Contacts of the helix formed by residues 303 - 317 (chain A) in PDB entry 1Y57
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 SER 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A LEU* 4.4 0.2 - - - -
301A THR 3.9 0.4 + - - -
302A MET* 1.3 76.5 - - - +
304A PRO* 1.3 73.1 - - - +
305A GLU* 3.7 14.6 + - - +
306A ALA* 3.0 26.6 + - - +
307A PHE* 3.0 21.0 + - - +
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Residues in contact with PRO 304 (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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255A LEU* 3.8 24.9 - - + -
297A LEU* 3.9 14.6 - - + -
302A MET 3.6 4.5 - - - +
303A SER* 1.3 87.0 - - - +
305A GLU* 1.3 63.0 + - - +
307A PHE* 3.3 2.1 + - - +
308A LEU* 2.9 36.9 + - - +
332A GLU* 4.5 17.0 - - + +
334A ILE* 3.9 20.6 - - + -
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Residues in contact with GLU 305 (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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95A ARG* 3.7 29.7 + - - +
252A THR* 4.1 13.0 + - - +
255A LEU* 3.1 32.8 - - + +
303A SER* 3.2 17.7 - - - +
304A PRO* 1.3 78.1 - - - +
306A ALA* 1.3 66.4 + - - +
308A LEU* 3.3 4.4 + - - +
309A GLN* 3.1 26.1 + - - +
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Residues in contact with ALA 306 (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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302A MET* 3.3 26.5 - - + +
303A SER* 3.0 23.7 + - - +
305A GLU* 1.3 75.9 - - - +
307A PHE* 1.3 62.8 + - - +
309A GLN* 3.3 36.5 + - - +
310A GLU* 4.4 0.3 + - - +
406A GLY 5.4 2.9 - - - +
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Residues in contact with PHE 307 (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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278A PHE* 5.1 4.0 - - + -
295A LYS* 3.8 47.3 - - + -
296A THR 3.9 4.0 - - - -
297A LEU* 3.8 41.5 - - + -
302A MET* 3.6 17.4 - - - +
303A SER 3.0 12.2 + - - +
304A PRO 3.5 7.0 - - - +
306A ALA* 1.3 79.3 - - - +
308A LEU* 1.3 60.4 + - + +
309A GLN 3.4 1.0 + - - -
310A GLU* 3.6 19.9 + - - +
334A ILE* 3.6 39.7 - - + -
336A ILE* 3.7 30.6 - - + +
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Residues in contact with LEU 308 (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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95A ARG* 3.6 29.4 - - - +
255A LEU* 3.7 20.0 - - + -
304A PRO 2.9 20.4 + - - +
305A GLU 3.7 3.8 - - - +
306A ALA 3.3 0.4 - - - -
307A PHE* 1.3 72.5 - - + +
309A GLN* 1.3 64.5 + - - +
310A GLU 3.0 2.7 - - - -
311A ALA* 2.9 16.4 + - + +
312A GLN* 3.0 12.5 + - - +
328A VAL* 4.2 21.1 - - + -
330A SER* 4.0 12.6 - - - +
334A ILE* 3.6 30.1 - - + -
336A ILE* 3.9 21.3 - - + -
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Residues in contact with GLN 309 (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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305A GLU* 3.1 16.9 + - - +
306A ALA* 3.3 26.5 - - - +
307A PHE 3.2 0.8 - - - -
308A LEU* 1.3 76.3 - - - +
310A GLU* 1.3 61.1 + - - +
312A GLN* 3.2 18.9 + - - +
313A VAL* 3.1 28.9 + - + +
405A PHE 5.2 0.4 - - - -
406A GLY 5.2 8.6 - - - +
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Residues in contact with GLU 310 (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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295A LYS* 2.8 38.7 + - - +
306A ALA 4.4 0.8 + - - +
307A PHE* 3.6 14.7 + - - +
309A GLN* 1.3 79.6 - - - +
311A ALA* 1.3 60.4 + - - +
313A VAL* 3.5 3.1 + - - +
314A MET* 3.2 45.4 + - - +
336A ILE* 4.2 16.0 - - + +
404A ASP* 4.7 5.4 + - - -
405A PHE* 3.9 28.6 + - - +
406A GLY* 4.0 24.8 + - - -
600A MPZ 5.0 4.2 + - - -
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Residues in contact with ALA 311 (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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308A LEU* 2.9 13.8 + - + +
310A GLU* 1.3 76.2 - - - +
312A GLN* 1.3 67.1 + - - +
314A MET* 3.2 5.1 + - - +
315A LYS* 2.9 31.9 + - - +
325A LEU* 3.6 19.5 - - + +
328A VAL* 3.7 30.5 - - + -
336A ILE* 4.3 12.4 - - + +
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Residues in contact with GLN 312 (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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94A SER* 3.5 22.9 + - - +
95A ARG* 3.7 33.9 - - - +
96A THR* 5.4 1.8 + - - -
308A LEU 3.0 11.5 + - - +
309A GLN* 3.5 21.0 - - - +
311A ALA* 1.3 77.9 - - - +
313A VAL* 1.3 63.1 + - + +
315A LYS* 3.4 26.0 + - + +
316A LYS* 3.7 7.4 + - - +
382A TYR* 5.4 0.2 + - - -
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Residues in contact with VAL 313 (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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309A GLN* 3.1 15.3 + - + +
310A GLU 3.6 8.1 - - - +
312A GLN* 1.3 78.3 - - + +
314A MET* 1.3 58.5 + - - +
316A LYS* 3.1 7.8 + - - +
317A LEU* 3.1 46.2 + - + +
382A TYR* 4.1 18.4 - - + -
405A PHE* 4.0 15.3 - - + +
408A ALA* 3.7 43.5 - - + +
409A ARG* 5.1 1.1 - - - -
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Residues in contact with MET 314 (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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260A TRP* 5.4 1.2 - - - -
310A GLU* 3.2 38.1 + - - +
311A ALA* 3.2 4.5 + - - +
313A VAL* 1.3 73.0 - - - +
315A LYS* 1.3 65.3 + - - +
316A LYS 3.2 0.4 + - - -
317A LEU* 3.3 22.2 - - - +
318A ARG* 5.3 1.6 - - - +
323A VAL* 3.2 31.9 - - + +
325A LEU* 3.6 40.0 + - + +
336A ILE* 4.9 2.0 - - - -
338A THR* 3.8 24.0 - - + -
405A PHE* 3.9 29.2 - - + -
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Residues in contact with LYS 315 (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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95A ARG* 4.3 7.9 + - - +
96A THR* 4.2 15.3 - - - +
97A GLU* 3.9 21.7 - - + +
258A ASP* 2.8 26.6 + - - +
260A TRP* 3.6 49.2 - - + +
311A ALA* 2.9 31.0 + - - +
312A GLN* 3.6 14.6 - - + +
313A VAL 3.2 0.6 - - - -
314A MET* 1.3 77.2 - - - +
316A LYS* 1.3 58.8 + - - +
317A LEU 5.2 0.4 - - - -
318A ARG* 5.7 2.6 - - - +
325A LEU* 3.5 15.0 - - + -
328A VAL* 5.2 6.8 - - - +
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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 GLN 3.7 6.2 + - - +
313A VAL 3.1 9.5 + - - +
315A LYS* 1.3 80.6 - - - +
317A LEU* 1.3 59.9 + - - +
318A ARG* 3.7 2.4 + - - +
376A TYR* 3.6 9.0 + - - -
380A MET* 3.9 24.6 - - + +
382A TYR* 3.4 33.7 - - + +
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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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313A VAL* 3.1 35.5 + - + +
314A MET* 3.3 17.1 - - - +
316A LYS* 1.3 77.8 - - - +
318A ARG* 1.3 58.4 + - - +
319A HIS 4.3 0.4 - - - -
322A LEU* 3.8 19.8 - - + +
323A VAL 5.3 3.5 - - - +
324A GLN* 6.1 0.3 - - - -
376A TYR* 3.5 8.3 - - + -
377A VAL* 4.3 14.1 - - + -
380A MET* 3.6 27.8 - - + -
382A TYR* 3.6 45.5 - - + -
405A PHE* 4.2 17.7 - - + -
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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