Contacts of the helix formed by residues 360 - 373 (chain B) in PDB entry 3V9G
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 LEU 360 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B VAL* 4.3 9.2 - - + -
324B HIS 3.4 10.3 - - - +
325B ARG* 3.1 42.4 - - - +
327B ALA* 4.5 8.7 - - + +
329B VAL* 3.6 26.5 - - + -
357B PRO* 3.1 15.5 + - + +
359B SER* 1.3 85.9 + - - +
361B TRP* 1.3 67.0 + - - +
362B PRO* 3.4 2.9 - - - -
363B GLN* 3.2 15.5 + - - +
364B ILE* 3.0 36.5 + - + +
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Residues in contact with TRP 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B VAL* 4.0 18.2 - - + -
357B PRO 3.1 12.4 + - - +
358B HIS* 3.6 11.4 - + - +
360B LEU* 1.3 75.6 - - - +
362B PRO* 1.3 64.5 - - + +
364B ILE* 3.1 9.8 + - + -
365B LYS* 2.7 78.5 + - + +
368B LEU* 4.7 8.5 - - + -
369B LEU* 6.3 0.4 - - + -
416B LEU* 3.6 31.0 - - + -
433B ILE* 5.7 0.7 - - + -
435B GLU* 3.8 19.6 + - - -
455B VAL* 3.8 28.0 - - + -
457B VAL* 3.6 33.9 - - + +
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Residues in contact with PRO 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B HIS* 3.4 17.3 - - + +
359B SER 3.9 7.2 - - - +
360B LEU 3.5 3.8 - - - -
361B TRP* 1.3 95.3 - - + +
363B GLN* 1.3 62.3 + - - +
365B LYS* 3.8 6.7 - - + +
366B GLY* 3.1 20.1 + - - -
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Residues in contact with GLN 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B VAL* 3.0 41.4 - - + +
359B SER 5.8 0.9 - - - +
360B LEU* 3.2 16.8 + - + +
362B PRO* 1.3 79.8 - - - +
364B ILE* 1.3 58.1 + - + +
366B GLY* 3.4 1.2 + - - -
367B ARG* 3.1 40.2 + - + +
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Residues in contact with ILE 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B VAL* 4.5 10.1 - - + -
329B VAL* 3.9 30.3 - - + -
332B VAL* 4.4 24.9 - - + -
333B VAL* 4.5 6.3 - - + -
354B LEU* 5.1 1.8 - - + -
356B VAL* 3.6 28.5 - - + -
360B LEU* 3.0 28.5 + - + +
361B TRP* 3.9 12.3 - - + +
363B GLN* 1.3 74.3 - - - +
365B LYS* 1.3 60.1 + - - +
367B ARG* 3.4 3.5 + - - +
368B LEU* 2.8 54.5 + - + +
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Residues in contact with LYS 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B TRP* 2.7 62.8 + - + +
362B PRO* 3.8 6.5 - - + +
364B ILE* 1.3 73.2 - - - +
366B GLY* 1.3 57.7 + - - +
368B LEU* 3.8 3.1 - - - +
369B LEU* 3.1 53.5 + - + +
416B LEU* 4.2 26.9 - - + +
435B GLU* 4.5 6.7 + - - -
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Residues in contact with GLY 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B PRO 3.1 14.6 + - - -
363B GLN* 3.9 2.7 - - - -
365B LYS* 1.3 77.6 - - - +
367B ARG* 1.3 59.4 + - - +
369B LEU* 3.4 5.1 + - - +
370B GLU* 2.9 30.3 + - - +
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Residues in contact with ARG 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B VAL* 4.6 3.8 - - + -
330B GLU* 3.4 36.0 + - - +
333B VAL* 3.8 24.7 - - + +
363B GLN* 3.1 28.7 + - + +
364B ILE 4.0 0.2 - - - +
366B GLY* 1.3 73.0 - - - +
368B LEU* 1.3 66.0 + - - +
370B GLU* 3.9 9.3 - - - +
371B GLU* 3.0 77.0 + - - +
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Residues in contact with LEU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B VAL* 4.0 21.8 - - + +
336B THR* 5.1 8.7 - - + -
337B LEU* 4.0 29.5 - - + +
354B LEU* 4.4 19.1 - - + -
361B TRP* 4.7 11.2 - - + -
364B ILE* 2.8 38.5 + - + +
365B LYS* 3.8 4.5 - - - +
367B ARG* 1.3 77.1 - - - +
369B LEU* 1.3 60.1 + - + +
371B GLU* 3.3 1.8 + - - +
372B HIS* 2.7 37.6 + - - +
433B ILE* 4.5 18.8 - - + +
453B LEU* 5.0 7.0 - - + -
455B VAL* 5.4 0.4 - - + -
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Residues in contact with LEU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B TRP* 6.3 0.4 - - + -
365B LYS* 3.1 45.2 + - + +
366B GLY* 3.9 5.4 - - - +
368B LEU* 1.3 79.4 - - + +
370B GLU* 1.3 65.7 + - - +
372B HIS* 3.6 5.7 + - - +
373B SER* 3.3 22.2 + - - -
416B LEU* 4.2 33.9 - - + +
417B ALA* 4.3 13.7 - - + -
433B ILE* 4.5 10.3 - - + -
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Residues in contact with GLU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B GLY 2.9 18.6 + - - +
367B ARG* 3.9 16.6 - - - +
368B LEU 3.3 0.2 - - - -
369B LEU* 1.3 77.0 - - - +
371B GLU* 1.3 63.9 + - - +
373B SER* 2.7 25.0 + - - -
374B ARG* 3.7 4.7 + - - +
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Residues in contact with GLU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A TRP* 3.0 33.4 + - + +
333B VAL* 4.2 6.5 - - + -
337B LEU* 3.7 20.6 - - + -
367B ARG* 3.0 58.2 + - - +
368B LEU 4.0 0.2 - - - +
370B GLU* 1.3 76.0 - - - +
372B HIS* 1.3 67.3 + - - +
374B ARG* 2.9 23.0 + - - +
375B ILE* 3.6 11.3 + - - +
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Residues in contact with HIS 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B LEU* 4.7 3.2 - - + +
341B PHE* 4.9 1.6 - + - -
368B LEU 2.7 21.9 + - - +
369B LEU* 3.6 10.4 + - - +
371B GLU* 1.3 72.6 - - - +
373B SER* 1.3 67.6 + - - +
375B ILE* 3.1 32.0 + - + +
417B ALA* 3.7 20.2 - - + +
418B GLY* 3.7 20.0 - - - -
430B GLU* 5.9 1.1 - - + -
431B PRO* 2.7 47.0 + - + +
433B ILE* 4.1 20.2 - - + -
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Residues in contact with SER 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B LEU 3.3 10.4 + - - -
370B GLU* 2.7 21.8 + - - -
371B GLU 3.1 0.4 - - - -
372B HIS* 1.3 85.2 + - - +
374B ARG* 1.3 57.9 + - - +
375B ILE 3.3 2.6 + - - +
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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