Contacts of the helix formed by residues 408 - 420 (chain B) in PDB entry 3VF1
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 GLY 408 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B VAL* 5.2 8.0 + - - +
175B GLN 5.7 3.1 - - - -
176B PHE* 4.9 2.1 - - - -
406B THR 3.3 1.4 + - - -
407B LYS* 1.3 76.0 - - - +
409B ILE* 1.3 63.5 + - - +
410B MET 3.4 2.5 - - - -
411B ALA* 3.5 11.8 + - - +
412B ILE* 3.2 24.8 + - - +
677B ILE 3.5 5.3 - - - +
678B ALA* 4.2 11.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B HIS 3.5 25.6 - - - +
381B MET* 3.5 27.8 - - + +
382B GLU* 3.5 11.9 - - - +
385B ALA* 3.6 24.2 - - + -
405B HIS 5.9 0.2 - - - +
406B THR* 3.3 23.1 - - - +
407B LYS 3.3 2.2 - - - -
408B GLY* 1.3 78.7 - - - +
410B MET* 1.3 67.4 + - + +
412B ILE* 3.2 2.6 - - - +
413B ASN* 3.1 32.3 + - - +
552B CYS* 5.1 4.7 - - - -
677B ILE* 3.3 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B TYR* 4.1 11.4 - - + -
162B VAL* 4.0 38.4 - - + -
170B LEU* 4.0 9.0 - - + -
174B VAL* 3.6 25.4 - - + -
382B GLU* 4.3 20.0 - - + -
385B ALA* 4.4 16.8 - - + -
386B VAL* 4.1 10.1 - - + -
389B TRP* 3.4 35.4 - - + +
406B THR 5.8 1.8 - - - +
408B GLY* 3.4 0.8 - - - +
409B ILE* 1.3 79.8 - - + +
411B ALA* 1.3 63.5 + - - +
413B ASN* 3.5 0.9 + - - +
414B THR* 2.8 30.8 + - - -
417B ARG* 4.5 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PRO* 4.4 4.1 - - + +
170B LEU* 3.8 12.4 - - + +
174B VAL 3.5 20.0 + - - +
175B GLN* 4.1 2.0 - - - -
176B PHE* 3.4 45.6 - - + +
408B GLY* 3.5 10.8 + - - +
409B ILE 3.4 0.2 - - - -
410B MET* 1.3 80.7 - - - +
412B ILE* 1.3 63.4 + - - +
414B THR* 3.6 2.9 - - - -
415B LEU* 3.2 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B PHE* 3.5 13.6 - - + -
181B THR* 5.0 1.3 - - + -
185B PHE* 3.8 34.5 - - + -
378B HIS* 4.0 19.1 - - + +
408B GLY 3.2 12.0 + - - +
409B ILE* 3.2 12.8 - - - +
411B ALA* 1.3 79.5 - - - +
413B ASN* 1.3 70.1 + - - +
415B LEU* 3.3 10.5 + - + +
416B GLY* 2.8 24.9 + - - -
420B LEU* 5.2 2.6 - - + +
677B ILE* 3.8 15.0 - - + +
678B ALA 4.3 7.0 - - - +
679B ILE* 4.0 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B HIS* 2.9 59.6 + - - +
379B LEU* 3.8 9.9 - - + +
382B GLU* 2.9 35.7 + - - +
409B ILE* 3.1 19.3 + - - +
410B MET 4.1 0.9 - - - +
412B ILE* 1.3 80.5 - - - +
414B THR* 1.3 61.3 + - - +
416B GLY* 3.6 2.5 - - - +
417B ARG* 2.9 41.9 + - - +
421B ILE* 5.6 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B VAL* 4.0 7.6 - - - +
164B ALA* 3.8 19.9 + - + +
165B GLU 4.3 1.3 - - - +
166B GLU* 3.4 39.9 - - - +
167B PRO 3.6 2.2 - - - -
170B LEU* 3.8 12.9 - - + +
410B MET 2.8 21.9 + - - -
411B ALA 3.3 4.9 + - - -
413B ASN* 1.3 76.2 - - - +
415B LEU* 1.3 62.4 + - - +
417B ARG* 3.4 28.3 + - - +
418B ASN* 3.4 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PRO* 4.2 20.1 - - + +
176B PHE* 4.1 17.5 - - + -
181B THR* 3.8 22.0 - - + +
182B SER* 3.5 22.2 - - - +
184B LEU 5.4 0.7 - - - +
185B PHE* 3.7 33.7 - - + -
411B ALA 3.2 10.4 + - - +
412B ILE* 3.5 10.3 - - + +
414B THR* 1.3 78.3 - - - +
416B GLY* 1.3 59.6 + - - +
418B ASN* 3.0 6.7 + - + +
419B ASP* 2.8 47.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ILE 2.8 15.6 + - - -
413B ASN* 3.2 5.1 + - - -
415B LEU* 1.3 76.5 - - - +
417B ARG* 1.3 57.7 + - - +
420B LEU* 3.0 34.7 + - - +
421B ILE* 2.9 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ASP* 5.0 2.5 - - - -
153B ARG* 3.3 16.2 + - - +
154B TYR* 2.7 62.1 + - + -
161B PHE* 3.3 32.7 - - - +
162B VAL* 3.9 9.3 + - - +
164B ALA 5.4 3.8 + - - -
379B LEU* 4.2 11.8 - - + +
382B GLU* 3.0 40.4 + - - -
410B MET 4.5 0.2 + - - -
413B ASN* 2.9 19.5 + - - +
414B THR* 3.6 37.4 + - - +
415B LEU 3.2 0.4 - - - -
416B GLY* 1.3 74.3 - - - +
418B ASN* 1.3 60.9 + - - +
421B ILE* 4.5 9.4 - - + -
422B PRO* 3.4 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ARG* 3.0 28.3 + - - +
165B GLU 3.1 26.8 + - - +
166B GLU* 4.3 11.1 - - - +
167B PRO* 4.7 3.6 - - - +
414B THR* 3.4 15.3 + - - +
415B LEU* 3.0 7.6 + - + +
417B ARG* 1.3 80.4 - - - +
419B ASP* 1.3 72.8 + - - +
422B PRO* 3.1 21.1 - - - +
424B GLY 5.8 0.3 - - - -
425B GLY* 5.1 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B SER 4.5 5.4 - - - +
185B PHE* 4.3 23.6 + - + +
186B ARG* 5.3 6.6 + - - +
415B LEU* 2.8 36.6 + - + +
418B ASN* 1.3 89.2 - - - +
420B LEU* 1.3 67.6 + - - +
425B GLY* 3.3 9.7 - - - -
426B ALA* 3.0 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PHE* 3.4 49.1 - - + -
374B LEU* 4.5 24.9 - - + -
378B HIS* 5.9 3.6 - - + +
412B ILE* 5.2 4.7 - - + +
416B GLY* 3.0 22.2 + - - +
419B ASP* 1.3 78.6 - - - +
421B ILE* 1.3 69.2 + - + +
422B PRO* 3.5 1.8 - - - +
425B GLY* 3.9 3.4 - - - -
426B ALA* 3.7 26.4 + - + +
427B ALA* 3.3 29.9 + - + +
609B VAL* 5.4 2.9 - - + -
613B LEU* 4.7 14.1 - - + -
679B ILE 6.0 0.4 - - - +
----------------------------------------------------------
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