Contacts of the helix formed by residues 312 - 329 (chain A) in PDB entry 2Y60
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 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A TYR* 3.8 12.9 + - - -
291A ASP* 4.6 5.6 - - - -
292A SER 3.4 6.7 - - - -
293A VAL* 3.8 18.0 - - - +
310A PRO 4.3 0.2 - - - -
311A LEU* 1.3 76.8 - - - +
313A TYR* 1.3 64.7 + - - +
314A GLY 3.8 1.0 + - - -
315A ASP* 3.3 31.8 + - - +
316A TYR* 3.0 20.6 + - - +
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Residues in contact with TYR 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU* 4.7 3.4 - - + -
218A SER* 3.2 19.6 - - - -
219A LEU* 3.2 6.6 + - + -
256A TYR* 3.5 48.2 + + + -
287A ASN* 2.6 47.4 + - + -
288A LEU* 3.6 35.0 - - + -
289A GLY 3.3 15.7 - - - +
290A TYR 3.9 0.6 + - - -
292A SER* 2.8 15.8 + - - +
311A LEU 3.7 0.4 + - - -
312A SER* 1.3 72.3 - - - +
314A GLY* 1.3 59.3 + - - +
316A TYR* 3.2 13.8 + + - +
317A LEU* 2.8 41.4 + - + +
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Residues in contact with GLY 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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123A THR* 4.7 0.5 - - - +
181A LEU* 4.5 5.8 - - - -
290A TYR* 2.8 49.3 + - - +
313A TYR* 1.3 78.3 - - - +
315A ASP* 1.3 56.2 + - - +
317A LEU* 3.4 1.8 + - - +
318A GLN* 3.0 39.2 + - - +
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Residues in contact with ASP 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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290A TYR* 4.5 5.7 + - - -
311A LEU* 4.1 15.6 - - + +
312A SER* 3.3 25.6 + - - +
314A GLY* 1.3 70.6 - - - +
316A TYR* 1.3 68.7 + - - +
318A GLN* 3.6 16.4 - - - +
319A ASN* 3.2 25.5 + - - +
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Residues in contact with TYR 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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217A VAL* 3.3 22.0 - - + -
218A SER 3.1 18.8 + - - -
255A SER* 2.6 31.9 + - - -
256A TYR* 3.1 41.0 + + + -
259A HIS* 6.2 0.7 - - + -
311A LEU* 3.8 25.7 - - + +
312A SER 3.0 13.9 + - - +
313A TYR* 3.5 40.6 - + - +
315A ASP* 1.3 77.3 - - - +
317A LEU* 1.3 59.7 + - - +
319A ASN* 3.8 4.1 + - - +
320A GLY* 2.8 30.0 + - - -
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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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87A ARG* 3.9 18.4 - - - +
123A THR* 4.2 9.0 - - + -
181A LEU* 3.8 35.7 - - + -
217A VAL* 3.8 16.2 - - + +
287A ASN* 3.8 29.6 - - - +
313A TYR* 2.8 24.8 + - + +
314A GLY 3.9 3.4 - - - +
316A TYR* 1.3 77.6 - - - +
318A GLN* 1.3 67.8 + - - +
321A LEU* 2.9 54.0 + - + +
1332A M8F 5.5 0.2 - - - +
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Residues in contact with GLN 318 (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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122A PRO* 3.5 26.4 - - + +
123A THR* 3.5 21.1 - - + -
290A TYR* 2.6 27.2 + - - -
314A GLY 3.0 22.8 + - - +
315A ASP* 3.6 15.0 - - - +
317A LEU* 1.3 81.2 - - - +
319A ASN* 1.3 62.8 + - + +
321A LEU* 3.6 3.9 + - - +
322A VAL* 3.4 25.7 + - - +
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Residues in contact with ASN 319 (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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315A ASP 3.2 17.5 + - - +
316A TYR* 4.0 3.8 + - - +
318A GLN* 1.3 75.6 - - + +
320A GLY* 1.3 70.8 + - - +
322A VAL* 3.5 5.7 + - - +
323A SER* 2.9 42.7 + - - -
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Residues in contact with GLY 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A VAL* 3.5 23.8 - - - +
316A TYR* 2.8 21.6 + - - -
317A LEU 3.8 0.4 - - - -
319A ASN* 1.3 84.5 - - - +
321A LEU* 1.3 57.6 + - - +
323A SER* 3.3 5.4 + - - -
324A LEU* 2.9 30.3 + - - +
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 3.9 18.6 - - + +
123A THR* 5.6 1.8 - - + -
217A VAL* 4.0 24.5 - - + +
317A LEU* 2.9 40.8 + - + +
318A GLN* 4.1 4.5 - - - +
320A GLY* 1.3 77.3 - - - +
322A VAL* 1.3 62.3 + - + +
324A LEU* 3.5 5.1 + - + +
325A ILE* 3.2 33.6 + - + +
1332A M8F 3.8 51.8 - - + +
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Residues in contact with VAL 322 (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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318A GLN 3.4 14.2 + - - +
319A ASN* 3.9 7.9 - - - +
320A GLY 3.4 0.2 - - - -
321A LEU* 1.3 77.1 - - + +
323A SER* 1.3 61.0 + - - +
325A ILE* 3.2 11.0 + - + +
326A ASN* 2.9 46.3 + - - +
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Residues in contact with SER 323 (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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319A ASN* 2.9 38.9 + - - -
320A GLY* 3.7 6.7 - - - -
322A VAL* 1.3 78.0 - - - +
324A LEU* 1.3 56.2 + - - +
326A ASN* 3.2 10.2 + - - +
327A LYS* 2.9 30.2 + - - +
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Residues in contact with LEU 324 (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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211A PHE* 4.2 16.3 - - + -
214A HIS* 3.8 29.2 - - + -
215A GLU 4.6 6.5 - - - +
217A VAL* 4.2 20.4 - - + +
320A GLY 2.9 16.6 + - - +
321A LEU* 3.8 6.1 - - + +
323A SER* 1.3 74.3 - - - +
325A ILE* 1.4 59.0 + - + +
327A LYS* 4.5 7.2 - - + +
328A ASN* 2.9 34.7 + - + +
329A GLY 3.9 1.3 + - - +
1332A M8F 3.8 45.8 - - + +
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Residues in contact with ILE 325 (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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86A VAL* 6.4 1.6 - - + -
321A LEU* 3.2 23.6 + - + +
322A VAL* 3.2 10.5 + - + +
324A LEU* 1.4 74.2 - - + +
326A ASN* 1.3 66.8 + - - +
329A GLY* 2.8 39.0 + - - +
330A GLN* 3.8 45.3 - - + +
331A THR* 5.5 1.6 - - + +
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Residues in contact with ASN 326 (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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322A VAL* 2.9 37.6 + - - +
323A SER* 3.2 10.6 + - - +
325A ILE* 1.3 84.5 - - - +
327A LYS* 1.3 64.1 + - - +
329A GLY* 4.5 0.7 + - - -
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Residues in contact with LYS 327 (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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212A GLU* 4.2 4.4 - - - +
213A TRP* 2.8 76.3 + - + +
214A HIS* 4.8 5.8 - - + +
323A SER 2.9 17.2 + - - +
324A LEU* 3.9 8.7 - - + +
326A ASN* 1.3 80.7 - - - +
328A ASN* 1.4 86.4 + - - +
329A GLY 3.6 0.4 + - - -
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Residues in contact with ASN 328 (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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201A LYS* 4.8 13.5 + - - -
211A PHE* 3.6 41.0 - - + -
212A GLU* 3.0 41.7 + - + +
213A TRP 3.1 11.1 + - - -
214A HIS* 3.8 6.1 - - - +
324A LEU* 2.9 14.6 + - + +
327A LYS* 1.4 105.5 + - - +
329A GLY* 1.3 60.7 + - - +
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Residues in contact with GLY 329 (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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211A PHE* 4.8 0.7 - - - -
324A LEU 4.5 0.9 - - - +
325A ILE* 2.8 29.0 + - - +
326A ASN 4.5 0.4 + - - -
327A LYS 3.6 1.4 - - - -
328A ASN* 1.3 80.7 - - - +
330A GLN* 1.3 66.4 + - - -
331A THR* 3.2 12.2 + - - +
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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