Contacts of the helix formed by residues 298 - 312 (chain N) in PDB entry 2DYS
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 ASP 298 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296N GLY 5.3 0.7 - - - +
297N MET* 1.3 78.8 - - - +
299N VAL* 1.3 66.2 + - - +
300N ASP* 4.4 7.0 - - + +
301N THR* 3.3 19.1 + - - +
302N ARG* 3.2 18.4 + - - -
308P PGV 3.8 30.2 + - - -
22U ASN* 3.5 36.9 + - - +
24U ASN* 6.0 0.5 - - - +
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Residues in contact with VAL 299 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297N MET 3.5 1.4 + - - -
298N ASP* 1.3 69.8 - - - +
300N ASP* 1.3 70.2 + - - +
302N ARG* 3.3 18.9 + - - +
303N ALA* 2.9 26.2 + - - +
84O LEU* 3.6 39.4 - - + +
85O TYR* 3.6 28.3 - - + -
88O ASP* 3.7 34.9 + - + +
22U ASN* 4.2 7.2 + - - +
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Residues in contact with ASP 300 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G CDL 3.1 44.5 + - - +
298N ASP* 3.3 5.2 - - + +
299N VAL* 1.3 81.4 - - - +
301N THR* 1.3 67.5 + - - +
303N ALA* 3.1 3.7 + - - +
304N TYR* 2.9 22.7 + - - +
85O TYR* 2.8 26.8 + - - -
304P CHD 3.6 22.9 + - - +
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Residues in contact with THR 301 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297N MET* 3.9 25.4 - - + -
298N ASP* 3.3 24.4 + - - +
299N VAL 3.3 0.2 - - - -
300N ASP* 1.3 79.7 - - - +
302N ARG* 1.3 56.8 + - - +
304N TYR* 3.2 2.6 + - - +
305N PHE* 3.0 53.5 + - + -
304P CHD 2.8 43.7 + - + +
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Residues in contact with ARG 302 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293N PHE* 3.8 38.8 + - + -
297N MET* 2.7 54.2 + - + +
298N ASP 3.2 4.9 + - - +
299N VAL* 3.5 32.5 - - - +
300N ASP 3.2 0.2 - - - -
301N THR* 1.3 77.3 - - - +
303N ALA* 1.3 59.5 + - - +
306N THR* 3.0 28.4 + - - -
361N SER* 3.7 13.9 + - - +
365N ILE* 5.1 6.1 - - - +
84O LEU* 3.3 31.1 + - + +
87O MET* 4.3 9.5 - - - +
88O ASP* 3.9 9.1 + - - +
23U GLN* 3.4 27.8 - - - +
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Residues in contact with ALA 303 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G CDL 4.3 14.7 - - + +
299N VAL 2.9 9.3 + - - +
300N ASP 3.1 6.0 + - - +
302N ARG* 1.3 74.0 - - - +
304N TYR* 1.3 64.6 + - - +
306N THR* 3.4 2.4 + - - -
307N SER* 3.1 26.7 + - - -
81O LEU* 3.9 13.3 - - + +
84O LEU* 3.8 15.0 - - + +
85O TYR* 3.4 31.4 - - + +
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Residues in contact with TYR 304 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G CDL 3.6 66.8 + - + +
286N ILE* 2.8 44.3 + - - +
300N ASP 2.9 8.0 + - - +
301N THR 3.5 4.0 - - - +
303N ALA* 1.3 76.0 - - - +
305N PHE* 1.3 91.4 + + - +
307N SER* 3.1 5.9 + - - -
308N ALA* 2.9 46.9 + - + +
304P CHD 3.3 42.0 - - + -
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Residues in contact with PHE 305 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286N ILE 3.6 18.2 - - - -
287N VAL* 3.6 26.2 - - - -
288N TRP* 3.9 25.4 - + - -
289N ALA* 3.5 38.4 - - + -
290N HIS 4.6 2.2 - - - +
293N PHE* 3.9 23.9 - - + -
297N MET* 5.0 1.1 - - + -
301N THR* 3.0 44.1 + - + +
303N ALA 3.4 0.2 - - - -
304N TYR* 1.3 96.9 - + - +
306N THR* 1.3 59.9 + - - +
308N ALA* 4.1 1.8 - - - +
309N THR* 2.8 30.5 + - - -
304P CHD 3.9 14.4 - - + -
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Residues in contact with THR 306 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293N PHE* 3.8 1.3 - - - -
302N ARG 3.0 21.2 + - - -
303N ALA* 3.8 5.3 - - - -
304N TYR 3.1 1.0 + - - -
305N PHE* 1.3 78.4 - - - +
307N SER* 1.3 64.4 + - - +
309N THR* 3.8 1.9 - - - -
310N MET* 3.2 31.0 + - - +
359N ALA 3.0 29.2 + - - +
360N ASN* 3.8 22.7 - - - +
361N SER* 3.1 19.6 + - - -
77O ALA* 5.7 3.1 - - + -
80O SER* 4.3 6.5 - - - +
81O LEU* 4.6 13.4 - - + +
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Residues in contact with SER 307 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G CDL 3.4 60.3 - - - +
303N ALA 3.1 12.4 + - - -
304N TYR 3.1 7.1 + - - -
306N THR* 1.3 76.9 - - - +
308N ALA* 1.3 66.0 + - - +
310N MET* 3.1 14.3 + - - +
311N ILE* 3.2 19.0 + - - +
77O ALA* 5.3 2.0 - - - +
81O LEU* 4.3 9.9 - - - +
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Residues in contact with ALA 308 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G CDL 4.2 16.7 - - + +
283N LEU* 4.8 4.0 - - - +
286N ILE* 4.1 3.6 - - + +
287N VAL* 3.7 19.7 - - + +
304N TYR* 2.9 51.8 + - + +
305N PHE* 4.5 2.5 - - - +
307N SER* 1.3 73.0 - - - +
309N THR* 1.3 63.6 + - - +
311N ILE* 3.5 17.2 + - - +
312N ILE* 3.9 5.4 - - - +
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Residues in contact with THR 309 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244N TYR* 5.9 0.2 - - - +
287N VAL* 3.4 15.5 + - + +
290N HIS* 2.8 37.2 + - + +
305N PHE 2.8 23.0 + - - -
306N THR 3.8 3.6 - - - -
307N SER 3.2 0.8 - - - -
308N ALA* 1.3 78.8 - - - +
310N MET* 1.3 60.9 + - - +
311N ILE 3.4 0.3 + - - -
312N ILE* 3.4 21.2 + - + +
356N ILE* 4.4 0.7 - - - +
359N ALA* 3.5 23.3 - - + -
605N HEA 3.6 25.0 - - + +
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Residues in contact with MET 310 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G CDL 5.0 3.8 - - + -
306N THR* 3.2 22.7 + - - +
307N SER* 3.1 8.2 + - - +
309N THR* 1.3 74.5 - - - +
311N ILE* 1.3 65.7 + - - +
313N ALA* 3.0 24.3 + - - +
356N ILE* 3.5 37.4 - - + +
359N ALA* 3.9 15.0 - - + -
360N ASN* 4.0 14.8 - - - +
73O LEU* 3.3 26.5 - - + +
76O ILE* 3.4 40.6 - - + -
77O ALA* 4.6 15.5 - - - -
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Residues in contact with ILE 311 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C PEK 4.4 21.5 - - + -
30G LEU* 4.2 22.7 - - + -
101G CDL 3.7 57.6 - - + +
283N LEU* 4.0 18.4 - - + -
307N SER 3.2 17.6 + - - +
308N ALA 3.6 7.9 - - - +
309N THR 3.3 0.2 - - - -
310N MET* 1.3 76.6 - - - +
312N ILE* 1.3 63.3 + - - +
313N ALA 2.9 1.7 + - - -
314N ILE* 3.0 21.9 + - + +
315N PRO* 3.2 6.8 - - - +
73O LEU* 4.3 7.4 - - - -
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Residues in contact with ILE 312 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244N TYR* 3.7 30.1 - - + +
280N ILE* 4.3 15.5 - - + +
283N LEU* 3.7 47.3 - - + +
284N GLY* 4.2 3.1 - - - +
287N VAL* 4.3 12.1 - - + -
308N ALA 3.9 5.2 - - - +
309N THR* 3.5 18.4 - - + +
310N MET 3.1 1.0 - - - -
311N ILE* 1.3 75.9 - - - +
313N ALA* 1.3 56.7 + - - +
314N ILE 3.2 0.4 - - - -
315N PRO* 3.2 2.5 - - - +
316N THR* 2.7 39.2 + - - +
605N HEA 3.7 22.4 - - - +
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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