Contacts of the strand formed by residues 409 - 419 (chain B) 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 LEU 409 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 5.9 0.9 - - + -
35B ILE* 3.5 36.1 - - + -
37B MET* 3.0 38.8 - - + -
42B ILE* 4.0 3.6 - - + -
65B VAL* 4.2 9.2 - - + -
66B ILE 3.5 7.9 - - - +
68B GLY* 3.9 2.8 - - - +
102B THR* 4.6 0.4 - - - +
401B ILE* 3.1 25.4 - - + -
407B ALA* 3.3 22.2 - - - +
408B ASP* 1.3 76.8 - - - +
410B VAL* 1.3 65.7 + - - +
411B ILE* 6.5 0.2 - - + -
445B VAL 4.0 0.2 - - - +
446B VAL* 3.5 3.5 - - - +
447B ILE* 2.8 51.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 3.2 7.0 - - - +
66B ILE* 2.9 46.3 + - + +
67B PRO 4.6 0.2 - - - +
68B GLY* 3.9 13.0 - - - -
100B GLY* 3.5 31.4 - - - +
409B LEU* 1.3 79.7 - - - +
411B ILE* 1.3 77.2 + - - +
412B TRP* 3.7 17.8 + - + +
443B PRO* 3.9 22.0 - - + -
445B VAL 3.4 8.3 - - - +
446B VAL* 4.3 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 4.3 18.6 - - + -
58B ILE* 3.8 30.3 - - + -
59B GLU 5.5 0.2 - - - +
60B ALA* 4.5 12.1 - - + +
63B ARG* 3.9 26.2 - - + -
64B MET 3.2 14.1 - - - +
65B VAL* 4.3 13.2 - - + -
409B LEU* 6.5 0.2 - - + -
410B VAL* 1.3 72.7 - - - +
412B TRP* 1.3 59.5 + - - +
444B LEU* 3.0 36.4 + - + +
445B VAL* 2.9 34.8 + - + +
447B ILE* 5.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG* 3.5 14.9 - - - +
64B MET* 3.3 43.7 + - + +
66B ILE* 4.0 24.2 - - + -
99B GLY 3.9 8.7 - - - -
100B GLY* 5.2 0.2 - - - -
362B MET* 3.2 44.4 - - + -
363B SER* 3.6 12.6 - - - -
366B TRP* 3.4 33.0 - + + -
380B PHE* 4.0 5.8 - + - -
410B VAL* 3.7 11.3 - - + +
411B ILE* 1.3 72.6 - - - +
413B ASP* 1.3 70.3 + - - +
414B PRO* 3.4 10.4 - - + +
441B GLY 3.6 5.6 - - - -
442B SER 3.5 18.6 - - - -
443B PRO* 3.6 36.6 - - + -
444B LEU* 4.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG* 4.9 6.3 + - - +
411B ILE 4.1 0.8 + - - -
412B TRP* 1.3 72.5 + - - +
414B PRO* 1.4 67.0 - - - +
415B ASP* 3.0 20.0 + - - +
416B SER* 2.8 38.0 + - - -
441B GLY* 3.5 2.9 - - - -
442B SER* 2.9 41.2 + - - +
444B LEU* 3.6 32.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
63B ARG* 4.6 10.8 - - + -
64B MET* 3.9 22.9 - - + +
366B TRP* 3.4 41.1 + - + +
412B TRP* 3.4 10.9 - - + +
413B ASP* 1.4 91.2 - - - +
415B ASP* 1.3 70.8 + - - +
440B ARG* 3.1 24.6 + - - +
441B GLY* 4.7 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG* 5.9 1.4 - - - -
413B ASP* 3.0 9.0 + - - +
414B PRO* 1.3 94.3 - - - +
416B SER* 1.3 71.2 + - - +
417B VAL* 3.5 6.4 + - - +
440B ARG* 3.2 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ASP* 2.8 28.1 + - - +
415B ASP* 1.3 82.6 - - - +
417B VAL* 1.3 61.4 + - - +
418B LYS* 5.1 5.0 - - - +
441B GLY* 3.2 23.9 + - - -
442B SER* 4.8 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B ASP 3.6 10.5 - - - +
416B SER* 1.3 77.7 - - - +
418B LYS* 1.3 72.1 + - - +
438B GLU* 3.9 23.8 - - + +
439B CYS 3.8 24.0 - - - +
440B ARG* 3.8 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B SER* 5.1 5.2 - - - +
417B VAL* 1.3 82.2 - - - +
419B THR* 1.3 66.8 + - - +
420B ILE* 5.9 1.1 - - + -
437B MET 3.1 1.9 - - - +
438B GLU* 4.3 3.1 - - - -
439B CYS* 2.6 47.1 + - + +
441B GLY 5.8 0.2 - - - +
442B SER* 3.3 39.6 + - - +
443B PRO* 4.3 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B LYS* 1.3 79.4 - - - +
420B ILE* 1.3 78.1 + - - +
421B SER* 4.1 9.3 + - - -
423B LYS* 5.4 3.4 - - - +
424B THR* 4.6 6.4 + - - -
435B GLU* 5.4 0.2 - - - +
436B GLY* 3.4 20.6 - - - +
437B MET 3.2 5.8 - - - -
438B GLU* 2.6 25.5 + - - -
----------------------------------------------------------
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