Contacts of the helix formed by residues 308 - 319 (chain Y) in PDB entry 1MVW
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 308 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219Y VAL* 3.0 19.5 - - - +
221Y LEU* 4.7 6.0 - - - +
306Y TYR 3.5 0.2 + - - -
307Y PRO* 1.3 72.2 - - - +
309Y ILE* 1.3 63.0 + - - +
310Y ALA* 3.3 3.5 - - - +
311Y ASP* 4.0 22.1 - - - +
312Y ARG* 3.3 21.5 + - - +
335Y ARG* 5.9 0.2 - - - +
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Residues in contact with ILE 309 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153Y LEU* 5.7 4.9 - - + -
219Y VAL* 3.9 14.8 - - + -
261Y LEU* 4.3 13.9 - - + -
262Y PHE* 4.6 9.3 - - + -
274Y ILE* 6.2 2.7 - - + -
299Y MET* 4.3 13.5 - - + -
303Y THR 3.9 7.4 - - - +
304Y THR* 3.2 52.3 - - + +
306Y TYR* 3.2 25.4 - - + +
307Y PRO 3.2 1.2 - - - -
308Y GLY* 1.3 78.4 - - - +
310Y ALA* 1.3 71.8 + - + +
312Y ARG* 3.8 2.3 + - - +
313Y MET* 3.0 32.6 + - + +
335Y ARG* 3.5 14.1 - - - +
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Residues in contact with ALA 310 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299Y MET* 4.0 22.9 - - + -
308Y GLY* 5.7 0.7 - - - -
309Y ILE* 1.3 82.7 - - + +
311Y ASP* 1.4 54.0 + - - +
313Y MET* 3.1 3.8 + - - +
314Y GLN* 2.8 38.4 + - + +
329Y ILE* 4.1 15.2 - - + +
331Y ALA* 4.1 13.9 - - + -
335Y ARG* 5.5 0.4 - - - +
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Residues in contact with ASP 311 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221Y LEU* 3.8 31.6 - - + +
308Y GLY* 3.8 16.9 + - - +
309Y ILE 3.5 0.4 - - - -
310Y ALA* 1.4 73.5 - - - +
312Y ARG* 1.3 65.2 + - - +
314Y GLN* 3.2 10.9 - - - +
315Y LYS* 3.0 26.7 + - - +
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Residues in contact with ARG 312 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219Y VAL* 3.6 12.8 - - + -
220Y ALA 3.0 20.9 + - - +
221Y LEU* 3.8 15.0 - - - +
222Y ASP 4.9 2.7 - - - +
223Y PHE* 2.9 41.5 - - - +
262Y PHE* 3.3 25.6 - - + +
263Y GLN* 3.4 26.7 + - - +
308Y GLY 3.3 13.8 + - - +
309Y ILE 3.9 3.1 - - - +
310Y ALA 3.4 0.2 - - - -
311Y ASP* 1.3 78.0 - - - +
313Y MET* 1.3 53.3 + - - +
315Y LYS* 3.6 3.7 - - - +
316Y GLU* 2.7 76.6 + - - +
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Residues in contact with MET 313 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153Y LEU* 4.5 9.4 - - + -
262Y PHE* 4.2 11.0 - - + -
274Y ILE* 3.9 17.0 - - + -
275Y HIS* 3.4 34.8 - - - -
278Y THR* 3.0 36.8 - - + +
297Y ASN* 4.4 11.0 - - - +
299Y MET* 4.8 8.3 - - - -
309Y ILE* 3.0 23.5 + - + +
310Y ALA* 3.1 4.7 + - - +
312Y ARG* 1.3 71.7 - - - +
314Y GLN* 1.3 58.8 + - - +
316Y GLU* 3.6 2.4 - - - +
317Y ILE* 2.9 39.4 + - + +
329Y ILE* 4.1 17.0 - - + -
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Residues in contact with GLN 314 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310Y ALA* 2.8 13.3 + - + +
311Y ASP* 3.2 17.0 - - - +
313Y MET* 1.3 76.1 - - - +
315Y LYS* 1.3 61.5 + - + +
318Y THR* 2.8 35.0 + - - +
327Y ILE* 3.5 32.2 + - - +
328Y LYS* 4.3 2.4 - - - +
329Y ILE* 3.5 30.1 - - + +
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Residues in contact with LYS 315 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221Y LEU* 6.3 4.3 - - + -
311Y ASP 3.0 12.8 + - - +
312Y ARG* 4.0 3.8 - - - +
314Y GLN* 1.3 83.8 - - + +
316Y GLU* 1.3 66.4 + - - +
318Y THR* 3.1 34.0 + - + +
319Y ALA* 3.5 30.5 - - - +
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Residues in contact with GLU 316 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262Y PHE* 4.6 2.2 - - + -
275Y HIS* 3.2 57.8 + - + +
312Y ARG* 2.7 60.6 + - - +
313Y MET* 3.2 7.4 + - - +
315Y LYS* 1.3 82.1 - - + +
317Y ILE* 1.3 62.9 + - - +
319Y ALA* 3.9 3.7 + - - +
320Y LEU* 3.8 17.0 + - - +
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Residues in contact with ILE 317 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275Y HIS* 3.8 23.6 - - + +
278Y THR* 4.1 16.2 - - + -
279Y TYR* 5.1 5.8 - - + +
294Y TYR* 4.0 25.3 - - + +
297Y ASN* 3.9 13.5 - - - +
313Y MET* 2.9 28.4 + - + +
316Y GLU* 1.3 76.1 - - - +
318Y THR* 1.3 66.5 + - - +
319Y ALA 3.2 2.5 - - - -
320Y LEU* 3.0 6.2 + - + +
321Y ALA* 2.9 25.6 + - - +
327Y ILE* 3.7 26.0 - - + -
329Y ILE* 3.6 21.5 - - + -
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Residues in contact with THR 318 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314Y GLN* 2.8 30.5 + - - +
315Y LYS* 3.1 30.6 + - + +
317Y ILE* 1.3 72.8 - - - +
319Y ALA* 1.3 60.7 + - - +
320Y LEU 3.1 5.5 + - - -
321Y ALA* 3.1 20.8 - - - +
323Y SER* 5.8 0.5 - - - -
325Y MET 6.1 0.4 - - - +
327Y ILE* 3.7 30.1 - - + -
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Residues in contact with ALA 319 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315Y LYS* 3.5 28.2 + - - +
316Y GLU* 4.0 4.5 - - - +
317Y ILE 3.2 0.8 - - - -
318Y THR* 1.3 79.7 + - - +
320Y LEU* 1.3 58.9 + - - +
321Y ALA 4.8 0.4 - - - -
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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
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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