Contacts of the helix formed by residues 302 - 319 (chain A) in PDB entry 1Y2C
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 302 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ASP* 1.3 85.2 + - - +
303A TYR* 1.3 67.1 + - - +
304A SER* 3.3 13.2 + - - +
305A ASP* 3.1 36.9 + - - +
306A ARG* 3.1 24.9 + - - +
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Residues in contact with TYR 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLU* 5.6 4.0 - - - -
259A SER* 5.9 0.7 - - - -
262A LYS* 3.9 21.4 - - + +
263A MET* 3.5 38.1 - - + +
266A ASP* 2.8 28.8 + - - -
302A ASN* 1.3 74.8 - - - +
304A SER* 1.3 66.8 + - - +
306A ARG* 3.1 9.3 + - + +
307A ILE* 2.8 57.6 + - + +
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Residues in contact with SER 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ASN* 3.3 12.2 + - - -
303A TYR* 1.3 81.5 - - - +
305A ASP* 1.3 65.2 + - - +
307A ILE* 3.6 8.6 - - - +
308A GLN* 3.2 28.8 + - - +
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Residues in contact with ASP 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A MET* 3.6 25.4 - - + +
300A LEU* 4.2 16.4 - - + +
301A ASP 5.2 2.3 + - - -
302A ASN* 3.1 30.6 + - - +
304A SER* 1.3 76.5 + - - +
306A ARG* 1.3 65.6 + - - +
308A GLN* 3.3 9.2 + - - +
309A VAL* 3.2 28.3 + - - +
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Residues in contact with ARG 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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184A VAL* 2.9 31.2 + - - +
185A PHE* 3.8 18.6 - - + +
186A THR* 4.0 12.1 - - - +
189A GLU* 2.7 44.8 + - - +
300A LEU* 2.7 53.0 + - + +
301A ASP 3.8 10.3 + - - -
302A ASN 3.1 18.9 + - - +
303A TYR* 3.1 10.6 + - + +
305A ASP* 1.3 76.8 - - - +
307A ILE* 1.3 62.5 + - - +
309A VAL* 3.3 2.4 + - - +
310A LEU* 3.1 27.9 + - + +
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Residues in contact with ILE 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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263A MET* 4.0 18.8 - - + +
266A ASP* 3.7 17.3 - - + +
267A ILE* 3.9 27.6 - - + -
303A TYR* 2.8 63.3 + - + +
304A SER* 3.6 9.9 - - - +
306A ARG* 1.3 71.9 - - - +
308A GLN* 1.3 64.8 + - - +
310A LEU* 3.2 8.6 + - + -
311A GLN* 2.8 46.1 + - + +
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Residues in contact with GLN 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 5.4 2.5 - - + -
282A ASP* 2.7 53.6 + - + +
283A LEU* 3.2 9.0 - - + +
286A MET* 4.2 15.8 - - + +
304A SER* 3.2 20.6 + - - +
305A ASP* 3.5 15.6 - - - +
306A ARG 3.2 0.2 - - - -
307A ILE* 1.3 82.6 - - + +
309A VAL* 1.3 57.4 + - - +
311A GLN* 3.4 15.3 + - - +
312A ASN* 3.0 44.4 + - - +
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Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU* 4.6 7.9 - - + -
185A PHE* 3.9 23.6 - - + -
283A LEU* 5.5 1.8 - - + -
286A MET* 3.4 32.5 - - - -
298A LEU* 5.0 0.9 - - + -
300A LEU* 3.7 16.2 - - + -
305A ASP 3.2 10.1 + - - +
306A ARG 3.8 6.7 - - - +
308A GLN* 1.3 75.8 - - - +
310A LEU* 1.3 58.0 + - - +
312A ASN* 3.5 4.3 + - - -
313A MET* 2.8 28.5 + - + +
384A TRP* 3.8 23.5 - - + -
387A LEU* 4.3 12.6 - - + -
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Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU* 4.4 8.7 - - + -
185A PHE* 3.6 42.4 - - + -
189A GLU* 4.2 27.6 - - + +
193A ALA* 4.2 19.1 - - + -
263A MET* 4.8 3.8 - - - -
267A ILE* 4.1 20.0 - - + -
306A ARG* 3.1 21.1 + - + +
307A ILE* 3.2 19.9 + - + +
309A VAL* 1.3 73.9 - - - +
311A GLN* 1.3 63.9 + - - +
313A MET* 3.3 7.9 + - + +
314A VAL* 3.1 29.8 + - - +
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Residues in contact with GLN 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ASP* 3.0 40.9 + - - +
267A ILE* 4.1 13.8 - - - +
270A ALA* 3.7 22.7 - - + +
271A THR* 5.9 0.3 - - - +
279A LEU* 4.0 17.7 - - + +
307A ILE* 2.8 34.1 + - + +
308A GLN* 3.5 21.2 - - - +
309A VAL 3.3 0.2 - - - -
310A LEU* 1.3 74.1 - - - +
312A ASN* 1.3 58.0 + - - +
314A VAL* 3.9 1.9 - - - +
315A HIS* 3.0 29.2 + - - +
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Residues in contact with ASN 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 3.7 44.5 + - - +
283A LEU* 3.8 38.7 - - + +
308A GLN* 3.0 39.2 + - - +
309A VAL 4.0 2.9 - - - +
311A GLN* 1.3 73.5 - - - +
313A MET* 1.3 60.6 + - - +
315A HIS* 3.6 5.3 - - - +
316A CYS* 2.8 35.0 + - - -
380A LEU* 4.1 10.6 - - - +
384A TRP* 4.2 7.0 - - + -
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Residues in contact with MET 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A THR* 4.2 13.5 - - + +
175A LEU* 3.6 30.2 - - + +
176A LEU* 3.7 43.5 - - + -
181A LEU* 3.4 33.0 - - + -
185A PHE* 4.2 10.3 - - + -
193A ALA* 5.3 1.6 - - - -
309A VAL* 2.8 17.4 + - + +
310A LEU* 3.6 12.8 - - + +
311A GLN 3.3 0.4 - - - -
312A ASN* 1.3 76.8 - - - +
314A VAL* 1.3 57.3 + - - +
316A CYS* 3.2 6.5 + - - +
317A ALA* 3.0 23.0 + - - +
384A TRP* 3.7 18.3 - - + -
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Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A VAL* 4.4 8.2 - - + +
172A THR* 3.8 17.7 - - + +
193A ALA* 4.0 14.4 - - + +
196A ALA 5.3 0.7 - - - -
197A SER* 3.7 31.4 - - - +
200A HIS* 5.4 3.4 - - + -
267A ILE* 3.7 30.7 - - + -
268A VAL* 6.4 0.2 - - + -
271A THR* 4.2 16.4 - - + -
310A LEU 3.1 14.3 + - - +
311A GLN 4.2 1.6 - - - +
313A MET* 1.3 74.5 - - + +
315A HIS* 1.3 60.3 + - - +
317A ALA* 3.3 1.6 + - - +
318A ASP* 2.9 27.8 + - + +
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Residues in contact with HIS 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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270A ALA 4.2 13.6 + - - +
271A THR* 4.6 12.3 + - + +
272A ASP 5.5 0.2 - - - -
273A MET* 3.7 20.8 - - - -
276A HIS* 2.9 34.8 + - + +
279A LEU* 3.9 21.8 - - + -
311A GLN 3.0 19.5 + - - +
312A ASN* 3.6 8.1 - - - +
314A VAL* 1.3 77.2 - - - +
316A CYS* 1.3 56.2 + - - +
318A ASP* 3.2 11.0 + - - +
319A LEU* 3.0 52.2 + - + +
380A LEU* 3.6 26.9 - - + -
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Residues in contact with CYS 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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175A LEU* 4.2 4.3 - - + -
312A ASN 2.8 22.2 + - - +
313A MET* 3.4 6.7 - - - +
315A HIS* 1.3 76.7 - - - +
317A ALA* 1.3 55.8 + - - +
319A LEU 3.1 4.9 - - - -
320A SER 3.0 23.7 + - - -
380A LEU* 3.7 34.8 - - - -
381A TRP* 3.3 32.9 - - + -
384A TRP* 3.9 33.9 - - + -
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Residues in contact with ALA 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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167A ASP* 5.2 0.9 - - - +
168A VAL* 3.8 17.1 - - + +
171A SER* 3.8 22.1 + - - -
172A THR* 3.4 28.7 - - - +
175A LEU* 4.2 5.5 - - + +
313A MET 3.0 10.5 + - - +
314A VAL 3.5 6.5 - - - +
316A CYS* 1.3 75.3 - - - +
318A ASP* 1.3 62.0 + - - +
320A SER* 2.6 29.1 + - - -
321A ASN* 5.4 0.5 + - - -
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Residues in contact with ASP 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TYR* 4.1 14.7 + - - -
164A HIS* 3.1 11.1 + - - -
168A VAL* 3.9 9.8 - - + +
200A HIS* 3.1 9.2 + - + +
271A THR* 4.2 20.8 - - + +
273A MET* 5.3 0.3 - - - +
314A VAL 2.9 13.5 + - - +
315A HIS* 3.3 16.3 + - - +
317A ALA* 1.3 78.5 - - - +
319A LEU* 1.3 64.2 + - + +
320A SER 3.6 1.6 + - - -
321A ASN* 4.9 3.6 + - - +
1001A ZN 2.2 36.6 - - - -
1003A 3DE 3.7 23.1 - - - +
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A MET* 4.0 7.9 - - - -
315A HIS* 3.0 47.2 + - + +
316A CYS 3.1 6.0 + - - +
318A ASP* 1.3 80.8 - - + +
320A SER* 1.3 58.4 + - - +
321A ASN* 3.5 3.1 - - - -
322A PRO* 3.8 3.8 - - - +
372A PHE* 4.1 14.4 - - + -
376A ILE* 3.9 26.9 - - + -
377A VAL* 3.6 22.6 - - + +
380A LEU* 3.9 15.9 - - + -
381A TRP* 3.2 13.7 + - - +
1003A 3DE 3.6 35.4 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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