Contacts of the helix formed by residues 54 - 65 (chain A) in PDB entry 2HGK
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 VAL 54 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 4.0 16.4 - - - +
34A PHE* 3.8 28.9 - - + -
41A PHE* 3.9 28.7 - - + -
49A GLU 4.0 8.7 - - - +
50A TRP* 3.5 17.5 - - + +
52A GLN 2.7 9.7 + - - -
53A TRP* 1.3 78.6 - - + +
55A LEU* 1.3 68.4 + - - +
57A PRO* 3.2 2.6 - - - +
58A ARG* 2.9 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 5.4 1.8 - - + -
14A LEU* 5.5 2.0 - - + -
50A TRP* 3.0 54.2 + - + +
51A LEU* 3.1 33.8 + - + +
54A VAL* 1.3 79.8 - - - +
56A ILE* 1.3 67.2 + - + +
58A ARG* 3.3 7.9 + - - +
59A MET* 2.9 50.1 + - + +
73A PHE* 3.6 23.1 - - + -
75A VAL* 4.8 1.6 - - + -
100A LEU* 4.3 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.4 44.2 - - + +
14A LEU* 4.1 24.2 - - + -
15A GLU* 4.6 12.3 - - + +
18A LEU* 4.8 1.3 - - + -
24A TRP* 4.2 27.1 - - + -
51A LEU 3.4 16.9 + - - +
52A GLN* 4.2 8.5 - - + -
53A TRP 5.0 0.4 - - - +
55A LEU* 1.3 78.7 - - + +
57A PRO* 1.4 66.0 - - + +
59A MET 3.3 0.3 + - - -
60A HIS* 2.9 48.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TRP* 6.3 2.0 - - + -
53A TRP* 3.1 35.9 - - + +
54A VAL 3.2 10.1 - - - +
56A ILE* 1.4 95.0 - - + +
58A ARG* 1.3 62.6 + - - +
60A HIS* 3.2 21.4 + - + +
61A ASP* 3.3 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PRO* 5.0 4.2 + - - +
41A PHE* 5.8 3.8 - - - -
50A TRP* 4.7 18.8 - - - +
54A VAL* 2.9 35.8 + - + +
55A LEU* 3.5 13.0 - - - +
57A PRO* 1.3 78.7 - - - +
59A MET* 1.3 71.1 + - - +
61A ASP* 3.5 6.2 + - - +
62A LEU* 3.2 26.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 5.7 0.4 - - + -
11A LEU* 3.7 23.1 - - + -
55A LEU* 2.9 47.3 + - + +
58A ARG* 1.3 84.4 - - + +
60A HIS* 1.3 58.7 + - - +
62A LEU* 3.9 26.2 - - + -
63A LEU* 2.7 45.1 + - + +
70A PRO* 4.7 5.4 - - + -
73A PHE* 3.7 22.4 - - + -
100A LEU* 6.3 0.4 - - + -
104A PHE* 3.9 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 3.7 37.1 - - + +
11A LEU* 3.6 16.1 - - + +
12A GLN* 4.6 12.6 - - + +
15A GLU* 5.4 2.8 + - - -
56A ILE* 2.9 49.2 + - + +
57A PRO* 3.3 14.1 - - + +
59A MET* 1.3 76.5 - - - +
61A ASP* 1.3 61.9 + - - +
63A LEU* 3.8 6.6 - - - +
64A ASP* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PRO 3.3 8.0 + - - +
58A ARG* 3.9 8.1 - - - +
59A MET 3.2 0.4 - - - -
60A HIS* 1.3 75.7 - - - +
62A LEU* 1.3 62.8 + - - +
64A ASP* 3.2 7.7 + - - +
65A ASN* 2.8 58.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 3.2 18.5 + - + +
59A MET* 3.1 33.1 + - + +
61A ASP* 1.3 82.2 + - - +
63A LEU* 1.3 65.5 + - + +
65A ASN* 3.3 6.7 + - - -
67A GLN* 3.2 60.4 + - + +
68A PRO 4.1 8.5 - - - +
69A LEU* 4.2 16.2 - - + -
70A PRO* 4.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A HIS* 3.3 57.6 + - + +
7A VAL* 3.7 21.8 - - + -
8A ARG* 3.5 28.7 - - + +
11A LEU* 3.9 11.0 - - + -
59A MET* 2.7 31.4 + - + +
60A HIS* 3.8 5.6 - - - +
62A LEU* 1.3 74.1 - - + +
64A ASP* 1.3 62.0 + - - +
66A LYS* 3.2 10.9 + - - +
69A LEU* 3.6 30.1 - - + -
104A PHE* 5.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A HIS 3.1 15.6 + - - +
61A ASP* 3.2 9.2 + - - +
63A LEU* 1.3 75.3 - - - +
65A ASN* 1.3 66.3 + - - +
66A LYS* 3.0 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASP* 2.8 53.7 + - - +
62A LEU* 3.3 5.4 + - - +
63A LEU 3.3 0.6 - - - -
64A ASP* 1.3 81.3 + - - +
66A LYS* 1.3 74.1 + - - +
67A GLN* 3.0 26.7 + - + +
----------------------------------------------------------
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