Contacts of the helix formed by residues 413 - 431 (chain B) in PDB entry 2VGB
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 PHE 413 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B MET* 3.5 29.0 + - + +
379B THR 3.9 12.3 - - - -
380B LYS* 3.6 20.0 - - - -
381B PRO* 4.0 28.9 - - + -
407B GLU 4.0 3.8 - - - -
411B GLY* 3.3 1.4 - - - -
412B ASN* 1.3 104.3 - - + +
414B PRO* 1.3 62.4 - - - +
416B GLU* 3.2 42.8 + - + +
417B ALA* 2.8 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ALA* 3.8 23.6 - - + +
103B ARG* 4.4 16.6 - - + +
107B MET* 4.4 10.1 - - - -
407B GLU 3.4 12.1 - - - +
408B THR* 3.7 31.7 - - + +
411B GLY 3.8 8.7 - - - +
412B ASN 3.6 5.8 - - - +
413B PHE* 1.3 89.5 - - - +
415B VAL* 1.3 64.8 + - + +
416B GLU* 4.5 0.9 - - - +
417B ALA* 3.2 3.8 + - - +
418B VAL* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ARG* 4.5 16.4 - - - +
106B GLU* 3.7 38.1 - - + +
107B MET* 3.6 26.2 - - + -
110B ALA* 4.1 12.6 - - + -
414B PRO* 1.3 74.7 - - + +
416B GLU* 1.3 69.3 + - - +
418B VAL* 3.1 3.4 + - - +
419B LYS* 2.8 51.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B MET* 3.9 18.6 - - + +
381B PRO* 4.7 6.1 - - + +
412B ASN 4.5 0.3 - - - +
413B PHE* 3.2 45.8 - - + +
414B PRO* 4.5 0.9 - - - +
415B VAL* 1.3 78.3 + - + +
417B ALA* 1.3 62.4 + - - +
419B LYS* 3.3 14.4 + - + +
420B MET* 3.0 24.6 + - - +
179D LYS* 5.9 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU* 3.6 11.2 - - + +
377B MET* 3.9 21.7 - - + +
404B LEU* 4.0 11.4 - - + -
407B GLU* 3.8 31.4 - - + +
413B PHE 2.8 22.0 + - - +
414B PRO 3.4 5.4 - - - +
415B VAL 3.2 0.2 - - - -
416B GLU* 1.3 73.6 - - - +
418B VAL* 1.3 59.7 + - - +
420B MET 3.4 1.2 + - - -
421B GLN* 3.3 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ILE* 4.0 10.2 - - + +
92B ALA* 4.6 5.8 - - + -
107B MET* 4.0 19.7 - - + +
110B ALA* 3.8 20.9 - - + +
111B GLY* 4.0 3.1 - - - -
112B MET* 3.7 26.9 - - + +
404B LEU* 3.7 20.6 - - + -
408B THR* 3.8 9.0 - - + -
414B PRO 3.0 16.9 + - - +
415B VAL* 3.7 7.2 - - - +
417B ALA* 1.3 71.4 - - - +
419B LYS* 1.3 68.3 + - - +
420B MET 3.2 0.2 + - - -
421B GLN* 3.3 4.2 + - - +
422B HIS* 3.0 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ALA* 3.7 24.5 - - + +
415B VAL* 2.8 36.6 + - - +
416B GLU* 3.5 13.2 - - + +
418B VAL* 1.3 76.8 - - - +
420B MET* 1.3 56.5 + - - +
422B HIS* 3.4 6.7 + - - +
423B ALA* 2.9 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU* 4.1 11.7 - - + -
377B MET* 4.4 7.4 - - + +
382B ARG* 4.4 13.9 - - - -
383B PRO* 3.8 31.6 - - + -
388B THR* 4.2 5.6 - - - +
416B GLU 3.0 16.0 + - - +
417B ALA 3.7 4.7 - - - +
418B VAL 3.2 0.2 - - - -
419B LYS* 1.3 73.0 - - - +
421B GLN* 1.3 67.4 + - - +
423B ALA* 3.0 3.9 + - + +
424B ILE* 2.9 63.6 + - + +
346D ALA* 4.3 1.1 - - - -
347D GLU* 3.4 40.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ILE* 3.5 31.3 - - + +
373B MET* 3.9 20.6 - - - +
374B LEU* 3.6 18.8 - - + +
391B VAL* 4.3 6.4 - - + +
402B ILE* 3.4 40.0 + - + +
403B MET 3.0 16.0 + - - +
404B LEU* 3.6 21.2 - - + +
417B ALA 3.3 7.1 + - - +
418B VAL 3.3 3.6 + - - +
420B MET* 1.3 76.9 - - - +
422B HIS* 1.3 63.8 + - - +
424B ILE* 4.2 6.5 - - - +
425B ALA* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ALA* 6.2 0.2 - - - -
86B ARG* 2.9 51.0 + - + +
90B ILE* 3.6 6.5 - - + +
110B ALA 3.8 18.5 + - - +
111B GLY* 5.1 0.4 - - - -
418B VAL 3.0 14.4 + - - +
419B LYS* 3.4 10.5 - - - +
421B GLN* 1.3 76.6 - - - +
423B ALA* 1.3 67.7 + - + +
426B ARG* 3.2 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B LYS 2.9 19.1 + - - +
420B MET* 3.0 8.6 + - + +
422B HIS* 1.3 80.4 - - + +
424B ILE* 1.3 62.8 + - - +
426B ARG* 3.5 11.5 + - - +
427B GLU* 3.5 17.8 + - - +
347D GLU* 3.1 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU* 4.5 2.2 - - + -
388B THR* 3.8 20.4 - - + +
391B VAL* 3.7 31.0 - - + -
392B ALA* 3.5 39.0 - - + +
420B MET* 2.9 49.8 + - + +
421B GLN 4.2 0.2 - - - +
423B ALA* 1.3 73.2 - - - +
425B ALA* 1.3 67.5 + - - +
427B GLU* 3.1 5.4 + - - +
428B ALA* 2.9 20.8 + - - +
347D GLU* 4.3 11.9 - - - +
350D PHE* 4.5 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ARG* 4.4 9.6 - - - +
88B THR* 4.1 13.7 - - - -
391B VAL* 4.6 1.1 - - - +
395B VAL* 4.2 15.3 - - + -
402B ILE* 4.4 7.6 - - + -
421B GLN 3.0 19.9 + - - +
422B HIS 3.9 2.5 - - - +
424B ILE* 1.3 76.6 - - - +
426B ARG* 1.3 57.9 + - - +
428B ALA* 4.5 0.4 - - - -
429B GLU* 2.8 53.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PRO* 3.8 41.4 + - + +
83B VAL* 4.5 1.0 - - - +
84B ALA 2.9 37.5 + - - +
85B ALA* 4.9 0.7 - - - +
86B ARG* 3.2 29.2 - - + +
422B HIS* 3.2 32.4 + - + +
423B ALA* 3.8 9.6 + - - +
424B ILE 3.1 1.2 - - - -
425B ALA* 1.3 76.3 - - - +
427B GLU* 1.3 61.3 + - - +
429B GLU* 3.9 6.9 - - - +
430B ALA* 3.3 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLN* 4.6 3.5 + - - +
80B SER 4.3 3.3 - - - +
81B GLU* 4.0 0.3 - - - +
82B PRO* 3.1 26.7 - - - +
423B ALA 3.5 14.3 + - - +
424B ILE 3.1 6.6 + - - +
426B ARG* 1.3 75.0 - - - +
428B ALA* 1.3 63.8 + - - +
430B ALA* 3.3 7.9 + - - +
431B ALA* 3.2 20.1 + - - +
347D GLU* 3.7 22.2 - - + +
348D LYS* 2.9 41.4 + - + +
350D PHE* 3.6 20.1 - - + -
351D LEU* 3.5 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B ALA* 3.8 28.0 - - + +
395B VAL* 3.5 28.7 - - + -
396B LEU* 3.5 12.2 - - + +
424B ILE 2.9 15.6 + - - +
425B ALA 3.9 1.1 - - - +
427B GLU* 1.3 76.1 - - - +
429B GLU* 1.3 65.3 + - - +
431B ALA 2.9 11.5 + - - +
432B VAL* 3.3 7.8 + - - +
350D PHE* 3.6 11.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ALA 4.2 1.4 - - - +
86B ARG* 3.1 12.2 - - - +
87B SER* 2.6 41.3 + - - +
88B THR* 2.5 39.5 + - - +
395B VAL* 3.8 10.5 - - + -
425B ALA* 2.8 32.7 + - - +
426B ARG* 3.9 5.6 - - - +
428B ALA* 1.3 71.6 - - - +
430B ALA* 1.3 61.0 + - - +
432B VAL* 3.1 24.2 + - - +
434B HIS* 4.2 8.5 + - - -
490B ARG* 4.3 0.2 + - - -
510B ARG* 4.9 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLN* 3.2 40.5 - - + +
60B GLN* 3.3 14.7 - - + +
72B HIS* 5.6 0.7 - - - -
80B SER 6.1 0.2 - - - +
82B PRO* 4.7 11.9 - - + -
83B VAL 5.8 0.2 - - - +
426B ARG 3.3 12.0 + - - +
427B GLU* 3.6 10.3 - - - +
429B GLU* 1.3 75.9 - - - +
431B ALA* 1.3 58.9 + - - +
432B VAL 3.3 0.9 - - - +
490B ARG* 3.2 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLN* 4.4 2.2 - - + -
72B HIS* 2.8 24.8 + - - -
76B LEU* 3.8 29.2 - - + -
396B LEU* 4.1 12.3 - - + +
427B GLU 3.2 10.1 + - - +
428B ALA* 2.9 13.1 + - - +
430B ALA* 1.3 77.9 - - - +
432B VAL* 1.3 65.6 + - - +
433B TYR 3.2 0.2 + - - -
350D PHE* 4.7 2.2 - - + -
351D LEU* 4.1 14.6 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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