Contacts of the helix formed by residues 309 - 325 (chain A) in PDB entry 4Y2P
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 CYS 309 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A GLU* 3.5 13.7 + - - +
307A GLU 3.6 0.4 - - - -
308A TYR* 1.3 81.1 - - - +
310A MET* 1.3 65.6 + - - +
311A GLU* 4.1 11.4 - - - -
312A VAL* 3.3 28.5 + - - +
313A LEU* 3.1 19.9 + - - +
468A ASN* 3.4 24.9 - - - +
471A ARG* 3.5 24.7 - - + -
472A ASN* 3.5 11.4 - - - +
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Residues in contact with MET 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A TYR 3.9 2.1 + - - +
309A CYS* 1.3 71.8 - - - +
311A GLU* 1.3 58.0 + - - +
313A LEU* 3.9 7.8 - - + +
314A CYS* 2.8 35.4 + - - +
336A TRP* 3.3 40.8 - - + +
339A MET* 4.2 7.9 - - + +
340A LEU* 3.7 32.1 - - + +
343A TYR* 4.4 17.0 - - + -
465A TRP* 3.8 23.3 - - + +
472A ASN* 2.8 33.1 + - + +
475A TRP* 3.6 20.6 - - + -
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Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A CYS* 3.3 11.6 - - - -
310A MET* 1.3 79.1 - - - +
312A VAL* 1.3 58.8 + - + +
314A CYS* 4.1 1.6 - - - +
315A LYS* 2.9 64.5 + - + +
472A ASN* 4.7 0.4 + - - -
475A TRP* 3.3 56.3 + - + +
478A LYS* 5.5 4.4 + - - -
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Residues in contact with VAL 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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245A LYS* 3.7 23.7 + - - +
294A LYS* 3.7 7.4 - - - +
306A GLU* 4.0 8.1 - - + +
307A GLU* 3.4 30.5 - - - +
309A CYS* 3.3 24.7 + - - +
311A GLU* 1.3 79.3 - - + +
313A LEU* 1.3 66.4 + - - +
315A LYS* 3.3 11.0 + - + +
316A GLU* 2.9 28.5 + - - +
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Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LYS* 3.6 42.0 - - + -
307A GLU 3.9 5.6 - - - +
308A TYR* 3.2 29.4 - - + +
309A CYS 3.1 15.2 + - - +
310A MET* 3.9 9.0 - - + +
312A VAL* 1.3 78.9 - - - +
314A CYS* 1.3 60.8 + - - +
316A GLU* 3.4 8.1 + - - +
317A MET* 3.0 26.3 + - - +
340A LEU* 3.7 16.4 - - + -
465A TRP* 3.7 40.2 - - + -
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Residues in contact with CYS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A MET* 2.8 27.5 + - - +
311A GLU 4.1 0.9 - - - +
313A LEU* 1.3 70.1 - - - +
315A LYS* 1.3 66.1 + - - +
317A MET* 3.0 5.8 + - - +
318A VAL* 3.0 24.3 + - - +
340A LEU* 3.9 27.4 - - - -
343A TYR* 3.9 19.5 - - - -
344A MET* 3.6 28.3 - - - +
348A TYR* 4.1 14.4 - - + -
475A TRP* 4.0 9.0 - - + -
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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
----------------------------------------------------------
311A GLU* 2.9 60.0 + - + +
312A VAL* 3.3 11.0 + - + +
314A CYS* 1.3 75.8 - - - +
316A GLU* 1.3 58.8 + - + +
318A VAL* 3.2 8.3 + - - +
319A THR* 3.0 30.2 + - - -
348A TYR* 3.3 25.8 + - - +
475A TRP* 5.1 1.6 - - - +
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Residues in contact with GLU 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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244A VAL* 3.6 20.3 - - + +
245A LYS* 2.7 32.6 + - + +
248A VAL* 3.9 12.7 - - - +
250A LEU* 4.8 7.6 - - + +
294A LYS* 2.6 50.3 + - - +
312A VAL* 2.9 17.8 + - - +
313A LEU* 3.4 13.0 - - - +
315A LYS* 1.3 75.5 - - + +
317A MET* 1.3 61.3 + - + +
319A THR* 3.3 9.0 + - - -
320A PHE* 2.8 27.9 + - - +
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Residues in contact with MET 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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250A LEU* 3.9 24.5 - - - -
262A CYS* 3.7 30.1 - - - -
264A CYS* 4.5 4.5 - - - -
291A MET* 4.0 20.6 - - + -
293A MET* 4.5 11.2 - - - +
313A LEU 3.0 16.8 + - - +
314A CYS 3.0 9.8 + - - +
316A GLU* 1.3 76.5 - - - +
318A VAL* 1.3 61.7 + - - +
320A PHE* 3.2 13.6 + - + +
321A LEU* 3.2 25.3 + - - +
331A PHE* 4.0 10.1 - - + -
340A LEU* 4.3 21.3 - - + -
344A MET* 4.0 17.9 - - + -
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Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A CYS 3.0 13.2 + - - +
315A LYS* 3.2 8.9 + - - +
317A MET* 1.3 72.9 - - - +
319A THR* 1.3 61.4 + - - +
321A LEU* 3.2 12.3 + - - +
322A ASP* 2.9 33.7 + - - +
344A MET* 3.9 9.9 - - + -
348A TYR* 3.6 46.9 - - + -
351A ARG* 3.5 28.9 - - + +
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Residues in contact with THR 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A VAL* 3.4 33.5 + - - +
315A LYS 3.0 13.6 + - - -
316A GLU* 3.5 10.0 - - - -
318A VAL* 1.3 77.9 - - - +
320A PHE* 1.4 53.4 + - - +
322A ASP* 3.4 11.7 + - + +
323A LYS* 2.8 62.8 + - + +
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Residues in contact with PHE 320 (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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242A VAL* 3.7 32.3 - - + +
244A VAL* 3.7 10.7 - - + +
250A LEU* 4.2 13.0 - - + -
252A PHE* 3.6 29.6 - + - -
262A CYS* 4.7 6.3 - - + -
289A LEU* 4.3 8.5 - - + -
291A MET* 3.6 37.7 - - + -
316A GLU 2.8 14.3 + - - +
317A MET* 3.3 26.0 - - + +
318A VAL 3.2 0.2 - - - -
319A THR* 1.4 75.5 - - - +
321A LEU* 1.3 75.1 + - + +
323A LYS* 4.0 1.9 - - - +
324A LEU* 3.2 46.3 + - + +
326A LEU* 5.6 0.2 - - + -
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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
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262A CYS* 5.6 2.5 - - + -
289A LEU* 6.3 0.2 - - + -
317A MET 3.2 12.1 + - - +
318A VAL* 3.2 9.5 + - - +
320A PHE* 1.3 89.0 - - + +
322A ASP* 1.3 60.1 + - - +
324A LEU* 3.2 4.3 + - - +
325A GLY 3.0 4.7 + - - -
326A LEU* 2.8 66.2 + - + +
328A GLN 4.5 0.4 - - - -
329A ALA* 3.9 21.3 - - + +
331A PHE* 3.8 21.3 - - + -
344A MET* 5.1 1.1 - - + -
351A ARG* 3.7 45.1 - - + +
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Residues in contact with ASP 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 VAL* 2.9 25.1 + - - +
319A THR* 3.1 18.1 + - + +
321A LEU* 1.3 75.2 - - - +
323A LYS* 1.3 66.6 + - + +
325A GLY* 3.1 14.4 + - - -
326A LEU 4.9 0.9 - - - +
351A ARG* 2.7 33.7 + - - +
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Residues in contact with LYS 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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242A VAL* 3.6 27.8 - - + -
243A THR* 3.1 24.3 + - - +
244A VAL 4.6 6.0 + - - -
245A LYS* 5.8 0.4 - - - +
319A THR* 2.8 40.7 + - + +
320A PHE 4.0 0.2 - - - +
321A LEU 3.3 0.2 - - - -
322A ASP* 1.3 76.5 - - + +
324A LEU* 1.3 58.7 + - - +
325A GLY 3.2 0.8 + - - -
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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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242A VAL* 4.3 11.0 - - + -
252A PHE* 4.1 15.9 - - + -
254A GLU* 5.1 0.9 - - - +
287A ARG* 4.3 19.5 + - - +
289A LEU* 3.8 16.2 - - + -
320A PHE* 3.2 54.3 + - + +
321A LEU 3.2 4.9 + - - +
323A LYS* 1.3 74.4 - - - +
325A GLY* 1.3 61.6 + - - +
326A LEU* 3.8 22.2 - - + +
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Residues in contact with GLY 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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321A LEU 3.0 2.4 + - - -
322A ASP* 3.1 14.2 + - - -
323A LYS 3.2 1.2 + - - -
324A LEU* 1.3 79.4 - - - +
326A LEU* 1.3 63.5 + - - +
327A SER 3.9 1.8 + - - -
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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
------------------------------------------------------------
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