Contacts of the helix formed by residues 314 - 323 (chain A) in PDB entry 3H60
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 GLY 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A ASP* 5.0 1.3 - - - -
275A ARG 4.9 0.9 - - - -
276A GLY 6.1 1.8 - - - -
279A SER* 5.7 0.2 - - - -
310A ASN 3.8 2.6 + - - -
311A GLN 5.0 0.6 + - - -
312A ILE 3.4 4.9 + - - -
313A TYR* 1.3 79.0 - - - +
315A PHE* 1.3 58.5 + - - +
316A GLU 3.5 1.8 - - - -
317A GLY 3.4 3.7 + - - -
318A GLU* 2.8 32.7 + - - +
487A MET* 4.5 3.1 - - - -
489A TYR* 3.5 6.1 - - - +
490A ALA* 3.9 24.7 - - - +
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Residues in contact with PHE 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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273A VAL* 3.7 20.9 - - + -
274A ASP* 3.0 27.5 + - - +
279A SER* 3.6 20.4 - - - -
280A VAL* 4.0 10.5 - - + -
283A ILE* 3.9 13.2 - - + -
310A ASN* 3.5 26.0 + - - +
313A TYR 4.0 0.2 + - - -
314A GLY* 1.3 69.8 - - - +
316A GLU* 1.3 61.6 + - - +
318A GLU* 3.2 4.2 + - - -
319A VAL* 2.9 57.0 + - + +
328A TYR* 3.9 7.2 - + - -
331A PHE* 3.7 33.4 - + + -
335A PHE* 3.6 24.9 - + - -
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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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310A ASN* 3.1 19.7 + - - +
311A GLN* 2.0 45.7 + - - +
315A PHE* 1.3 76.7 - - - +
317A GLY* 1.3 53.5 + - - +
319A VAL* 3.4 2.4 + - - +
320A LYS* 2.9 66.5 + - + +
328A TYR* 3.7 39.5 - - + -
329A GLU* 4.8 2.6 - - - +
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Residues in contact with GLY 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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310A ASN 4.5 0.8 + - - -
311A GLN 5.5 1.8 + - - -
314A GLY 3.4 4.0 + - - -
315A PHE 3.3 0.2 - - - -
316A GLU* 1.3 77.2 - - - +
318A GLU* 1.3 57.0 + - - +
320A LYS* 3.5 8.0 + - - +
321A ALA* 3.0 31.5 + - - +
489A TYR* 3.3 26.1 - - - -
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Residues in contact with GLU 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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276A GLY 3.8 3.1 - - - +
277A SER* 3.3 17.4 - - - +
279A SER* 3.1 33.6 + - - -
280A VAL* 3.1 30.7 + - + +
281A GLU* 3.3 1.2 - - - +
314A GLY 2.8 21.4 + - - +
315A PHE* 3.2 6.0 + - - +
317A GLY* 1.3 74.9 - - - +
319A VAL* 1.3 55.5 + - - +
321A ALA* 3.3 2.4 + - - +
322A LYS* 2.8 56.1 + - - +
489A TYR* 3.4 27.4 - - + +
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Residues in contact with VAL 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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280A VAL* 3.8 12.3 - - + -
315A PHE* 2.9 59.0 + - + +
316A GLU 3.9 3.4 - - - +
318A GLU* 1.3 69.4 - - - +
320A LYS* 1.3 57.7 + - - +
322A LYS 4.5 0.2 - - - +
323A TYR* 2.6 36.8 + - + +
324A THR 3.4 3.8 + - - +
327A MET* 3.9 17.3 - - + -
328A TYR* 3.4 40.8 - - + +
331A PHE* 3.9 7.6 - - + -
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Residues in contact with LYS 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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316A GLU* 2.9 53.6 + - + +
317A GLY* 3.9 6.1 - - - +
319A VAL* 1.3 76.4 - - - +
321A ALA* 1.3 62.1 + - - +
323A TYR 3.5 13.5 - - - +
324A THR* 4.2 10.3 - - - +
325A ALA* 4.1 33.4 - - + +
328A TYR* 5.0 2.5 - - + -
329A GLU* 5.6 0.9 - - - -
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Residues in contact with ALA 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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203A LYS* 4.8 2.8 + - - -
317A GLY 3.0 18.1 + - - +
318A GLU 3.5 4.9 - - - +
320A LYS* 1.3 78.4 - - - +
322A LYS* 1.3 60.4 + - + +
323A TYR 4.9 0.6 - - - +
489A TYR* 4.0 24.0 - - + -
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Residues in contact with LYS 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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203A LYS* 2.9 49.5 + - + +
277A SER 3.8 8.9 + - - -
278A PHE* 5.2 1.8 - - - -
280A VAL* 4.1 14.4 - - + -
281A GLU* 3.0 26.3 + - - +
318A GLU* 2.8 52.1 + - + +
319A VAL* 5.0 0.4 - - - -
321A ALA* 1.3 81.8 - - + +
323A TYR* 1.3 76.1 + - + +
489A TYR* 3.6 20.9 + - + +
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Residues in contact with TYR 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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198A TYR* 4.9 0.5 + - - -
203A LYS* 3.6 18.5 - - + +
204A LEU* 2.6 36.8 + - - +
206A ARG* 3.7 25.8 - - + -
209A ALA* 3.8 14.2 - - + +
280A VAL* 4.1 23.9 - - + +
284A LEU* 4.1 9.7 - - + +
319A VAL* 2.6 22.4 + - + +
320A LYS 3.5 7.8 - - - +
321A ALA 4.9 0.7 - - - +
322A LYS* 1.3 88.1 - - + +
324A THR* 1.3 78.1 + - + +
327A MET* 3.5 38.6 - - + -
331A PHE* 5.1 2.5 - + - -
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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