Contacts of the helix formed by residues 95 - 115 (chain A) in PDB entry 6BZE
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 95 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 6.2 2.0 - - + -
30A GLU* 3.6 26.5 - - + +
31A LYS* 3.7 29.5 - - + +
32A ILE* 5.5 4.0 - - + -
38A PHE* 4.9 4.7 - - + -
81A THR* 5.8 3.6 - - + -
85A SER* 3.4 36.6 - - - +
91A THR* 4.1 11.8 + - - +
93A ASN* 4.3 1.0 - - - +
94A PHE* 1.3 82.1 - - - +
96A ILE* 1.3 53.9 + - + +
98A LYS* 3.1 7.2 - - + +
99A ILE* 2.3 47.3 + - + +
102A GLU* 5.2 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU 5.1 0.2 - - - +
85A SER* 4.0 10.3 - - - +
86A ILE* 4.0 24.7 - - + +
91A THR 3.5 5.2 - - - +
92A GLN* 3.2 59.0 - - - +
93A ASN 3.1 1.8 + - - -
95A LEU* 1.3 74.6 - - + +
97A GLN* 1.3 57.5 + - - +
98A LYS 2.9 0.4 - - - -
99A ILE* 2.1 95.7 - - + +
100A THR* 2.5 24.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLN 4.9 1.3 - - - +
93A ASN* 2.7 48.3 + - + +
94A PHE* 4.7 7.1 + - - +
96A ILE* 1.3 74.3 - - - +
98A LYS* 1.3 59.3 + - + +
100A THR* 2.2 27.0 + - - -
101A ASP* 2.7 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 5.2 1.2 - - + +
27A TYR* 2.5 64.4 + - + +
30A GLU* 5.8 0.2 - - + -
94A PHE* 2.3 36.1 - - + +
95A LEU* 3.1 13.0 - - + +
97A GLN* 1.3 84.7 - - + +
99A ILE* 1.3 49.8 - - - -
101A ASP* 2.7 27.4 + - + +
102A GLU* 2.0 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 4.9 14.2 - - + +
85A SER* 5.0 2.9 - - - -
86A ILE* 4.7 11.4 - - + -
92A GLN* 4.6 1.1 - - - +
95A LEU* 2.3 60.7 + - + +
96A ILE* 2.1 84.6 + - + +
98A LYS* 1.3 70.2 - - - +
100A THR* 1.3 59.7 - - + +
102A GLU* 3.2 20.8 - - - +
103A VAL* 2.3 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE* 2.5 24.1 + - + +
97A GLN* 2.2 35.5 + - - -
99A ILE* 1.3 80.8 - - + +
101A ASP* 1.3 51.1 + - - +
103A VAL* 3.0 13.5 + - + +
104A LEU* 2.4 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 4.2 7.4 - - - +
97A GLN 2.7 15.5 + - - +
98A LYS* 2.7 37.6 + - + +
100A THR* 1.3 76.0 + - - +
102A GLU* 1.3 52.1 + - - -
104A LEU* 3.0 23.7 - - + +
105A LYS* 2.5 57.5 + - - +
108A ASN* 5.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 5.1 1.9 - - + +
21A LEU* 5.1 6.6 - - - +
24A LEU* 3.4 35.5 - - + +
81A THR* 5.6 2.4 - - - +
82A LEU* 3.1 37.5 - - + +
95A LEU* 5.1 6.6 - - - +
98A LYS 2.0 27.6 + - - +
99A ILE* 3.2 16.4 - - - +
101A ASP* 1.3 65.3 + - - +
103A VAL* 1.3 66.4 + - - +
105A LYS* 3.4 9.9 + - - +
106A LEU* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 5.9 8.7 - - + -
99A ILE* 2.3 34.9 + - + +
100A THR* 3.1 16.6 - - + +
102A GLU* 1.3 69.0 - - - +
104A LEU* 1.3 52.5 + - + +
106A LEU* 3.1 14.6 + - + +
107A ARG* 2.5 54.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A THR* 2.4 35.9 + - - +
101A ASP* 3.0 34.3 - - + +
103A VAL* 1.3 70.7 - - + +
105A LYS* 1.3 52.5 + - - +
107A ARG* 2.8 14.1 + - + -
108A ASN* 2.3 59.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 3.7 17.4 - - + +
23A ASN* 3.5 41.9 + - - +
24A LEU* 3.7 22.0 - - + -
101A ASP* 2.5 35.5 + - - +
102A GLU* 3.5 7.2 - - + +
104A LEU* 1.3 71.1 - - - +
106A LEU* 1.3 60.6 + - - +
108A ASN* 3.5 10.0 + - + +
109A ILE* 3.2 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 3.6 22.2 - - + -
17A LYS* 3.6 45.5 - - + +
20A ALA* 3.7 10.6 - - + +
79A LEU* 5.6 8.3 - - + -
102A GLU 3.0 13.3 + - - +
103A VAL* 3.2 16.6 - - + +
105A LYS* 1.3 73.6 - - - +
107A ARG* 1.3 60.1 + - - +
109A ILE* 3.0 3.5 + - - +
110A LYS* 2.5 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 2.5 34.1 + - + +
104A LEU* 2.8 18.3 + - + +
106A LEU* 1.3 76.9 - - - +
108A ASN* 1.3 61.7 + - - +
110A LYS* 3.0 39.0 - - - +
111A LEU* 2.7 65.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASP* 5.5 0.2 - - - +
104A LEU* 2.3 61.2 + - - +
105A LYS* 3.5 12.0 + - - +
107A ARG* 1.3 76.1 - - - +
109A ILE* 1.3 65.1 + - + +
111A LEU* 4.3 1.9 - - - +
112A GLU* 2.9 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 3.5 38.1 - - + +
19A ASP* 4.0 12.3 - - + +
20A ALA 4.6 0.2 - - - +
23A ASN* 3.1 33.2 - - + +
105A LYS* 3.2 31.2 + - - +
106A LEU* 3.0 2.7 + - - +
108A ASN* 1.3 85.2 - - + +
110A LYS* 1.3 64.4 + - - +
112A GLU* 3.4 8.6 + - - +
113A HIS* 3.1 22.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 5.4 16.3 - - + +
16A VAL* 4.0 21.3 - - + +
17A LYS* 6.1 0.2 - - - +
106A LEU* 2.5 39.1 + - + +
107A ARG* 3.0 35.2 - - - +
109A ILE* 1.3 73.3 - - - +
111A LEU* 1.3 84.4 + - - +
113A HIS* 3.0 21.9 + - - +
114A LEU* 3.3 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ARG* 2.7 47.2 + - + +
108A ASN* 4.3 1.6 - - - +
110A LYS* 1.3 93.3 - - - +
112A GLU* 1.3 64.9 + - - +
114A LEU* 3.0 30.9 + - + +
115A LYS* 3.5 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ASN 2.9 20.5 + - - +
109A ILE* 3.5 9.6 - - - +
110A LYS 3.2 0.2 - - - -
111A LEU* 1.3 77.0 - - - +
113A HIS* 1.3 61.4 + - - +
115A LYS* 2.7 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASP* 4.1 29.8 - - + +
16A VAL* 4.0 20.7 - - + +
109A ILE* 3.1 12.2 + - + +
110A LYS* 3.0 17.3 + - - +
112A GLU* 1.3 84.3 + - - +
114A LEU* 1.3 63.6 + - + +
115A LYS* 3.3 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU* 5.4 11.0 - - - +
110A LYS* 3.3 30.5 - - + +
111A LEU* 3.0 27.9 + - + +
113A HIS* 1.3 83.0 - - + +
115A LYS* 1.3 79.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU 3.5 2.7 + - - -
112A GLU* 2.7 32.8 + - - +
113A HIS 4.1 9.0 - - - +
114A LEU* 1.3 92.5 - - - +
----------------------------------------------------------
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