Contacts of the helix formed by residues 117 - 137 (chain A) in PDB entry 1S0O
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 ASP 117 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ILE* 4.3 11.4 - - - +
115A VAL* 3.7 3.5 - - - +
116A ARG* 1.3 82.4 - - - +
118A TYR* 1.3 59.4 + - - +
119A ARG* 2.8 44.1 + - - +
120A GLU* 2.9 20.8 + - - +
121A ALA* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 4.8 1.7 + - - -
2A ILE* 3.8 31.3 - - + +
117A ASP* 1.3 74.1 - - - +
119A ARG* 1.3 57.3 + - - +
121A ALA* 3.4 2.2 - - - +
122A TYR* 2.7 36.0 + - - +
144A ILE* 3.9 18.8 - - + -
145A SER* 3.2 9.7 - - - -
146A LYS* 3.0 34.1 + - - +
165A VAL* 3.5 29.1 - - + +
166A ILE 4.1 2.1 + - - -
167A ASP* 3.6 31.4 - - + -
168A ASP* 3.9 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASP* 2.8 23.6 + - - +
118A TYR* 1.3 78.9 - - - +
120A GLU* 1.3 86.7 + - - +
122A TYR* 3.3 7.9 + - - +
123A ASN* 3.1 48.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LYS 4.6 1.6 - - - +
115A VAL* 3.5 22.2 - - + +
116A ARG* 3.0 57.5 + - - +
117A ASP* 2.9 14.2 + - - +
119A ARG* 1.3 101.6 + - - +
121A ALA* 1.3 66.1 + - - +
123A ASN* 3.2 9.9 + - - +
124A LEU* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ILE* 4.1 4.7 - - + -
4A LEU* 4.1 2.1 - - - +
111A ILE* 4.0 15.9 - - + -
115A VAL* 3.9 13.7 - - + +
117A ASP 3.0 15.0 + - - +
118A TYR* 3.2 14.1 + - - +
120A GLU* 1.3 76.0 - - - +
122A TYR* 1.3 64.2 + - - +
124A LEU* 3.2 4.3 + - - +
125A GLY 2.9 17.7 + - - -
144A ILE* 3.4 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR 2.7 20.8 + - - +
119A ARG* 3.4 7.9 - - - +
121A ALA* 1.3 72.4 - - - +
123A ASN* 1.3 66.8 + - - +
125A GLY* 2.8 17.3 + - - -
126A LEU* 3.0 37.5 + - + +
144A ILE* 3.8 8.5 - - - +
163A ILE* 3.5 50.9 + - + +
164A LYS* 5.1 1.3 - - - -
165A VAL* 3.9 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ARG* 3.1 42.9 + - - +
120A GLU* 3.2 8.8 + - - +
122A TYR* 1.3 86.1 - - - +
124A LEU* 1.3 63.5 + - - +
126A LEU* 3.1 16.7 + - - +
127A GLU* 2.9 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.5 2.9 - - + -
95A TYR* 3.6 33.0 - - + +
111A ILE* 3.9 37.7 - - + -
114A LYS* 4.5 7.6 - - + -
115A VAL* 3.9 15.7 - - + -
120A GLU 2.9 13.7 + - - +
121A ALA 3.4 8.7 - - - +
123A ASN* 1.3 75.4 - - - +
125A GLY* 1.3 57.4 + - - +
127A GLU* 3.2 22.9 + - - +
128A ILE* 2.9 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.0 15.2 - - - +
121A ALA 2.9 10.1 + - - -
122A TYR 2.8 9.9 + - - -
124A LEU* 1.3 77.1 - - - +
126A LEU* 1.3 62.1 + - - +
128A ILE* 3.2 5.5 + - - +
129A LYS* 3.0 26.9 + - - +
142A VAL* 4.1 9.4 - - - +
163A ILE* 3.9 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR* 3.0 41.8 + - + +
123A ASN* 3.1 17.9 + - - +
125A GLY* 1.3 74.9 - - - +
127A GLU* 1.3 61.9 + - - +
129A LYS* 3.3 14.0 + - + +
130A ASN* 3.0 37.2 + - - +
163A ILE* 3.8 25.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 3.8 20.5 + - + +
123A ASN* 2.9 10.8 + - - +
124A LEU* 3.2 33.2 + - + +
126A LEU* 1.3 77.7 - - - +
128A ILE* 1.3 57.2 + - - +
130A ASN* 3.3 9.7 + - - +
131A LYS* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.1 22.7 - - + -
6A VAL* 4.5 9.4 - - + -
92A LEU* 3.6 24.5 - - + -
95A TYR* 3.7 39.5 - - + -
109A LEU* 4.0 21.8 - - + -
124A LEU* 2.9 22.3 + - + +
125A GLY* 3.6 7.4 - - - +
127A GLU* 1.3 73.0 - - - +
129A LYS* 1.3 65.2 + - - +
131A LYS* 3.3 6.6 + - - +
132A ILE* 3.0 34.9 + - + +
140A VAL* 5.4 0.4 - - + -
142A VAL* 5.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLY 3.0 20.8 + - - +
126A LEU* 3.7 13.7 - - - +
127A GLU 3.3 0.2 - - - -
128A ILE* 1.3 75.6 - - - +
130A ASN* 1.3 66.0 + - - +
132A ILE* 3.6 2.0 + - - +
133A LEU* 3.1 24.7 + - - +
138A ILE 4.7 1.7 - - - +
139A THR* 6.0 0.2 - - - -
140A VAL* 2.9 43.7 + - + +
142A VAL* 3.8 18.4 - - + -
161A ASN* 2.9 27.6 + - - -
162A GLY* 3.3 25.2 + - - +
163A ILE* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 3.0 31.6 + - - +
127A GLU* 3.7 7.2 - - - +
129A LYS* 1.3 76.5 - - - +
131A LYS* 1.3 57.9 + - - +
133A LEU* 3.2 10.3 + - - +
134A GLU* 2.8 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 4.2 21.8 - - + +
95A TYR* 3.4 31.0 - - + +
127A GLU 2.9 16.4 + - - +
128A ILE* 3.5 6.1 - - - +
130A ASN* 1.3 77.0 - - - +
132A ILE* 1.3 58.3 + - + +
134A GLU* 3.3 24.1 + - - +
135A LYS* 2.9 57.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 4.6 3.8 - - + -
88A ILE* 3.7 40.8 - - + -
91A LEU* 3.9 19.3 - - + -
92A LEU* 4.2 8.5 - - + -
128A ILE* 3.0 33.6 + - + +
129A LYS* 4.1 4.0 - - - +
131A LYS* 1.3 76.2 - - + +
133A LEU* 1.3 58.8 + - - +
136A GLU* 2.9 26.8 + - + +
137A LYS 3.3 3.6 + - - -
138A ILE* 3.6 27.3 + - + +
140A VAL* 4.0 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LYS 3.1 19.5 + - - +
130A ASN* 3.6 10.5 - - - +
132A ILE* 1.3 76.7 - - - +
134A GLU* 1.3 58.5 + - - +
137A LYS* 2.7 65.0 + - + +
138A ILE 3.7 14.1 + - - +
139A THR* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ASN 2.8 16.1 + - - +
131A LYS* 3.5 33.1 + - - +
133A LEU* 1.3 78.6 - - - +
135A LYS* 1.3 80.4 + - + +
137A LYS* 3.3 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 3.8 31.9 - - + -
131A LYS* 2.9 43.5 + - + +
134A GLU* 1.3 98.7 + - + +
136A GLU* 1.3 70.6 - - + +
137A LYS* 5.4 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 3.8 12.6 - - - +
84A VAL* 4.7 6.2 - - + +
87A ARG* 2.8 56.4 + - + +
88A ILE* 4.1 21.3 - - + -
91A LEU* 4.7 6.3 - - + +
132A ILE 2.9 13.3 + - - +
135A LYS* 1.3 88.8 - - + +
137A LYS* 1.3 74.9 + - - +
138A ILE* 3.3 20.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLN* 4.1 3.1 - - - +
18A VAL* 3.4 26.4 - - + +
24A LYS* 6.2 1.6 - - - +
132A ILE 3.3 0.6 + - - -
133A LEU* 2.7 59.6 + - + +
134A GLU* 3.3 22.8 + - - +
135A LYS 5.5 0.4 - - - +
136A GLU* 1.3 75.2 - - - +
138A ILE* 1.3 58.4 + - - +
139A THR* 5.6 0.5 - - - +
----------------------------------------------------------
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