Contacts of the helix formed by residues 63 - 75 (chain A) in PDB entry 4HH3
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 THR 63 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 1.3 75.3 - - - +
64A ALA* 1.3 59.6 + - - +
65A GLU* 2.8 30.3 + - - -
66A SER* 3.1 7.6 + - - -
67A VAL* 2.8 26.8 + - - +
89A ASN* 3.1 22.9 + - + +
91A ILE* 3.6 16.2 - - + -
97A GLU* 3.6 24.7 - - - +
338C GLU* 3.6 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 1.3 71.6 - - - +
65A GLU* 1.3 63.3 + - - +
67A VAL* 3.2 10.8 + - - +
68A ALA* 3.1 21.8 + - - +
337C THR* 3.6 23.3 - - - +
338C GLU* 2.7 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 2.8 12.3 + - - +
64A ALA* 1.3 77.9 - - - +
66A SER* 1.3 86.9 + - - +
68A ALA* 3.5 7.4 + - - +
69A LYS* 2.9 46.3 + - - +
87A GLU 4.8 0.3 - - - +
89A ASN* 2.7 22.8 + - - -
239C LEU* 5.4 9.5 - - + +
240C ALA* 6.0 0.3 - - - -
246C ARG* 6.3 0.9 - - - +
336C GLY* 5.3 14.4 - - - -
337C THR 6.0 0.6 - - - +
338C GLU* 5.1 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 3.9 8.6 - - - +
63A THR* 3.1 19.9 + - - -
65A GLU* 1.3 100.9 + - - +
67A VAL* 1.3 56.2 + - - +
69A LYS* 4.1 0.9 - - - -
70A PHE* 2.8 34.8 + - - +
87A GLU 4.2 0.3 + - - -
88A LEU* 3.5 20.6 - - - +
89A ASN* 2.8 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU* 3.6 38.6 - - + +
62A LEU* 3.9 21.5 - - + +
63A THR 2.8 19.8 + - - +
64A ALA* 3.2 11.6 + - - +
66A SER* 1.3 76.7 - - - +
68A ALA* 1.3 57.9 + - - +
70A PHE* 3.2 4.0 + - - +
71A ARG* 2.9 64.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ALA 3.1 10.0 + - - +
65A GLU* 3.7 9.9 - - - +
67A VAL* 1.3 82.0 - - + +
69A LYS* 1.3 57.5 + - - +
71A ARG* 3.5 8.5 + - - +
72A LEU* 3.0 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLU* 2.9 30.1 + - - +
66A SER* 3.8 6.1 - - - +
68A ALA* 1.3 76.0 - - - +
70A PHE* 1.3 64.3 + - - +
72A LEU* 3.3 9.6 + - + +
73A ARG* 3.1 26.6 + - + +
86A VAL* 3.4 23.4 - - + +
87A GLU* 3.4 21.1 + - - +
88A LEU* 4.1 1.1 - - + -
239C LEU* 2.8 41.4 + - - +
240C ALA* 3.6 18.2 - - - +
242C ASP* 2.9 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 4.9 8.7 - - + -
33A GLY* 5.8 4.5 - - - -
58A LEU* 3.5 33.7 - - + -
59A GLU* 5.4 8.3 - - + -
62A LEU* 4.2 9.9 - - + -
66A SER 2.8 22.7 + - - +
67A VAL* 3.2 4.2 + - - +
69A LYS* 1.3 74.6 - - - +
71A ARG* 1.3 63.0 + - + +
73A ARG* 3.9 1.0 - - - +
74A SER* 2.7 45.9 + - - -
86A VAL* 5.2 0.7 - - - -
88A LEU* 4.2 11.8 - - + +
104A LEU* 4.3 22.6 - - + +
113A ILE* 3.9 26.9 - - + -
115A MET* 3.9 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU* 2.5 45.1 + - - +
67A VAL* 2.9 33.2 + - - +
68A ALA* 3.9 7.9 - - - +
70A PHE* 1.3 80.6 - - + +
72A LEU* 1.3 58.5 + - - +
74A SER* 3.7 6.1 - - - -
75A GLU* 2.9 62.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ALA 3.0 18.4 + - - +
69A LYS* 3.5 7.2 - - - +
70A PHE 3.3 0.2 - - - -
71A ARG* 1.3 79.3 - - - +
73A ARG* 1.3 88.6 + - + +
74A SER 3.6 0.2 + - - -
75A GLU* 4.3 4.1 + - - +
76A GLY 4.8 4.9 + - - -
240C ALA* 3.8 24.7 - - + +
241C GLU* 5.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LYS* 3.1 19.0 + - + +
72A LEU* 1.3 100.4 + - + +
74A SER* 1.3 59.3 + - - +
76A GLY 5.1 0.7 - - - -
77A LEU* 3.5 25.0 + - - +
83A SER* 4.3 9.0 - - - -
84A VAL* 3.6 28.1 - - + +
86A VAL* 4.2 20.6 - - + -
104A LEU* 4.0 18.6 - - + +
241C GLU* 3.0 40.4 + - - +
242C ASP* 4.6 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PHE* 2.7 39.6 + - - -
71A ARG* 3.6 4.5 + - - -
73A ARG* 1.3 78.5 - - - +
75A GLU* 1.3 68.3 + - - +
76A GLY 3.3 2.7 - - - -
77A LEU* 3.0 13.6 + - - +
104A LEU* 4.3 6.7 - - - -
106A ARG* 2.7 25.6 + - - -
113A ILE* 3.5 26.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG* 2.9 49.3 + - + +
72A LEU* 4.3 2.6 + - - +
73A ARG 3.8 0.2 - - - -
74A SER* 1.3 80.7 + - - +
76A GLY* 1.3 57.6 + - - +
77A LEU 3.8 0.2 + - - -
78A GLU* 4.7 3.5 - - - +
106A ARG* 4.6 6.4 + - - +
111A ARG* 5.2 2.6 + - - -
----------------------------------------------------------
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