Contacts of the helix formed by residues 302 - 317 (chain G) in PDB entry 1R4N
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 PRO 302 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168G GLU* 5.2 1.3 - - - +
293G ARG* 3.9 27.1 - - - +
300G GLN 3.2 6.2 - - - +
301G THR* 1.3 101.6 - - + +
303G SER* 1.3 70.5 + - - +
304G PHE* 3.2 5.2 + - + +
305G TRP* 3.4 30.2 + - + +
306G ILE* 3.5 3.1 + - - +
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Residues in contact with SER 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302G PRO* 1.3 74.0 - - - +
304G PHE* 1.3 68.5 + - - +
306G ILE* 3.2 14.1 + - - +
307G LEU* 3.4 14.9 + - - +
375G ILE* 4.0 21.8 - - - +
379G GLU* 3.5 23.7 + - - -
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Residues in contact with PHE 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170G PRO* 3.6 32.3 - - + -
171G VAL 4.4 5.6 - - - -
172G ILE* 4.0 21.1 - - + -
288G ILE* 4.4 12.6 - - + -
302G PRO* 3.2 4.9 + - + +
303G SER* 1.3 78.1 - - - +
305G TRP* 1.3 105.4 + + + +
307G LEU* 2.8 33.0 + - + +
308G ALA* 3.0 12.2 + - + -
383G LEU* 5.7 1.1 - - + -
390G LEU* 3.7 33.7 - - + -
392G VAL* 3.8 30.1 - - + -
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Residues in contact with TRP 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168G GLU* 3.1 25.7 + - - -
170G PRO* 5.3 0.8 - - + +
288G ILE* 3.2 43.1 - - + -
291G ASP* 3.9 12.6 - - + -
293G ARG* 3.4 32.0 - - + +
294G CYS* 3.7 21.4 - - + -
297G ILE* 6.4 0.7 - - - -
301G THR* 3.9 17.5 - - + -
302G PRO* 3.4 27.6 + - + -
304G PHE* 1.3 99.7 - + + +
306G ILE* 1.3 63.3 + - - +
308G ALA* 2.9 19.5 + - + +
309G ARG* 2.9 15.1 + - - +
392G VAL* 4.2 12.3 - - + -
394G ARG* 3.3 28.0 - - - -
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Residues in contact with ILE 306 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297G ILE* 4.2 10.5 - - + -
301G THR* 3.7 24.7 - - + +
302G PRO 3.5 3.9 + - - +
303G SER* 3.2 10.4 + - - +
304G PHE 3.2 0.6 - - - -
305G TRP* 1.3 76.2 - - - +
307G LEU* 1.3 55.8 + - - +
309G ARG* 3.1 7.9 + - - +
310G ALA* 2.6 36.6 + - + +
361G VAL* 4.4 10.1 - - + -
364G LEU* 3.7 17.5 - - + +
365G LEU* 3.6 30.3 - - + +
368G ILE* 4.1 19.7 - - + -
370G GLN* 4.4 11.2 - - - +
375G ILE* 4.2 18.4 - - + -
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Residues in contact with LEU 307 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172G ILE* 4.1 20.6 - - + -
303G SER* 3.6 20.6 - - - +
304G PHE* 2.8 13.5 + - + +
306G ILE* 1.3 77.7 - - - +
308G ALA* 1.3 61.0 + - - +
310G ALA* 3.4 6.0 - - - +
311G LEU* 2.9 26.2 + - - +
361G VAL* 3.7 22.9 - - + -
375G ILE* 3.8 26.2 - - + -
379G GLU* 4.7 15.0 - - + +
380G LEU* 4.6 5.4 - - + -
383G LEU* 3.0 41.0 - - + +
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Residues in contact with ALA 308 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288G ILE* 4.1 17.0 - - + -
289G PHE* 3.4 8.6 - - + -
294G CYS* 4.2 6.3 - - - -
304G PHE* 3.0 12.9 + - + +
305G TRP* 2.9 36.7 + - + +
307G LEU* 1.3 74.4 - - - +
309G ARG* 1.3 66.8 + - - +
311G LEU* 2.8 21.9 + - - +
312G LYS 2.9 10.4 + - - -
383G LEU* 5.3 0.6 - - - +
390G LEU* 5.3 5.2 - - + -
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Residues in contact with ARG 309 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294G CYS* 3.4 27.8 + - - +
295G ILE* 2.7 42.4 + - - +
297G ILE* 3.7 19.0 - - + +
305G TRP 2.9 9.2 + - - +
306G ILE 3.6 5.4 - - - +
308G ALA* 1.3 74.8 - - - +
310G ALA* 1.3 54.8 + - - +
311G LEU 2.7 12.1 + - - -
312G LYS* 2.8 20.9 + - - +
313G GLU* 2.8 54.6 + - + +
364G LEU* 3.2 27.6 - - + +
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Residues in contact with ALA 310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306G ILE 2.6 21.2 + - - +
307G LEU* 3.4 8.1 - - - +
308G ALA 3.2 0.2 - - - -
309G ARG* 1.3 72.8 - - - +
311G LEU* 1.3 58.1 + - - +
313G GLU* 4.1 1.6 - - - -
314G PHE* 3.5 12.0 + - - +
357G VAL* 3.6 12.1 - - + +
360G HIS* 3.6 17.1 - - - +
361G VAL* 3.3 45.3 - - + +
364G LEU* 3.6 8.7 - - + +
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Residues in contact with LEU 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289G PHE* 3.8 10.3 - - + -
307G LEU 2.9 6.7 + - - +
308G ALA* 2.8 10.2 + - - +
309G ARG 2.7 4.4 + - - -
310G ALA* 1.3 73.4 - - - +
312G LYS* 1.3 58.0 + - - +
313G GLU 3.1 1.6 - - - -
314G PHE* 2.7 24.4 + - - +
315G VAL* 2.8 14.1 + - - +
323G LEU* 4.1 17.7 - - + -
324G PRO* 4.0 13.5 - - + -
357G VAL* 3.3 35.2 - - + -
383G LEU* 3.8 32.1 - - + -
384G CYS* 4.9 2.7 - - - -
387G SER* 4.3 14.4 - - - -
390G LEU* 3.8 19.7 - - + -
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Residues in contact with LYS 312 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289G PHE* 3.3 65.3 + - + +
290G ASN* 4.9 6.2 + - - -
294G CYS* 4.4 7.4 - - - -
295G ILE* 3.7 23.4 - - - +
308G ALA 2.9 6.3 + - - +
309G ARG* 2.8 28.6 + - - +
311G LEU* 1.3 71.6 - - - +
313G GLU* 1.3 60.7 + - - +
315G VAL* 2.9 6.0 + - + +
316G ALA* 2.9 29.6 + - + +
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Residues in contact with GLU 313 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309G ARG* 2.8 59.0 + - + +
310G ALA* 4.1 2.5 - - - +
312G LYS* 1.3 77.3 - - - +
314G PHE* 1.3 57.0 + - - +
316G ALA* 3.6 9.8 + - - +
317G LYS* 3.0 31.7 + - - +
360G HIS* 3.8 26.2 + - + +
364G LEU* 4.8 10.3 - - + -
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Residues in contact with PHE 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310G ALA 3.5 11.5 + - - +
311G LEU* 2.7 17.8 + - - +
313G GLU* 1.3 71.5 - - - +
315G VAL* 1.3 62.2 + - - +
317G LYS 3.3 6.6 + - - -
318G GLU* 4.0 13.9 - - + -
319G GLY* 2.6 52.4 + - - -
322G ASN 3.6 13.7 - - - -
323G LEU* 3.7 0.9 - - - -
324G PRO* 3.6 26.0 - - + -
353G ASP* 3.0 38.8 - - + -
356G ALA* 3.2 32.8 - - + -
357G VAL* 3.4 21.5 - - + -
360G HIS* 3.6 11.0 - - + -
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Residues in contact with VAL 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281G ILE* 3.6 11.2 - - + -
289G PHE* 3.8 27.4 - - + -
311G LEU* 2.8 18.5 + - + +
312G LYS* 3.2 7.2 - - + +
314G PHE* 1.3 78.8 - - + +
316G ALA* 1.3 64.6 + - - +
320G GLN 3.4 3.1 + - - -
321G GLY* 2.9 57.7 + - - +
322G ASN 4.0 20.4 - - - +
323G LEU* 4.2 10.8 - - + +
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Residues in contact with ALA 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312G LYS* 2.9 15.6 + - + +
313G GLU* 3.8 11.9 - - - +
315G VAL* 1.3 79.7 - - - +
317G LYS* 1.3 64.1 + - + +
320G GLN* 4.8 1.0 + - - -
321G GLY* 4.8 2.2 + - - -
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Residues in contact with LYS 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313G GLU* 3.0 15.3 + - - +
314G PHE 3.4 0.2 - - - -
316G ALA* 1.3 81.7 - - + +
318G GLU* 1.3 86.9 + - - +
319G GLY 2.7 18.1 + - - -
320G GLN* 2.9 15.9 + - - +
360G HIS* 3.8 10.5 - - + -
363G LYS* 4.0 20.8 - - - +
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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