Contacts of the helix formed by residues 379 - 395 (chain B) in PDB entry 3GV5
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 VAL 379 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329B LEU* 4.0 27.6 - - + -
368B VAL* 3.7 29.2 - - + +
371B LYS* 3.8 37.0 - - + -
377B TYR* 3.6 8.1 + - + +
378B ASP* 1.3 72.0 + - - +
380B MSE 1.3 70.5 + - + +
381B THR 3.4 1.8 - - - -
382B PRO* 3.3 5.4 - - + +
383B MSE 3.1 31.1 + - + +
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Residues in contact with MSE 380 (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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322B GLU* 3.6 47.8 - - + +
325B LEU* 3.8 12.8 - - - -
326B ALA* 4.3 14.4 - - + -
329B LEU* 3.7 25.1 - - + -
378B ASP* 3.5 9.6 + - - +
379B VAL* 1.3 80.6 - - + +
381B THR* 1.3 56.9 + - - +
383B MSE 3.8 2.0 - - - +
384B VAL* 2.9 42.4 + - + +
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Residues in contact with THR 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ASP* 3.2 29.4 + - + +
380B MSE 1.3 79.8 - - - +
382B PRO* 1.4 75.3 - - + +
384B VAL* 3.4 10.1 - - - +
385B ASP* 3.1 31.9 + - - -
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Residues in contact with PRO 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B VAL* 4.2 26.9 - - + -
378B ASP 3.4 15.0 - - - +
379B VAL* 3.3 14.1 - - - +
381B THR* 1.4 103.2 - - + +
383B MSE 1.3 61.1 + - - +
385B ASP* 3.4 11.0 - - + +
386B ILE* 3.1 29.6 + - + +
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Residues in contact with MSE 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU* 3.6 22.2 - - + -
329B LEU* 5.1 5.4 - - + -
342B VAL* 3.3 46.4 - - + -
364B ILE* 4.2 21.3 - - - -
368B VAL* 4.1 4.9 - - + -
371B LYS* 5.8 2.5 - - - -
379B VAL* 3.1 37.5 + - + +
382B PRO* 1.3 74.9 - - - +
384B VAL* 1.3 60.2 + - - +
386B ILE* 3.3 14.5 + - + +
387B LEU* 3.0 41.1 + - + +
410B PHE* 3.9 14.4 - - + -
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Residues in contact with VAL 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LYS* 4.6 16.4 - - + +
321B ILE* 5.1 5.2 - - + -
322B GLU* 3.7 39.0 - - + +
325B LEU* 3.5 20.9 - - + -
380B MSE 2.9 29.8 + - + +
381B THR* 3.4 15.9 - - - +
383B MSE 1.3 68.9 - - - +
385B ASP* 1.3 64.3 + - - +
387B LEU* 3.3 6.9 + - - +
388B MSE 2.9 38.2 + - + +
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Residues in contact with ASP 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B LYS* 5.6 4.0 + - - -
381B THR* 3.1 25.4 + - - +
382B PRO* 3.4 16.4 - - + +
384B VAL* 1.3 79.2 - - - +
386B ILE* 1.3 62.2 + - + +
388B MSE 3.6 4.5 + - - +
389B LYS* 3.3 37.3 + - - +
392B ARG* 4.9 1.2 + - - -
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Residues in contact with ILE 386 (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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342B VAL* 5.3 4.9 - - + -
362B CYS* 3.5 29.2 - - - -
363B PRO 4.7 3.8 - - - +
364B ILE* 4.9 1.8 - - + -
365B PRO* 3.4 36.1 - - + -
368B VAL* 5.2 4.0 - - + -
382B PRO* 3.1 16.6 + - + +
383B MSE 3.6 23.6 - - + +
385B ASP* 1.3 78.8 - - + +
387B LEU* 1.3 62.7 + - + +
389B LYS* 3.3 23.5 + - + +
390B LEU* 3.0 29.2 + - + +
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ILE* 3.7 31.6 - - + -
325B LEU* 3.9 20.6 - - + -
342B VAL* 3.7 22.0 - - + -
343B ARG 4.4 1.1 - - - +
344B LEU* 3.6 30.5 - - + +
383B MSE 3.0 30.9 + - + +
384B VAL* 3.3 3.8 + - - +
386B ILE* 1.3 76.2 - - + +
388B MSE 1.3 58.7 + - - +
390B LEU* 3.3 11.6 + - + +
391B PHE* 2.8 27.2 + - - +
408B VAL* 3.9 24.0 - - + -
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Residues in contact with MSE 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLU* 3.6 33.0 - - + +
318B LYS* 3.9 50.3 - - + +
321B ILE* 3.7 27.8 - - - -
384B VAL* 2.9 26.6 + - + +
385B ASP* 4.1 4.7 - - - +
387B LEU* 1.3 70.0 - - - +
389B LYS* 1.3 60.4 + - - +
391B PHE* 3.5 23.4 - - + +
392B ARG* 2.9 52.6 + - - +
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Residues in contact with LYS 389 (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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385B ASP* 3.3 26.5 + - - +
386B ILE* 3.3 25.8 + - - +
388B MSE 1.3 72.0 - - - +
390B LEU* 1.3 68.3 + - + +
392B ARG* 3.5 20.8 + - - +
393B ASN* 3.1 23.9 + - - +
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Residues in contact with LEU 390 (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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342B VAL* 4.0 16.6 - - + +
344B LEU* 4.1 18.6 - - + +
360B ARG* 3.4 43.6 - - + +
361B GLN* 4.1 7.6 - - - +
362B CYS* 4.0 27.6 - - + -
386B ILE* 3.0 18.9 + - + +
387B LEU* 3.5 17.9 - - + +
389B LYS* 1.3 76.4 - - + +
391B PHE* 1.3 61.1 + - - +
393B ASN* 3.4 9.5 + - + +
394B MSE 3.3 23.8 + - - +
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Residues in contact with PHE 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLU* 4.4 8.1 - - + -
317B ALA* 3.9 22.7 - - + -
321B ILE* 4.2 9.4 - - + -
344B LEU* 3.6 21.9 - - + +
346B ILE* 4.6 2.9 - - + -
387B LEU 2.8 19.3 + - - +
388B MSE 3.5 25.6 - - + +
389B LYS 3.3 0.4 - - - -
390B LEU* 1.3 72.5 - - - +
392B ARG* 1.3 57.2 + - + +
394B MSE 3.0 7.4 + - - +
395B VAL* 2.7 60.8 + - + +
397B VAL* 3.9 17.5 - - + -
401B PHE* 3.9 20.0 - + - -
403B LEU* 3.6 21.3 - - + -
406B LEU* 4.3 7.0 - - + -
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Residues in contact with ARG 392 (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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314B GLU* 2.8 44.3 + - - +
385B ASP 4.9 1.0 + - - -
388B MSE 2.9 35.2 + - - +
389B LYS* 3.7 33.4 - - - +
391B PHE* 1.3 70.8 - - + +
393B ASN* 1.3 63.4 + - - +
395B VAL 3.2 18.3 - - - +
396B ASN* 4.9 1.7 - - - -
397B VAL* 3.9 24.5 - - + -
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Residues in contact with ASN 393 (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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360B ARG* 3.2 37.5 + - + +
389B LYS 3.1 14.1 + - - +
390B LEU* 3.4 15.7 - - + +
392B ARG* 1.3 78.3 - - - +
394B MSE 1.3 59.6 + - - +
867P G 5.3 0.2 + - - -
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Residues in contact with MSE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 3.7 36.3 - - + +
346B ILE* 4.0 23.8 - - + -
348B ARG* 3.3 19.4 + - - -
358B GLU* 3.8 28.4 - - + +
359B SER 3.7 8.3 - - - -
360B ARG* 3.5 58.6 - - + +
390B LEU 3.3 14.5 + - - +
391B PHE* 3.0 5.4 + - - +
393B ASN* 1.3 81.4 - - - +
395B VAL* 1.3 59.9 + - + +
396B ASN 4.0 1.6 + - - -
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Residues in contact with VAL 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ILE* 3.8 24.9 - - + -
348B ARG* 3.8 9.0 - - - +
391B PHE* 2.7 48.2 + - + +
392B ARG* 3.2 18.0 - - - +
394B MSE 1.3 76.7 - - + +
396B ASN* 1.3 63.4 + - - +
397B VAL* 3.1 15.3 + - + +
401B PHE* 3.5 48.7 - - + -
403B LEU* 4.4 5.4 - - + -
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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