Contacts of the helix formed by residues 108 - 118 (chain A) in PDB entry 1ZQB
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 PRO 108 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS* 4.4 15.0 - - + +
28A ASN* 3.5 44.6 - - + +
97A ILE* 5.1 2.2 - - + -
101A THR* 4.1 8.7 - - - +
107A GLY* 1.4 82.7 - - - +
109A SER* 1.4 52.9 + - - +
111A ALA* 3.0 7.8 + - + +
112A ARG* 2.9 49.1 + - + +
5P A 3.7 7.2 - - - +
6P T 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PRO* 1.4 76.2 - - - +
110A ALA* 1.3 61.7 + - - +
112A ARG* 3.6 23.0 + - - +
113A LYS* 3.1 21.5 + - - +
4P A 3.0 33.7 + - - -
5P A 2.8 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ILE* 4.2 6.3 - - + -
107A GLY 3.3 11.2 - - - +
109A SER* 1.3 71.8 + - - +
111A ALA* 1.3 58.1 + - - +
113A LYS* 3.0 13.3 + - + +
114A PHE* 2.8 47.6 + - + -
136A GLN* 4.2 17.5 - - - +
5P A 2.6 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE* 3.7 33.2 - - + +
100A LEU* 4.6 9.4 - - + +
101A THR* 4.0 4.9 - - - +
106A ILE* 4.2 10.5 - - + -
107A GLY 2.7 19.4 + - - +
108A PRO* 3.0 12.5 + - + +
110A ALA* 1.3 74.2 - - - +
112A ARG* 1.3 60.2 + - - +
114A PHE* 3.5 3.5 + - - +
115A VAL* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LYS 5.0 2.6 + - - -
28A ASN 3.6 20.5 + - - +
29A VAL 3.9 11.0 - - - -
30A SER 4.6 2.5 + - - -
31A GLN* 2.9 50.0 - - - +
97A ILE* 3.4 25.1 - - + -
108A PRO* 2.9 19.1 + - - +
109A SER* 3.9 28.3 + - - +
111A ALA* 1.3 72.2 - - - +
113A LYS* 1.3 68.1 - - - +
115A VAL* 3.1 4.2 + - - +
116A ASP* 2.9 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A SER 3.1 15.1 + - - +
110A ALA* 3.0 14.0 + - - +
112A ARG* 1.3 76.9 - - - +
114A PHE* 1.3 97.9 - - - +
116A ASP* 3.0 14.8 + - - +
117A GLU* 3.2 31.6 + - - +
131A LYS* 4.0 8.4 + - - -
136A GLN* 5.1 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 4.8 5.2 - - + -
106A ILE* 4.4 20.6 - - + -
110A ALA* 2.8 36.5 + - + +
111A ALA* 4.0 4.5 - - - +
113A LYS* 1.3 102.3 - - - +
115A VAL* 1.3 62.8 + - - +
117A GLU* 3.3 16.0 + - - -
118A GLY 3.0 5.0 + - - -
119A ILE* 2.8 59.5 + - + +
125A LEU* 4.5 4.7 - - + -
131A LYS* 3.4 30.3 - - + -
132A LEU* 3.4 23.1 - - + -
136A GLN* 4.1 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A THR* 4.7 19.3 - - + +
96A SER* 4.3 14.8 - - - +
97A ILE* 4.4 12.1 - - + -
100A LEU* 4.1 19.1 - - + -
111A ALA 2.9 25.2 + - - +
112A ARG* 3.1 8.0 + - - +
114A PHE* 1.3 79.9 - - - +
116A ASP* 1.3 63.4 - - - +
118A GLY* 2.7 22.7 + - - -
119A ILE 4.2 5.4 - - - +
120A LYS* 3.4 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A THR* 5.7 3.3 - - - +
112A ARG* 2.9 29.2 + - - +
113A LYS* 3.0 4.4 + - - +
115A VAL* 1.3 86.7 - - - +
117A GLU* 1.3 59.6 - - - +
118A GLY* 4.7 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LYS* 3.2 25.5 + - - +
114A PHE* 3.6 32.6 - - - +
115A VAL 3.1 0.4 - - - -
116A ASP* 1.3 75.6 - - - +
118A GLY* 1.4 58.6 + - - +
119A ILE* 3.9 10.6 - - + +
131A LYS* 3.8 31.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL 2.7 15.9 + - - -
116A ASP 3.2 0.4 - - - -
117A GLU* 1.4 80.2 - - - +
119A ILE* 1.3 60.6 + - - +
120A LYS* 3.2 20.5 + - - +
124A ASP* 3.0 13.7 - - - +
----------------------------------------------------------
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