Contacts of the helix formed by residues 360 - 370 (chain C) in PDB entry 2VM8
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 360 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C THR* 3.8 2.0 - - + -
356C ASN* 2.9 27.7 + - - +
357C GLY* 3.3 15.3 + - - -
359C GLU* 1.3 89.3 + - + +
361C ARG* 1.3 56.5 + - - +
362C MET 3.5 2.0 - - - -
363C SER* 3.2 8.0 + - - +
364C VAL* 2.8 39.3 + - + +
420C ILE* 3.7 23.9 - - + +
425C HIS* 4.3 9.4 + - - +
432C ASN* 3.0 18.4 - - - +
434C PHE* 3.2 28.4 - - + -
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Residues in contact with ARG 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLY* 3.6 2.8 - - - -
70C ILE 3.4 13.5 + - - +
71C ASP* 3.3 36.2 + - - +
101C THR* 3.1 24.8 + - - -
280C THR* 3.1 27.1 - - - +
329C THR* 2.7 41.1 + - - -
330C GLY* 3.6 28.5 - - - +
357C GLY 2.9 11.1 + - - +
358C THR* 4.2 7.6 + - - +
359C GLU 3.5 1.6 - - - -
360C GLU* 1.3 75.7 - - - +
362C MET* 1.3 70.9 + - + +
364C VAL* 3.8 1.4 - - - +
365C ILE* 3.2 39.6 + - + +
384C THR* 3.5 24.4 + - - +
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Residues in contact with MET 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ILE* 3.6 29.8 - - + -
67C PRO 4.5 1.3 - - - +
69C GLY* 3.8 15.7 - - - +
99C GLY 3.7 13.4 + - - +
100C GLY* 3.0 37.2 - - - +
101C THR* 3.6 15.9 - - - +
358C THR 5.3 0.8 + - - -
359C GLU 5.0 0.2 + - - -
360C GLU 3.5 0.4 - - - -
361C ARG* 1.3 87.6 - - - +
363C SER* 1.3 63.0 + - - +
365C ILE* 3.3 5.4 + - - -
366C TRP* 3.1 17.7 + - - +
380C PHE* 3.3 20.6 - - + -
384C THR* 3.4 28.7 - - - +
412C TRP* 3.8 12.1 - - + -
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Residues in contact with SER 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C GLY* 4.8 3.0 + - - -
359C GLU 5.1 2.8 + - - -
360C GLU* 3.2 10.6 + - - -
362C MET* 1.3 74.4 - - - +
364C VAL* 1.3 66.4 + - - +
366C TRP* 3.5 0.8 + - - -
367C ASP* 3.0 18.4 + - - +
412C TRP* 3.4 19.2 - - - -
420C ILE* 6.1 1.1 - - - -
439C CYS* 3.3 19.8 - - - -
440C ARG 3.5 3.6 - - - +
441C GLY 2.8 27.0 + - - -
442C SER* 3.8 5.2 - - - -
443C PRO* 4.1 5.0 - - - +
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Residues in contact with VAL 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C THR* 4.0 17.5 - - + +
283C LEU* 4.3 9.6 - - + +
284C GLY* 4.0 25.1 - - - +
360C GLU* 2.8 34.3 + - + +
361C ARG 3.8 3.8 - - - +
363C SER* 1.3 78.4 - - - +
365C ILE* 1.3 58.5 + - + +
367C ASP* 3.4 1.7 + - - +
368C LYS* 2.9 41.9 + - + +
420C ILE* 4.0 17.7 - - + -
434C PHE* 4.6 5.6 - - + -
437C MET* 4.0 12.8 - - - -
439C CYS* 4.0 4.9 - - - -
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Residues in contact with ILE 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C THR* 6.4 0.4 - - - -
283C LEU* 4.2 18.6 - - + -
318C ASN* 4.4 6.7 - - - +
321C LEU* 4.1 18.2 - - + -
329C THR* 3.4 35.7 - - + +
361C ARG* 3.2 27.4 + - + +
362C MET* 3.8 3.4 - - - +
363C SER 3.2 0.2 - - - -
364C VAL* 1.3 75.6 - - + +
366C TRP* 1.3 68.4 + - - +
369C ALA* 2.9 34.7 + - + +
370C VAL* 4.6 0.2 - - - +
375C MET* 4.6 1.3 - - + -
380C PHE* 4.0 16.8 - - + -
383C VAL* 4.5 7.9 - - + -
384C THR* 3.7 16.2 - - + -
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Residues in contact with TRP 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C MET* 3.6 29.2 - - + -
362C MET 3.1 15.3 + - - +
363C SER 3.7 4.9 - - - +
365C ILE* 1.3 79.4 - - - +
367C ASP* 1.3 62.8 + - - +
370C VAL* 3.2 33.1 + - + +
371C VAL* 3.0 35.9 + - + +
377C GLU* 3.9 12.1 - - + -
380C PHE* 3.5 51.0 - + + -
412C TRP* 3.6 15.7 - - + +
414C PRO* 3.4 41.2 + - + +
440C ARG 3.2 20.4 - - - +
441C GLY* 3.8 9.4 - - - -
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Residues in contact with ASP 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363C SER 3.0 17.9 + - - +
364C VAL 3.6 4.3 - - - +
366C TRP* 1.3 78.3 - - - +
368C LYS* 1.3 76.2 + - + +
369C ALA 3.6 0.2 + - - -
371C VAL* 3.2 27.8 - - - +
372C THR* 3.6 8.7 - - - +
437C MET* 5.0 5.5 - - - +
438C GLU 3.8 9.1 - - - +
439C CYS* 3.7 14.3 - - - -
440C ARG* 2.8 36.6 + - - +
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Residues in contact with LYS 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C LEU 3.3 24.5 - - - +
284C GLY* 4.2 12.8 + - - +
314C PRO* 4.2 16.0 - - - +
315C ASP* 4.2 19.0 + - - +
318C ASN* 3.6 26.7 - - - +
364C VAL* 2.9 32.4 + - + +
367C ASP* 1.3 92.4 - - + +
369C ALA* 1.3 56.6 + - - +
372C THR* 2.9 19.4 + - - +
374C LYS* 4.1 10.2 - - - +
437C MET* 5.3 7.6 - - + +
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Residues in contact with ALA 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C ASN* 3.8 16.6 - - + +
322C SER* 4.1 5.8 - - - +
365C ILE* 2.9 15.9 + - + +
368C LYS* 1.3 77.3 - - - +
370C VAL* 1.3 54.6 + - + +
372C THR* 3.2 8.1 - - - -
374C LYS* 2.7 37.0 + - - +
375C MET* 2.8 43.1 + - + -
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Residues in contact with VAL 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C TRP* 3.2 47.8 + - + +
369C ALA* 1.3 75.8 - - + +
371C VAL* 1.3 71.4 + - - +
372C THR 3.1 1.3 - - - -
373C GLY* 3.0 12.5 + - - -
375C MET* 3.2 40.9 - - + +
376C ASP* 4.3 1.1 - - - +
377C GLU 4.6 6.7 - - - +
380C PHE* 4.0 24.7 - - + -
484D ALA* 4.4 7.4 - - - +
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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
------------------------------------------------------------
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