Contacts of the helix formed by residues 94 - 105 (chain A) in PDB entry 1BX4
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 LYS 94 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASP* 1.3 72.3 - - - +
95A PHE* 1.3 72.0 + - + +
97A GLU* 3.1 18.3 + - - +
98A ILE* 3.2 18.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.4 27.6 - - + +
19A ILE* 4.8 4.9 - - + -
60A TYR* 4.2 21.3 - + - -
93A ASP* 3.3 6.7 + - - +
94A LYS* 1.3 84.1 - - + +
96A GLY* 1.3 62.0 + - - +
98A ILE* 3.2 25.3 + - + +
99A LEU* 3.3 17.2 + - - +
120A THR* 3.9 24.0 - - + -
122A THR* 3.8 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ILE* 4.0 7.9 - - - +
91A GLY 4.2 8.5 - - - -
93A ASP* 2.8 16.0 + - - -
94A LYS 3.2 0.2 - - - -
95A PHE* 1.3 78.1 - - - +
97A GLU* 1.3 59.5 + - - +
99A LEU* 3.4 4.9 + - - +
100A LYS* 3.2 33.0 + - - +
120A THR* 3.3 20.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASP 3.1 18.2 + - - +
94A LYS* 3.1 11.2 + - - +
96A GLY* 1.3 73.4 - - - +
98A ILE* 1.3 60.6 + - + +
100A LYS* 2.9 29.3 + - - +
101A ARG* 3.0 35.0 + - - +
114A GLU* 5.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.9 37.7 - - + -
60A TYR* 5.6 5.6 - - + -
61A HIS* 6.2 0.2 - - - -
62A ALA* 4.9 4.7 - - + +
94A LYS* 3.2 17.8 + - + +
95A PHE* 3.3 15.3 - - + +
97A GLU* 1.3 77.2 - - + +
99A LEU* 1.3 58.0 + - - +
101A ARG* 3.6 32.4 - - - +
102A LYS* 3.0 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PRO* 3.8 34.3 - - + -
16A LEU 3.7 21.1 - - - +
17A LEU* 4.1 10.3 - - + -
62A ALA* 3.6 30.3 - - + -
63A GLY 4.2 0.9 - - - +
67A GLN* 4.4 11.8 + - - +
71A LYS* 5.1 0.7 + - - -
90A ILE* 4.1 7.9 - - + -
95A PHE 3.3 10.4 + - - +
96A GLY* 3.8 6.5 - - - +
97A GLU 3.3 0.2 - - - -
98A ILE* 1.3 79.9 - - - +
100A LYS* 1.3 55.8 + - + +
102A LYS* 3.5 2.3 + - - +
103A ALA* 3.1 28.4 + - - +
112A TYR* 3.8 8.5 + - + +
120A THR* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ILE* 4.0 11.0 - - + +
96A GLY 3.2 19.6 + - - +
97A GLU* 2.9 41.9 + - - +
99A LEU* 1.3 72.6 - - - +
101A ARG* 1.3 66.4 + - - +
103A ALA* 3.3 2.3 + - - +
104A ALA* 3.1 24.3 + - - +
112A TYR* 3.8 34.1 - - + -
114A GLU* 3.6 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLU* 3.0 20.2 + - - +
98A ILE* 3.6 41.7 - - - +
100A LYS* 1.3 78.3 - - - +
102A LYS* 1.3 86.5 + - - +
104A ALA* 3.4 5.3 + - - +
105A GLU* 3.1 48.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA* 3.9 27.4 - - + -
71A LYS* 4.0 9.9 - - - +
98A ILE* 3.0 23.8 + - + +
99A LEU 4.1 1.3 - - - +
101A ARG* 1.3 101.5 - - - +
103A ALA* 1.3 64.9 - - - +
105A GLU* 3.0 30.0 + - + +
106A ALA* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLN* 4.5 4.3 - - + +
71A LYS* 4.1 13.2 - - - +
99A LEU 3.1 11.1 + - - +
100A LYS* 3.3 5.4 + - - +
102A LYS* 1.3 76.8 - - - +
104A ALA* 1.3 62.5 + - - +
106A ALA* 3.3 8.0 + - - +
108A VAL* 3.2 31.1 + - + +
110A ALA* 3.9 19.1 - - + -
112A TYR* 3.5 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS 3.1 16.5 + - - +
101A ARG* 3.7 6.1 - - - +
103A ALA* 1.3 73.8 - - - +
105A GLU* 1.3 61.4 + - + +
106A ALA 3.0 1.3 - - - -
107A HIS* 2.9 25.6 + - - -
108A VAL 4.7 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 3.1 42.1 + - + +
102A LYS* 3.0 36.9 + - + +
104A ALA* 1.3 77.2 - - + +
106A ALA* 1.3 57.1 + - - +
107A HIS* 3.2 21.6 + - - -
----------------------------------------------------------
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