Contacts of the helix formed by residues 310 - 323 (chain F) in PDB entry 3DUF
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 ASN 310 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212F MET* 5.8 0.2 - - - -
215F GLU* 3.5 18.2 - - - +
305F SER 4.7 8.3 + - - -
308F LEU 3.8 11.6 + - - +
309F PRO* 1.3 74.1 - - - +
311F PHE* 1.3 69.8 + - + +
312F LYS* 2.8 59.8 + - - +
313F ASP* 2.8 29.1 + - - +
314F VAL* 3.3 16.9 + - - +
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Residues in contact with PHE 311 (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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215F GLU* 3.0 42.0 + - - +
218F LYS* 4.0 38.8 - - + -
219F ALA 4.2 4.3 - - - +
222F GLU* 5.5 9.6 - - + -
310F ASN* 1.3 84.2 - - + +
312F LYS* 1.3 83.2 + - + +
314F VAL* 3.0 5.6 + - - +
315F ILE* 2.8 41.6 + - + +
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Residues in contact with LYS 312 (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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310F ASN* 2.8 33.5 + - - +
311F PHE* 1.3 97.5 - - + +
313F ASP* 1.3 57.4 + - - +
315F ILE* 3.3 10.1 + - - +
316F GLU* 3.0 27.7 + - - +
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Residues in contact with ASP 313 (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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291F VAL* 4.1 18.4 - - + -
308F LEU 4.3 0.9 - - - +
309F PRO* 3.6 8.7 - - - +
310F ASN* 2.8 40.8 + - - +
312F LYS* 1.3 72.9 - - - +
314F VAL* 1.3 64.4 + - - +
315F ILE 2.9 4.7 - - - -
316F GLU* 3.3 12.8 + - - +
317F THR* 3.0 31.7 + - - +
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Residues in contact with VAL 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206F ILE* 4.5 10.8 - - + -
212F MET* 5.9 0.7 - - - -
215F GLU* 4.5 9.4 - - + +
216F SER* 4.4 13.5 - - - +
219F ALA* 3.5 22.2 - - + -
223F LEU* 6.2 0.2 - - + -
257F ILE* 4.0 17.1 - - + +
259F VAL* 3.9 31.2 - - + -
291F VAL* 4.3 11.2 - - + -
310F ASN 3.5 13.7 - - - +
311F PHE* 3.0 10.4 + - - +
313F ASP* 1.3 77.1 - - - +
315F ILE* 1.3 58.0 + - - +
318F ALA* 3.2 24.8 + - - +
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Residues in contact with ILE 315 (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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219F ALA* 3.2 42.8 - - + +
222F GLU* 4.1 18.8 - - + -
223F LEU* 3.8 14.4 - - + -
226F GLU* 4.7 7.0 - - - +
311F PHE* 2.8 28.6 + - + +
312F LYS* 3.3 12.3 - - - +
313F ASP 2.9 0.2 - - - -
314F VAL* 1.3 77.1 - - - +
316F GLU* 1.3 67.7 + - + +
318F ALA* 3.2 3.1 + - - +
319F LYS* 3.1 46.1 + - + +
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Residues in contact with GLU 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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312F LYS 3.0 16.6 + - - +
313F ASP* 3.3 11.7 + - - +
315F ILE* 1.3 79.6 - - + +
317F THR* 1.3 64.6 + - - +
319F LYS* 3.6 6.7 + - - +
320F LYS* 3.3 26.1 + - + +
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Residues in contact with THR 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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257F ILE* 4.1 13.6 - - + +
289F LEU* 4.0 28.3 - - + -
290F ARG 4.4 6.2 + - - +
291F VAL* 3.4 28.1 - - + +
313F ASP* 3.0 17.3 + - - +
314F VAL 4.4 1.3 - - - -
316F GLU* 1.3 78.4 + - - +
318F ALA* 1.3 63.3 + - - +
320F LYS* 3.4 9.0 + - + +
321F VAL* 3.3 22.2 + - - +
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Residues in contact with ALA 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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204F ILE* 4.3 13.5 - - + +
206F ILE* 5.2 2.7 - - + -
223F LEU* 4.0 27.4 - - + -
228F ILE* 5.4 0.2 - - - -
257F ILE* 4.2 14.5 - - + +
314F VAL 3.2 19.2 + - - +
315F ILE 3.2 5.9 + - - +
317F THR* 1.3 78.9 - - - +
319F LYS* 1.3 59.2 + - - +
320F LYS 3.2 0.4 - - - -
321F VAL* 3.4 2.9 + - - +
322F MET* 3.0 33.4 + - + +
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Residues in contact with LYS 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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223F LEU* 4.2 12.8 - - + -
226F GLU* 2.8 32.3 + - - +
228F ILE* 4.3 10.8 - - + -
315F ILE* 3.1 34.9 + - + +
316F GLU* 3.6 6.7 + - - +
317F THR 3.4 0.2 - - - -
318F ALA* 1.3 76.2 - - - +
320F LYS* 1.3 57.4 + - - +
322F MET* 3.8 6.3 - - - -
323F ASN* 2.6 47.3 + - - +
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Residues in contact with LYS 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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289F LEU* 4.2 22.9 - - + +
316F GLU* 3.3 20.8 + - + +
317F THR* 3.7 9.6 - - + +
318F ALA 3.2 0.6 - - - -
319F LYS* 1.3 75.4 - - - +
321F VAL* 1.3 63.9 + - - +
322F MET 3.3 0.4 - - - -
323F ASN* 3.9 3.8 - - - +
324F PHE* 3.5 23.8 + - + +
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Residues in contact with VAL 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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204F ILE* 4.0 9.0 - - + -
255F ARG* 3.1 44.2 + - + -
256F ALA 4.4 8.1 - - - +
257F ILE* 3.7 15.9 - - + -
286F ALA* 3.8 13.5 - - + +
287F PRO* 3.9 10.5 - - + +
289F LEU* 3.5 35.9 - - + -
317F THR 3.3 12.2 + - - +
318F ALA 4.0 4.0 - - - +
320F LYS* 1.3 75.8 - - - +
322F MET* 1.3 61.6 + - - +
324F PHE* 3.6 11.8 - - - +
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Residues in contact with MET 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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203F ASP* 3.6 29.8 - - + +
204F ILE* 4.0 20.9 - - + -
228F ILE* 3.9 35.9 - - + -
255F ARG* 3.6 39.5 + - - +
318F ALA 3.0 25.6 + - - +
319F LYS* 4.1 6.5 - - - +
320F LYS 3.3 0.2 - - - -
321F VAL* 1.3 79.0 - - - +
323F ASN* 1.3 61.8 + - - +
324F PHE* 3.1 9.2 + - - +
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Residues in contact with ASN 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 LYS* 2.6 41.5 + - - +
320F LYS* 3.9 5.4 - - - -
322F MET* 1.3 78.2 - - - +
324F PHE* 1.3 64.9 + - - +
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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