Contacts of the helix formed by residues 360 - 370 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D THR* 4.2 7.0 - - + -
333D HIS* 5.7 0.2 - - - -
356D ASN* 3.4 21.7 + - - +
357D GLY* 3.5 17.5 + - - -
358D THR 3.4 0.2 - - - -
359D GLU* 1.3 93.3 + - + +
361D ARG* 1.3 65.9 + - - +
362D MET 3.2 3.0 + - - -
363D SER* 3.3 7.6 + - - -
364D VAL* 2.9 42.5 + - + +
420D ILE* 4.1 29.6 - - + +
425D HIS* 4.3 8.8 + - - +
432D ASN* 2.9 22.1 + - - -
434D PHE* 4.3 6.4 - - + -
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Residues in contact with ARG 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D GLY* 3.3 7.7 - - - -
70D ILE 3.1 42.0 + - - +
71D ASP* 4.1 9.7 - - - -
101D THR* 3.1 25.0 + - - +
280D THR* 3.2 25.5 - - - +
283D LEU* 5.9 0.2 - - + -
329D THR* 3.1 40.6 + - - -
330D GLY* 3.8 14.4 - - - +
357D GLY 3.4 8.4 + - - +
358D THR* 4.3 7.2 - - - +
359D GLU 3.5 2.6 - - - -
360D GLU* 1.3 78.8 - - - +
362D MET* 1.3 65.2 + - + +
364D VAL* 3.3 2.3 + - - +
365D ILE* 3.2 43.1 + - + +
384D THR* 2.8 26.9 + - - +
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Residues in contact with MET 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D ILE* 4.1 15.7 - - + -
67D PRO 4.9 1.3 - - - +
69D GLY* 3.6 31.9 - - - +
99D GLY 4.2 7.4 - - - +
100D GLY* 3.9 24.5 - - - +
101D THR* 4.3 2.2 - - - +
359D GLU 4.9 1.8 + - - -
360D GLU 3.3 0.2 - - - -
361D ARG* 1.3 92.9 - - + +
363D SER* 1.3 63.9 + - - +
365D ILE* 4.1 3.1 - - - -
366D TRP* 3.3 23.9 + - - +
380D PHE* 3.4 29.6 - - + -
384D THR* 3.6 26.0 - - + +
410D VAL* 5.0 2.0 - - + -
412D TRP* 3.4 21.5 - - + -
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Residues in contact with SER 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D GLY* 5.0 3.3 + - - -
359D GLU 5.1 3.1 + - - -
360D GLU* 3.3 11.9 + - - -
362D MET* 1.3 77.2 - - - +
364D VAL* 1.3 60.4 + - - +
366D TRP* 3.5 0.3 + - - +
367D ASP* 2.9 33.1 + - - +
412D TRP* 3.8 5.1 - - - -
420D ILE* 5.1 4.3 - - - -
439D CYS* 3.3 15.3 - - - -
440D ARG 3.6 1.7 - - - +
441D GLY 2.6 29.7 + - - -
442D SER* 3.8 9.5 - - - -
443D PRO* 4.6 4.0 - - - +
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Residues in contact with VAL 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D THR* 3.8 19.3 - - + +
283D LEU* 4.1 7.6 - - + +
284D GLY* 3.5 32.1 - - - +
360D GLU* 2.9 37.1 + - + +
361D ARG 3.8 3.8 - - - +
363D SER* 1.3 76.5 - - - +
365D ILE* 1.3 59.1 + - + +
367D ASP* 4.0 1.5 - - - +
368D LYS* 2.9 35.8 + - + +
420D ILE* 4.5 5.6 - - + -
434D PHE* 4.6 5.6 - - + -
437D MET* 4.5 18.8 - - - -
439D CYS* 4.3 4.7 - - - -
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Residues in contact with ILE 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D THR* 6.4 0.2 - - - -
283D LEU* 3.9 19.5 - - + -
318D ASN* 4.2 6.1 - - - +
321D LEU* 4.3 5.4 - - + -
329D THR* 3.6 37.0 - - + +
361D ARG* 3.2 26.3 + - + +
362D MET* 4.6 0.2 - - - -
364D VAL* 1.3 75.2 - - + +
366D TRP* 1.3 61.2 + - - +
368D LYS 3.0 0.5 + - - -
369D ALA* 2.6 51.5 + - + +
375D MET* 4.2 3.8 - - + -
380D PHE* 4.1 19.3 - - + -
383D VAL* 4.2 16.6 - - + -
384D THR* 4.2 14.1 - - + -
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Residues in contact with TRP 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D MET* 3.6 34.5 - - + -
362D MET 3.3 19.3 + - - +
363D SER 3.7 2.9 - - - +
365D ILE* 1.3 77.8 - - - +
367D ASP* 1.3 55.0 + - - +
370D VAL* 2.9 68.6 + - + +
371D VAL* 3.0 24.4 + - + +
377D GLU* 4.2 13.5 - - + -
380D PHE* 3.7 26.1 - + + -
412D TRP* 3.3 20.4 - + + -
414D PRO* 3.2 41.7 + - + +
440D ARG* 3.3 18.8 - - - -
441D GLY* 3.8 7.2 - - - -
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Residues in contact with ASP 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D SER 2.9 21.5 + - - +
364D VAL* 4.0 2.2 - - - +
366D TRP* 1.3 74.3 - - - +
368D LYS* 1.3 74.6 + - - +
369D ALA 3.4 0.2 - - - -
371D VAL* 3.8 22.8 - - - +
372D THR* 3.9 10.0 - - - +
437D MET* 5.3 3.7 - - - +
438D GLU 4.1 5.4 - - - +
439D CYS* 3.6 16.1 - - + +
440D ARG* 2.9 41.5 + - - +
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Residues in contact with LYS 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D LEU 3.9 18.6 - - - +
284D GLY* 5.0 7.7 + - - +
314D PRO* 4.2 20.1 - - - +
315D ASP* 5.1 6.0 - - - +
318D ASN* 3.7 28.2 - - - +
364D VAL* 2.9 32.4 + - + +
367D ASP* 1.3 85.5 - - - +
369D ALA* 1.3 58.0 - - - +
372D THR* 2.9 24.6 + - + +
374D LYS* 4.0 8.3 + - - +
437D MET* 5.7 5.8 - - + -
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Residues in contact with ALA 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D ASN* 3.5 18.8 - - + +
322D SER* 4.2 5.4 - - - +
365D ILE* 2.6 21.4 + - + +
368D LYS* 1.3 72.9 - - - +
370D VAL* 1.3 57.0 + - - +
372D THR* 3.1 8.7 - - - -
374D LYS* 2.8 32.5 + - - +
375D MET* 2.9 40.5 + - + -
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Residues in contact with VAL 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484C ALA* 4.3 10.6 - - - +
365D ILE 4.5 0.9 - - - +
366D TRP* 2.9 70.4 + - + +
369D ALA* 1.3 70.8 - - - +
371D VAL* 1.3 61.8 + - + +
372D THR 3.2 1.3 - - - -
373D GLY* 3.2 17.3 + - - -
375D MET* 3.4 34.9 - - + +
376D ASP* 4.1 8.7 - - - +
377D GLU 4.4 1.1 - - - +
380D PHE* 3.8 15.7 - - + -
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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