in PDB entry 6C3P
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 ALA 315 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311F LEU 3.7 3.0 + - - +
312F LEU* 2.6 29.5 + - + +
314F PHE* 1.3 71.6 - - - +
316F GLY* 1.3 63.1 + - - +
317F PRO 3.6 0.2 - - - -
318F LEU* 3.7 23.8 - - + +
319F CYS* 3.6 14.9 + - - +
362F LEU* 4.4 3.4 - - - +
365F ALA* 6.1 3.8 - - + -
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Residues in contact with GLY 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313F GLY 2.9 15.5 + - - -
314F PHE 3.0 1.2 - - - -
315F ALA* 1.3 74.2 - - - +
317F PRO* 1.3 65.4 - - - +
319F CYS* 2.8 28.1 + - - +
320F ILE* 3.3 10.7 + - - +
362F LEU* 3.6 20.5 - - - +
366F LEU* 6.0 1.6 - - - -
585F ILE* 4.9 0.7 - - - -
1288F LEU* 4.7 8.5 - - - -
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Residues in contact with PRO 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313F GLY 4.2 0.2 - - - +
314F PHE* 3.3 18.6 - - + +
316F GLY* 1.3 88.7 - - - +
318F LEU* 1.3 61.8 + - + +
320F ILE* 2.8 26.8 + - + +
321F PHE* 2.9 14.6 + - - +
451F LEU* 5.8 2.5 - - + -
578F ALA* 4.2 14.2 - - + +
582F LEU* 3.8 39.9 - - + +
585F ILE* 3.6 28.0 - - + -
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Residues in contact with LEU 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314F PHE* 4.8 5.2 - - + +
315F ALA* 3.7 29.4 - - + +
316F GLY 3.1 0.4 + - - -
317F PRO* 1.3 76.4 - - - +
319F CYS* 1.3 63.2 + - - +
321F PHE* 3.4 8.3 + - + +
322F GLY* 2.9 20.3 + - - -
358F LEU* 5.9 0.2 - - - +
451F LEU* 4.1 30.1 - - + -
454F TYR* 6.5 0.4 - - + -
455F ILE* 3.9 28.0 - - + -
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Residues in contact with CYS 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315F ALA 3.6 4.5 + - - +
316F GLY 2.8 12.7 + - - +
318F LEU* 1.3 78.0 - - - +
320F ILE* 1.3 57.9 + - - +
323F ILE* 2.8 48.0 + - - +
358F LEU* 3.2 36.5 - - + +
359F ALA* 4.0 0.9 - - - -
362F LEU* 3.3 42.4 - - + -
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Residues in contact with ILE 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316F GLY 3.7 5.8 - - - +
317F PRO* 2.8 20.5 + - + +
319F CYS* 1.3 77.9 - - - +
321F PHE* 1.3 62.7 + - - +
323F ILE* 3.2 9.7 + - - +
324F VAL* 3.0 38.0 + - + +
362F LEU* 5.0 3.4 - - + -
577F PHE* 4.6 9.2 - - + -
578F ALA* 4.7 8.1 - - + -
581F SER* 3.6 22.9 - - - +
1281F GLY 4.7 0.7 - - - +
1284F LEU* 3.5 26.9 - - + -
1285F THR* 3.3 23.6 - - - +
1288F LEU* 3.8 26.7 - - + -
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Residues in contact with PHE 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317F PRO 2.9 10.7 + - - +
318F LEU* 3.7 10.8 - - + +
320F ILE* 1.3 76.9 - - - +
322F GLY* 1.3 63.6 + - - +
324F VAL* 3.2 4.9 + - - +
325F ASP* 2.9 51.4 + - + +
455F ILE* 4.8 21.1 - - + -
456F LEU* 4.4 12.3 - - + -
574F SER* 3.1 29.4 - - - -
575F VAL* 4.1 18.2 - - + -
578F ALA* 4.1 20.3 - - + +
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Residues in contact with GLY 322 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318F LEU 2.9 14.8 + - - -
319F CYS 3.7 2.9 - - - -
321F PHE* 1.3 76.2 - - - +
323F ILE* 1.3 63.6 + - - +
325F ASP* 2.6 16.6 - - - +
326F HIS* 2.3 42.6 + - - -
358F LEU* 4.1 9.0 - - - -
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Residues in contact with ILE 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319F CYS* 2.8 40.0 + - - +
320F ILE* 3.3 9.6 - - + +
322F GLY* 1.3 71.3 - - - +
324F VAL* 1.3 69.4 + - + +
326F HIS* 3.8 1.6 - - - +
327F LEU* 3.0 23.1 + - + +
355F ALA* 4.7 17.5 - - + +
358F LEU* 3.6 13.4 - - + +
359F ALA* 4.4 14.1 - - + -
362F LEU* 5.2 3.1 - - + -
1263F ALA* 5.2 4.7 - - + -
1267F ILE* 3.5 27.8 - - + -
1280F VAL* 4.6 3.4 - - + -
1284F LEU* 3.6 36.6 - - + -
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Residues in contact with VAL 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320F ILE* 3.0 24.6 + - + +
321F PHE* 4.7 0.2 - - - -
323F ILE* 1.3 81.5 - - + +
325F ASP* 1.3 58.4 + - - +
327F LEU* 3.2 8.9 + - - +
328F GLY* 2.9 22.5 + - - -
573F PRO 4.7 3.1 - - - +
574F SER* 3.5 37.5 - - - +
577F PHE* 5.8 2.5 - - + -
578F ALA* 6.2 0.2 - - + -
1277F ALA* 4.7 21.1 - - + +
1278F GLY* 5.2 4.0 - - - +
1280F VAL* 6.3 0.2 - - + -
1281F GLY* 4.3 24.5 - - - +
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Residues in contact with ASP 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321F PHE* 2.9 43.1 + - + +
322F GLY* 2.6 17.1 - - - +
324F VAL* 1.3 75.9 - - - +
326F HIS* 1.3 95.6 + - - +
328F GLY* 3.1 14.4 + - - +
329F LYS* 4.2 2.4 + - - +
574F SER* 4.4 12.1 - - - +
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Residues in contact with HIS 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322F GLY* 2.3 36.2 + - - +
323F ILE 3.9 2.7 - - - +
325F ASP* 1.3 93.4 + - - +
327F LEU* 1.3 61.5 + - - +
328F GLY 3.6 0.2 + - - -
329F LYS 4.0 12.0 + - - -
354F ASN* 2.9 43.5 + - - +
355F ALA* 4.3 11.7 - - + -
358F LEU* 3.8 23.2 - - + +
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Residues in contact with LEU 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323F ILE* 3.0 14.0 + - + +
324F VAL* 3.4 10.8 - - - +
325F ASP 3.2 0.2 - - - -
326F HIS* 1.3 73.0 - - - +
328F GLY* 1.3 68.3 + - - +
329F LYS* 2.8 11.5 + - - -
355F ALA* 5.4 2.2 - - + +
1267F ILE* 4.0 27.4 - - + +
1270F SER* 3.4 32.3 - - - +
1271F LEU* 4.4 24.7 - - + +
1277F ALA* 3.5 27.8 - - + -
1280F VAL* 4.6 4.0 - - + -
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Residues in contact with GLY 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324F VAL 2.9 13.8 + - - -
325F ASP* 3.1 12.1 + - - -
327F LEU* 1.3 76.6 - - - +
329F LYS* 1.3 73.5 + - - +
1277F ALA* 6.4 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