Contacts of the helix formed by residues 98 - 109 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 4.2 16.3 - - + +
69C LEU* 4.2 8.0 - - - +
96C PRO* 3.4 6.5 - - - +
97C ARG* 1.3 79.5 - - - +
99C VAL* 1.3 65.5 + - - +
100C GLN* 3.3 39.1 + - + +
101C GLN* 3.2 39.9 + - + +
102C GLY 3.4 4.7 + - - -
156C ALA* 3.6 22.6 - - + +
160C VAL* 3.5 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C GLU* 1.3 73.2 - - - +
100C GLN* 1.3 63.9 + - - +
102C GLY* 3.0 13.3 + - - -
103C GLU* 3.1 21.4 + - - +
156C ALA 4.6 1.0 + - - +
159C PRO* 4.1 31.6 - - + +
160C VAL* 3.7 6.4 - - + +
163C PHE* 3.3 49.9 - - + -
164C TYR* 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU* 3.7 12.2 - - + +
98C GLU* 3.3 38.5 + - + +
99C VAL* 1.3 78.0 - - - +
101C GLN* 1.3 60.2 + - - +
103C GLU* 3.5 15.7 + - - +
104C GLU* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 4.8 2.8 - - - +
67C VAL 4.5 2.8 + - - -
69C LEU* 3.7 26.3 - - + +
72C VAL* 4.1 7.3 - - - +
95C TYR* 2.7 41.0 + - - +
96C PRO* 3.6 7.4 - - + -
97C ARG* 2.8 30.4 + - - +
98C GLU* 3.2 32.2 + - + +
100C GLN* 1.3 80.1 - - - +
102C GLY* 1.3 60.1 + - - +
104C GLU* 3.7 0.3 + - - -
105C PHE 3.1 12.5 + - - -
633C AP5 3.0 41.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PHE* 5.0 1.5 - - - -
96C PRO* 3.4 15.8 - - - +
98C GLU 3.4 4.2 + - - -
99C VAL* 3.0 8.6 + - - -
101C GLN* 1.3 76.4 - - - +
103C GLU* 1.3 64.2 + - - +
105C PHE* 3.4 6.0 + - - +
106C GLU* 3.0 28.2 + - - +
163C PHE* 5.5 0.4 - - - -
164C TYR* 3.4 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LYS* 3.6 41.5 - - + +
99C VAL* 3.1 20.9 + - - +
100C GLN* 3.8 15.1 - - - +
101C GLN 3.4 0.2 - - - -
102C GLY* 1.3 74.7 - - - +
104C GLU* 1.3 61.9 + - - +
106C GLU* 3.3 4.9 + - - +
107C ARG* 3.0 31.2 + - + +
163C PHE* 3.9 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LEU* 4.1 16.4 - - + -
70C GLU* 5.0 0.4 - - - +
73C LEU* 3.5 24.5 - - + -
100C GLN 3.1 16.0 + - - +
101C GLN 4.3 1.6 - - - +
103C GLU* 1.3 78.4 - - - +
105C PHE* 1.3 62.2 + - - +
107C ARG* 3.4 11.7 + - - +
108C ARG* 2.9 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 4.0 18.4 - - + -
12C PHE* 3.9 32.3 - + + -
73C LEU* 4.1 9.9 - - + -
76C LEU* 3.8 20.6 - - + -
80C MET* 4.0 20.0 - - + -
92C ILE* 4.4 5.4 - - + -
95C TYR* 3.7 25.4 + + + +
101C GLN 3.1 18.9 + - - +
102C GLY* 3.5 6.3 - - - +
103C GLU 3.3 0.2 - - - -
104C GLU* 1.3 77.1 - - - +
106C GLU* 1.3 55.1 + - + +
109C ILE* 2.7 62.1 + - + +
110C GLY 3.3 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LYS 3.9 2.7 - - - +
167B ARG* 3.6 35.0 - - - +
168B GLY* 3.8 4.5 - - - -
6C LYS* 6.1 0.3 - - - -
12C PHE* 5.2 0.4 - - + -
102C GLY 3.0 15.4 + - - +
103C GLU* 3.8 4.6 + - - +
105C PHE* 1.3 77.3 - - + +
107C ARG* 1.3 61.8 + - - +
108C ARG 3.5 0.2 + - - -
109C ILE 3.9 1.0 + - - -
110C GLY* 3.5 31.3 + - - +
111C GLN* 3.0 16.6 - - - +
112C PRO* 3.7 13.0 - - + -
163C PHE* 4.6 1.9 - - - -
164C TYR* 2.8 17.8 + - - +
167C ARG* 2.7 46.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLU* 3.4 45.8 + - - +
166B LYS* 3.8 19.0 - - - +
168B GLY* 4.3 10.6 - - - -
6C LYS* 5.9 2.6 - - - -
103C GLU* 3.0 32.4 + - + +
104C GLU* 3.8 15.2 + - - +
105C PHE 3.3 0.2 - - - -
106C GLU* 1.3 76.5 - - - +
108C ARG* 1.3 64.3 + - + +
109C ILE 5.4 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C GLU* 5.7 5.1 - - - +
5C LEU* 4.9 1.4 - - - +
6C LYS* 6.4 0.4 - - - -
70C GLU* 2.8 42.7 + - - -
73C LEU* 3.7 21.0 - - + +
74C ASP* 2.8 20.2 + - - -
77C ARG* 3.4 29.9 + - - +
104C GLU* 2.9 59.5 + - - +
105C PHE 4.5 0.2 - - - +
107C ARG* 1.3 80.7 - - + +
109C ILE* 1.3 69.5 + - + +
645C ZN 3.9 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C GLU* 4.7 0.7 - - - +
5C LEU* 3.9 27.3 - - + +
6C LYS* 3.4 26.6 - - - +
10C ILE* 4.3 4.0 - - + -
73C LEU* 4.2 9.2 - - + -
76C LEU* 5.2 0.2 - - + -
77C ARG* 3.6 39.9 - - + +
80C MET* 3.8 33.9 - - + -
105C PHE* 2.7 49.5 + - + +
106C GLU 4.1 2.2 - - - -
107C ARG 3.6 0.6 - - - -
108C ARG* 1.3 83.7 - - + +
110C GLY* 1.3 59.2 + - - +
----------------------------------------------------------
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