Contacts of the helix formed by residues 66 - 74 (chain D) in PDB entry 2HVY
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 HIS 66 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C TYR* 3.9 41.5 - + + +
44C TYR* 3.7 19.4 - - + +
45C ARG* 4.4 5.5 - - + +
37D THR* 3.7 9.9 - - + -
41D THR* 2.9 42.4 + - + +
62D GLU 4.2 5.6 + - - +
63D ILE 3.1 28.3 + - - -
64D VAL* 4.1 0.6 - - - -
65D ALA* 1.3 76.7 - - - +
67D LEU* 1.3 75.7 + - + +
69D PRO* 3.4 7.0 - - - +
70D LEU* 3.2 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D THR* 4.5 5.8 - - + -
40D THR* 4.4 12.8 - - + -
41D THR* 3.7 27.1 - - - +
44D VAL* 4.4 9.6 - - + -
52D VAL* 4.5 0.4 - - + -
54D ILE* 4.0 17.5 - - + -
64D VAL* 3.1 19.0 + - + +
66D HIS* 1.3 92.5 - - + +
68D PRO* 1.4 67.5 - - + +
70D LEU* 3.0 10.7 + - + +
71D CYS* 2.8 39.7 + - - -
99D SER* 3.5 34.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D TYR* 3.6 13.9 - - + +
9D LYS* 3.9 16.4 - - + +
54D ILE* 4.2 10.3 - - + -
64D VAL 3.4 14.1 - - - +
65D ALA* 3.5 11.0 - - - +
67D LEU* 1.4 88.9 - - + +
69D PRO* 1.4 62.1 - - + +
71D CYS* 3.4 2.4 + - - +
72D GLU* 3.1 34.8 + - - +
78D TYR* 3.7 21.7 - - + +
80D TYR* 3.4 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C TYR* 3.2 36.2 - - + +
47C ARG* 4.2 26.6 + - + -
48C TRP* 4.8 4.0 - - + +
9D LYS* 4.4 9.2 - - - +
65D ALA 3.5 11.4 - - - +
66D HIS 3.4 14.8 - - - +
68D PRO* 1.4 92.1 - - + +
70D LEU* 1.3 61.6 + - - -
72D GLU* 3.7 10.9 + - + +
73D GLU* 3.2 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C TYR* 4.6 5.8 - - + -
44C TYR* 3.8 36.3 - - + +
41D THR* 3.7 31.6 - - + +
44D VAL* 3.9 22.0 - - + -
45D GLU* 5.0 7.2 - - + +
66D HIS* 3.2 26.8 + - + +
67D LEU* 3.0 10.4 + - + +
69D PRO* 1.3 74.1 - - - +
71D CYS* 1.3 61.4 + - - +
73D GLU* 3.2 2.5 + - + +
74D LYS* 3.0 50.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D VAL* 4.3 17.3 - - - -
52D VAL* 3.7 40.2 - - - -
67D LEU* 2.8 28.8 + - - +
68D PRO 3.6 0.4 - - - +
70D LEU* 1.3 73.6 - - - +
72D GLU* 1.3 56.2 + - - +
74D LYS 3.5 0.3 + - - -
75D GLU 2.9 8.5 + - - -
76D ILE* 2.7 46.7 + - - +
78D TYR* 3.6 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LYS* 4.6 10.4 - - - +
68D PRO* 3.1 18.8 + - - +
69D PRO* 4.1 8.2 - - + +
70D LEU 3.3 0.2 - - - -
71D CYS* 1.3 74.2 - - - +
73D GLU* 1.3 62.8 + - - +
75D GLU* 3.3 20.9 - - - +
76D ILE 5.0 0.7 - - - -
78D TYR* 2.7 28.4 + - + -
123D MET* 3.7 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C TYR* 4.2 19.5 - - + +
47C ARG* 2.6 37.1 + - - +
69D PRO 3.2 16.5 + - - +
70D LEU 3.2 5.7 + - - +
72D GLU* 1.3 80.4 - - - +
74D LYS* 1.3 66.2 + - + +
75D GLU* 3.2 8.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C TYR* 5.1 7.5 + - - -
44D VAL* 3.8 28.9 - - + +
45D GLU* 3.7 33.2 + - - +
47D GLY* 5.7 3.1 - - - +
70D LEU* 3.0 32.3 + - + +
71D CYS 4.4 0.4 - - - +
72D GLU 3.4 0.2 - - - -
73D GLU* 1.3 82.5 - - + +
75D GLU* 1.3 70.3 + - - +
76D ILE* 3.4 13.5 + - + +
----------------------------------------------------------
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