Contacts of the helix formed by residues 73 - 87 (chain A) in PDB entry 4HE2
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 73 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 5.4 0.9 - - + +
47A ALA* 4.2 16.4 - - + +
48A VAL* 4.1 23.8 - - + -
51A ALA* 3.9 26.2 - - + -
72A LYS* 1.3 76.5 - - - +
74A ASP* 1.3 61.8 + - - +
76A LEU* 4.1 22.4 - - + -
77A SER* 2.7 39.9 + - - +
120A LEU* 4.6 6.7 - - + -
126A ILE* 3.9 39.9 - - + +
132A ILE* 4.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS* 3.2 6.0 + - - +
73A LEU* 1.3 76.4 - - - +
75A VAL* 1.3 60.5 + - + +
77A SER* 3.9 1.2 - - - -
78A ASN* 3.0 31.6 + - - +
98A GLU* 3.5 33.6 - - - +
119A PRO* 4.3 3.0 - - - +
120A LEU* 3.5 25.7 + - - +
123A SER* 3.0 32.0 + - - -
126A ILE* 5.0 3.8 - - - +
405A MG 4.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS* 3.3 24.8 + - + +
73A LEU 3.3 0.6 - - - -
74A ASP* 1.3 80.6 - - + +
76A LEU* 1.3 62.4 + - - +
78A ASN* 3.5 5.9 + - - +
79A SER* 3.1 29.2 + - - +
98A GLU* 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA* 3.8 30.1 - - + -
72A LYS* 3.1 20.9 + - + +
73A LEU* 4.0 14.4 - - + +
75A VAL* 1.3 74.4 - - - +
77A SER* 1.3 66.1 + - - +
79A SER* 3.3 8.1 + - - -
80A LEU* 3.0 44.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 3.7 33.7 - - - +
73A LEU* 2.7 29.4 + - - +
74A ASP 4.0 1.1 - - - -
76A LEU* 1.3 76.7 - - - +
78A ASN* 1.3 63.2 + - - +
80A LEU* 3.3 3.6 + - - +
81A VAL* 3.0 28.8 + - - +
119A PRO* 3.6 29.4 - - - -
120A LEU* 4.0 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASP 3.0 20.1 + - - +
75A VAL* 3.7 6.1 - - - +
77A SER* 1.3 77.9 - - - +
79A SER* 1.3 59.3 + - - +
81A VAL* 3.9 0.7 - - - +
82A ILE* 3.0 46.9 + - - +
96A SER* 2.7 28.1 + - - -
98A GLU* 3.6 15.1 + - + +
99A ASN* 2.8 25.1 + - - +
117A PHE* 3.3 13.3 - - - -
119A PRO* 3.7 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 3.1 23.0 + - - +
76A LEU* 3.7 7.2 - - - -
78A ASN* 1.3 76.0 + - - +
80A LEU* 1.3 64.2 - - - +
82A ILE* 4.1 5.6 - - - +
83A ASN* 3.0 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA* 4.2 11.4 - - + -
43A ALA* 3.9 29.4 - - + +
44A ILE* 3.9 25.8 - - + +
76A LEU* 3.0 43.0 + - + +
77A SER 3.6 5.8 - - - +
79A SER* 1.3 75.9 - - - +
81A VAL* 1.3 63.4 + - - +
83A ASN* 4.0 2.7 - - - +
84A MET* 3.0 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A MET* 4.0 22.2 - - + -
40A ALA* 3.9 21.8 - - + -
44A ILE* 4.0 14.1 - - + -
77A SER 3.0 21.8 + - - +
78A ASN 4.0 0.2 - - - +
80A LEU* 1.3 75.8 - - - +
82A ILE* 1.3 57.4 + - - +
84A MET* 3.8 0.7 - - - +
85A LEU* 2.9 53.7 + - + +
117A PHE* 3.6 37.0 - - + -
119A PRO* 4.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASN* 3.0 48.3 + - - +
79A SER* 4.1 4.9 - - - +
81A VAL* 1.3 74.3 - - - +
83A ASN* 1.3 63.2 + - - +
86A GLN* 2.9 58.5 + - + +
94A LEU* 4.1 11.0 - - + -
99A ASN* 3.8 5.2 - - - +
103A ILE* 3.8 27.8 - - + -
117A PHE* 3.8 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A SER* 3.0 33.9 + - - +
80A LEU* 4.1 3.1 - - - +
82A ILE* 1.3 84.8 - - - +
84A MET* 1.3 69.2 + - + +
86A GLN* 4.1 8.1 - - - +
87A SER* 2.9 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER* 3.4 43.1 + - - +
39A THR* 4.4 19.1 - - - -
40A ALA* 3.9 17.0 - - + +
80A LEU* 3.0 33.1 + - + +
81A VAL 3.8 2.7 - - - +
83A ASN* 1.3 86.4 - - + +
85A LEU* 1.3 64.6 + - + +
87A SER* 3.3 18.3 + - - +
88A SER 3.4 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 4.1 22.7 - - + +
36A SER* 4.5 0.9 - - - -
37A MET* 4.0 38.1 - - + +
81A VAL* 2.9 39.4 + - + +
82A ILE 4.0 1.8 - - - +
84A MET* 1.3 78.9 - - + +
86A GLN* 1.3 60.3 + - - +
88A SER* 2.5 26.5 + - - -
89A TYR 4.3 0.2 + - - -
91A THR* 3.6 15.3 + - + +
94A LEU* 3.8 22.7 - - + -
115A VAL* 3.8 27.8 - - + -
117A PHE* 4.2 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ILE* 2.9 35.9 + - - +
83A ASN* 4.2 8.6 - - - +
85A LEU* 1.3 76.4 - - - +
87A SER* 1.3 61.0 + - - +
88A SER 3.2 1.0 + - - -
89A TYR 3.5 8.3 + - - -
91A THR* 4.0 7.3 + - - -
94A LEU* 4.0 13.0 - - + +
103A ILE* 3.3 31.7 + - - +
104A ILE 4.6 1.6 + - - -
105A THR* 4.4 28.5 + - + +
106A ALA 5.5 1.1 - - - +
109A LYS* 3.7 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER* 5.3 0.2 + - - -
83A ASN 2.9 21.9 + - - -
84A MET* 3.3 17.0 + - - +
86A GLN* 1.3 76.2 - - - +
88A SER* 1.3 55.6 + - - +
89A TYR* 3.2 23.7 - - - -
109A LYS* 4.5 19.3 - - - +
----------------------------------------------------------
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