Contacts of the helix formed by residues 63 - 72 (chain H) in PDB entry 2VUT
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 ASN 63 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H PRO* 2.8 32.8 + - + +
60H LEU 3.4 8.8 + - - +
61H LEU 3.2 4.0 - - - +
62H ASN* 1.3 78.4 - - - +
64H VAL* 1.3 64.1 + - - +
65H PRO* 3.2 16.4 - - - +
66H LEU* 3.2 14.1 + - - +
67H MET* 3.5 15.0 + - - +
94H ASP* 5.1 1.4 + - - -
688O PRO* 5.5 0.7 - - + -
701O LEU* 3.8 16.5 - - - +
702O LYS* 5.4 0.5 - - - +
705O GLY* 2.9 40.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H ASN* 4.0 1.5 - - - -
63H ASN* 1.3 72.3 - - - +
65H PRO* 1.3 81.1 - - + +
67H MET* 3.3 9.9 + - - +
68H ASP* 3.0 30.3 + - - +
94H ASP* 4.3 29.8 - - + +
101H ARG* 4.6 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 65 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G LYS* 4.7 1.0 + - - -
205G LYS* 5.8 0.2 - - - +
63H ASN* 3.1 13.7 - - - +
64H VAL* 1.3 102.4 - - + +
66H LEU* 1.3 59.4 + - - +
68H ASP* 3.5 9.6 + - + +
69H THR* 3.1 24.8 + - - -
702O LYS 4.0 20.0 - - - +
703O LEU 4.1 8.7 - - - +
704O HIS 3.9 6.8 - - - +
705O GLY* 3.9 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H GLN* 3.8 21.5 - - + -
56H PHE* 3.5 34.8 - - + +
57H GLN 4.8 0.4 - - - -
58H GLY* 3.7 27.4 - - - +
59H PRO 3.7 4.3 - - - +
60H LEU* 4.6 5.6 - - + -
63H ASN* 3.2 27.9 + - + +
64H VAL 3.1 0.6 - - - -
65H PRO* 1.3 75.9 - - - +
67H MET* 1.3 63.5 + - + +
68H ASP 3.1 1.6 - - - -
69H THR* 3.0 7.1 + - - -
70H LEU* 2.8 31.2 + - + +
704O HIS 4.9 0.7 - - - -
705O GLY* 3.3 22.2 - - - +
706O VAL* 4.4 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 67 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H LEU* 3.5 34.8 - - + +
63H ASN 3.7 12.3 - - - +
64H VAL* 3.3 11.2 + - + +
66H LEU* 1.3 75.8 - - - +
68H ASP* 1.3 61.8 + - - +
70H LEU* 3.3 8.9 + - - +
71H PHE* 3.3 30.2 + - + -
91H ILE* 3.9 15.7 - - + +
94H ASP* 3.3 35.9 - - + +
95H LEU* 3.3 44.6 - - + -
98H ALA* 3.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 68 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G GLN* 4.4 20.9 + - - +
5G LYS* 5.3 2.5 - - - +
64H VAL* 3.0 25.6 + - - +
65H PRO* 3.6 9.6 - - + +
67H MET* 1.3 79.2 - - - +
69H THR* 1.3 62.4 + - - +
71H PHE* 3.5 3.3 + - - +
72H GLU* 3.4 25.3 + - - +
98H ALA* 4.2 8.3 - - - +
101H ARG* 3.2 37.5 + - - +
102H ALA* 5.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G LYS* 2.6 36.2 + - + +
28G VAL 3.3 23.5 + - - +
29G GLY* 4.3 0.7 - - - -
33H ARG* 2.7 35.3 + - - +
56H PHE* 3.8 20.4 - - + -
65H PRO 3.1 11.2 + - - -
66H LEU* 3.0 13.9 + - - -
68H ASP* 1.3 78.3 - - - +
70H LEU* 1.3 60.9 + - - +
72H GLU* 3.2 13.7 + - - +
704O HIS 4.7 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ALA* 3.7 14.4 - - + +
10H VAL 3.5 13.5 - - - +
11H VAL* 3.5 31.9 - - + -
33H ARG* 3.0 61.7 + - + +
34H ALA* 4.0 7.9 - - - +
35H GLN* 4.2 5.8 - - + +
56H PHE* 4.2 9.6 - - + -
60H LEU* 5.7 0.9 - - + -
66H LEU* 2.8 16.4 + - + +
67H MET* 3.3 12.6 - - - +
68H ASP 3.2 0.2 - - - -
69H THR* 1.3 76.4 - - - +
71H PHE* 1.3 72.7 + - + +
79H ILE* 5.0 0.4 - - + -
95H LEU* 4.6 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 71 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ALA* 3.4 26.5 - - + -
67H MET 3.3 23.2 + - - +
68H ASP* 3.5 3.1 + - - +
69H THR 3.3 0.4 - - - -
70H LEU* 1.3 80.0 - - + +
72H GLU* 1.3 65.6 + - - +
73H GLY 3.0 1.6 + - - -
74H ALA* 2.9 17.3 + - - +
77H ALA* 3.8 17.0 - - + -
79H ILE* 4.4 13.9 - - + -
95H LEU* 3.3 37.7 - - + -
98H ALA* 3.5 17.7 - - + +
99H ALA* 3.6 9.0 - - + -
102H ALA* 3.8 29.4 - - + +
104H THR* 3.9 2.1 + - - -
105H ILE* 3.7 17.0 - - + -
108H TYR* 4.0 16.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 72 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G GLN 4.1 0.9 - - - +
4G GLN* 3.3 35.6 - - + +
5G LYS* 2.5 63.3 + - - +
33H ARG* 3.1 29.7 + - - +
68H ASP* 3.4 14.3 + - - +
69H THR* 3.2 18.0 + - - +
71H PHE* 1.3 74.1 - - - +
73H GLY* 1.3 62.4 + - - +
74H ALA 3.2 1.0 + - - -
102H ALA* 5.4 2.7 - - - -
----------------------------------------------------------
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