Contacts of the helix formed by residues 308 - 322 (chain A) in PDB entry 1YV5
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 GLU 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A GLN* 3.2 26.7 - - - +
307A LYS* 1.3 79.9 + - - +
309A ALA* 1.3 67.4 + - - +
310A GLU* 4.4 9.0 - - + +
311A LYS* 2.8 50.0 + - + +
312A VAL* 3.0 13.9 + - - +
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Residues in contact with ALA 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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277A GLN* 6.1 0.4 - - - +
307A LYS 3.5 5.0 + - - -
308A GLU* 1.3 70.7 - - - +
310A GLU* 1.3 62.7 + - - +
312A VAL* 3.3 10.1 + - - +
313A ALA* 3.0 24.3 + - - +
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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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308A GLU* 4.4 8.9 - - + +
309A ALA* 1.3 80.0 - - - +
311A LYS* 1.3 81.8 + - + +
313A ALA* 3.4 8.5 + - - +
314A ARG* 2.5 68.1 + - - +
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Residues in contact with LYS 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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302A GLU 4.0 8.3 - - - +
303A ASN* 3.3 35.4 - - - +
306A GLN* 3.3 38.5 + - + +
308A GLU* 2.8 39.7 + - + +
310A GLU* 1.3 96.0 + - - +
312A VAL* 1.3 64.0 + - - +
314A ARG* 3.2 15.3 + - - +
315A VAL* 3.3 16.5 + - - +
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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
----------------------------------------------------------
262A LEU* 5.0 7.0 - - + -
276A ILE* 3.8 34.1 - - + +
277A GLN* 3.7 34.8 - - - +
303A ASN 5.6 0.2 - - - +
306A GLN 3.6 23.1 - - - +
307A LYS 4.9 0.2 - - - -
308A GLU 3.0 14.7 + - - +
309A ALA* 3.3 10.1 + - - +
311A LYS* 1.3 75.6 - - - +
313A ALA* 1.3 57.5 + - - +
315A VAL* 3.4 4.5 + - - +
316A LYS* 3.1 24.9 + - + +
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Residues in contact with ALA 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 ALA 3.0 16.1 + - - +
310A GLU* 3.6 9.0 - - - +
311A LYS 3.1 0.4 - - - -
312A VAL* 1.3 75.1 - - - +
314A ARG* 1.3 60.8 + - - +
316A LYS* 3.7 8.6 - - - +
317A ALA* 2.9 30.7 + - - +
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Residues in contact with ARG 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ILE* 4.5 11.2 - - + +
303A ASN* 3.3 35.7 + - - +
310A GLU* 2.5 50.2 + - - +
311A LYS* 3.2 10.8 + - - +
313A ALA* 1.3 76.8 - - - +
315A VAL* 1.3 55.2 + - - +
317A ALA* 3.4 6.4 + - - +
318A LEU* 3.0 27.6 + - - +
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Residues in contact with VAL 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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276A ILE* 3.8 24.7 - - + -
299A ILE* 5.5 1.3 - - - -
300A LEU* 3.8 18.6 - - + -
303A ASN* 3.8 24.7 - - + -
304A TYR* 4.0 9.9 - - + +
311A LYS 3.3 13.9 + - - +
312A VAL 3.6 7.0 - - - +
314A ARG* 1.3 74.3 - - - +
316A LYS* 1.3 64.9 + - - +
318A LEU* 3.1 8.9 + - - +
319A TYR* 2.9 54.9 + - + +
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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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262A LEU* 3.4 57.1 + - + +
263A PHE* 3.9 13.8 - - + +
276A ILE* 4.5 0.8 - - - +
312A VAL* 3.1 12.9 + - + +
313A ALA* 3.7 11.0 - - - +
315A VAL* 1.3 77.9 - - - +
317A ALA* 1.3 57.6 + - - +
319A TYR* 3.3 3.1 + - - +
320A GLU* 2.9 52.3 + - - +
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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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313A ALA 2.9 18.8 + - - +
314A ARG* 3.7 7.6 - - - +
316A LYS* 1.3 73.1 - - - +
318A LEU* 1.3 60.5 + - - +
320A GLU* 3.7 14.4 - - - +
321A GLU* 2.8 30.5 + - - +
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Residues in contact with LEU 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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288A CYS* 3.8 21.1 - - - -
296A GLN* 3.2 68.2 - - + +
299A ILE* 4.3 19.3 - - + -
300A LEU* 4.2 13.9 - - + -
314A ARG 3.0 14.0 + - - +
315A VAL* 3.1 9.4 + - - +
317A ALA* 1.3 74.1 - - - +
319A TYR* 1.3 58.8 + - + +
321A GLU* 3.2 5.0 + - + +
322A LEU* 2.9 39.4 + - + +
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Residues in contact with TYR 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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262A LEU* 3.2 31.4 - - + -
263A PHE* 4.1 11.7 - + + -
276A ILE* 4.4 6.1 - - + -
282A SER* 5.5 0.3 - - - -
284A LEU* 3.7 28.4 - - + +
285A VAL* 3.3 26.7 + - - +
288A CYS* 3.6 32.3 - - + -
300A LEU* 4.3 2.0 - - + -
304A TYR* 3.4 16.3 + - - -
315A VAL* 2.9 33.4 + - + +
316A LYS* 3.4 7.4 - - - +
318A LEU* 1.3 73.5 - - + +
320A GLU* 1.3 56.3 + - - +
322A LEU* 2.9 18.5 + - - -
323A ASP 3.1 9.4 + - - -
324A LEU* 3.2 34.7 + - + +
325A PRO* 4.8 0.4 - - - -
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Residues in contact with GLU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A PHE* 3.7 19.5 - - + -
316A LYS* 2.9 48.0 + - - +
317A ALA* 3.8 13.6 - - - +
319A TYR* 1.3 71.7 - - - +
321A GLU* 1.3 63.1 + - - +
323A ASP* 3.1 19.5 + - - +
325A PRO* 4.6 10.5 - - + -
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Residues in contact with GLU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLN* 4.4 16.2 - - - +
317A ALA 2.8 22.1 + - - +
318A LEU* 3.2 9.6 + - + +
320A GLU* 1.3 74.0 - - - +
322A LEU* 1.3 60.0 + - - +
323A ASP* 3.3 9.1 + - - +
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Residues in contact with LEU 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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288A CYS* 3.6 45.3 - - + +
291A ARG* 4.0 30.2 + - + +
292A ALA* 4.5 4.9 - - - +
296A GLN* 3.9 26.2 - - - +
318A LEU* 2.9 26.8 + - + +
319A TYR* 2.9 4.9 + - - +
321A GLU* 1.3 76.7 - - - +
323A ASP* 1.3 72.7 + - - +
324A LEU* 3.3 15.7 + - + +
327A VAL* 4.7 3.5 - - - +
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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