Contacts of the helix formed by residues 98 - 109 (chain B) in PDB entry 1Z83
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 GLU 98 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 3.9 16.3 - - + +
69B LEU* 4.4 8.1 - - - +
96B PRO* 3.5 6.4 - - - +
97B ARG* 1.3 78.2 - - - +
99B VAL* 1.3 66.2 + - - +
100B GLN* 3.9 17.3 - - - +
101B GLN* 3.2 44.3 + - + +
102B GLY* 3.4 6.9 + - - -
156B ALA* 3.7 17.2 - - + +
160B VAL* 3.6 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLU* 1.3 74.9 - - - +
100B GLN* 1.3 63.8 + - - +
102B GLY* 3.0 11.9 + - - +
103B GLU* 3.1 25.3 + - - +
156B ALA 4.7 1.4 + - - -
159B PRO* 4.3 16.8 - - + +
160B VAL* 3.9 10.9 - - - +
163B PHE* 3.8 53.2 - - + -
164B TYR* 6.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 4.0 9.2 - - + +
98B GLU* 3.3 19.0 - - + +
99B VAL* 1.3 77.9 - - - +
101B GLN* 1.3 61.9 + - - +
103B GLU* 3.4 12.1 + - - +
104B GLU* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 4.6 3.2 - - - +
67B VAL 4.5 4.8 + - - -
69B LEU* 3.9 17.9 - - + +
72B VAL* 4.3 6.4 - - - +
95B TYR* 2.7 47.0 + - + +
96B PRO* 3.8 4.0 - - + -
97B ARG* 2.9 26.0 + - - +
98B GLU* 3.2 36.2 + - + +
100B GLN* 1.3 79.5 - - - +
102B GLY* 1.3 63.4 + - - +
104B GLU* 3.5 0.3 + - - -
105B PHE 3.1 12.5 + - - -
632B AP5 2.9 41.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 5.0 1.7 - - - -
96B PRO* 3.6 15.1 - - - +
98B GLU 3.4 4.8 + - - -
99B VAL* 3.0 8.3 + - - -
101B GLN* 1.3 79.0 - - - +
103B GLU* 1.3 61.8 + - - +
105B PHE* 3.4 6.3 + - - +
106B GLU* 3.1 29.8 + - - +
164B TYR* 3.4 24.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 3.1 26.6 + - - +
100B GLN* 3.9 12.7 - - - +
101B GLN 3.4 0.2 - - - -
102B GLY* 1.3 76.8 - - - +
104B GLU* 1.3 63.8 + - - +
106B GLU* 3.5 9.6 + - - +
107B ARG* 3.3 25.4 + - - +
163B PHE* 4.2 23.1 - - + -
166C LYS* 4.0 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLU* 3.5 4.3 - - - +
74A ASP* 3.0 1.9 - - - +
69B LEU* 3.6 24.8 - - + +
70B GLU* 4.2 0.2 - - - +
73B LEU* 3.8 9.0 - - + -
100B GLN 3.1 16.4 + - - +
101B GLN 4.3 2.0 - - - +
102B GLY 3.3 0.2 - - - -
103B GLU* 1.3 74.3 - - - +
105B PHE* 1.3 66.2 + - - +
107B ARG* 3.4 31.9 + - - +
108B ARG* 2.6 53.2 + - + +
642B ZN 2.0 37.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 4.0 13.2 - - + -
12B PHE* 3.8 33.2 - + + -
73B LEU* 4.1 10.5 - - + -
76B LEU* 3.9 21.1 - - + -
80B MET* 3.9 24.7 - - + -
92B ILE* 4.6 3.8 - - + -
95B TYR* 3.8 23.6 + + + +
101B GLN 3.1 18.0 + - - +
102B GLY* 3.6 6.3 - - - +
104B GLU* 1.3 77.1 - - - +
106B GLU* 1.3 55.0 + - + +
108B ARG* 3.3 0.6 + - - -
109B ILE* 2.8 71.4 + - + +
110B GLY 3.3 22.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 5.3 0.2 - - + -
102B GLY 3.1 16.8 + - - +
103B GLU* 3.8 9.7 - - - +
104B GLU 3.3 0.2 - - - -
105B PHE* 1.3 79.7 - - + +
107B ARG* 1.3 60.9 + - - +
109B ILE 3.8 0.7 + - - -
110B GLY* 3.6 27.3 + - - +
111B GLN* 3.2 26.7 - - - +
112B PRO* 3.5 9.8 - - + +
163B PHE* 4.5 2.1 - - - -
164B TYR* 3.3 14.9 + - - +
167B ARG* 2.6 46.2 + - - -
166C LYS 4.3 10.5 - - - +
167C ARG* 4.0 19.7 - - - +
168C GLY* 4.7 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLU* 5.9 0.9 - - - +
53A ARG* 3.7 50.0 - - - +
70A GLU* 4.1 8.9 + - - -
71A THR* 6.4 0.4 - - - +
74A ASP* 4.2 3.4 + - - +
103B GLU* 3.3 16.9 + - - +
104B GLU* 3.4 51.8 + - - +
105B PHE 3.3 0.2 - - - -
106B GLU* 1.3 79.5 - - - +
108B ARG* 1.3 72.7 + - + +
109B ILE 3.9 0.2 + - - -
166C LYS 4.2 12.7 + - - +
168C GLY* 5.4 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASP* 3.4 22.7 + - - +
77A ARG* 6.0 0.2 - - - +
78A ASP* 2.9 43.6 + - - +
108A ARG* 4.2 1.8 - - - +
5B LEU* 4.7 1.2 - - - +
70B GLU* 2.9 20.2 + - - -
73B LEU* 3.6 20.3 + - + +
74B ASP* 4.0 15.0 + - - +
77B ARG* 3.2 33.8 + - - +
104B GLU* 2.6 59.0 + - + +
105B PHE* 4.5 1.1 - - - +
107B ARG* 1.3 91.7 - - + +
109B ILE* 1.3 62.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B GLU* 4.5 1.6 - - - +
5B LEU* 3.8 24.8 - - + +
6B LYS* 3.7 26.9 + - - +
10B ILE* 4.2 5.2 - - + -
73B LEU* 4.3 8.3 - - + -
77B ARG* 3.7 38.1 - - + +
80B MET* 3.9 23.3 - - + -
105B PHE* 2.8 58.6 + - + +
106B GLU 4.1 1.8 - - - -
107B ARG 3.6 1.6 - - - -
108B ARG* 1.3 84.5 - - + +
110B GLY* 1.3 59.1 + - - +
----------------------------------------------------------
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