Contacts of the helix formed by residues 120 - 134 (chain A) in PDB entry 6R7Y
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 THR 120 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LYS* 5.1 3.8 - - - +
117A ASP* 5.0 6.5 - - - +
118A PHE 3.5 8.3 + - - +
119A LEU* 1.3 77.1 - - - +
121A MET* 1.3 59.7 + - - +
122A ALA* 3.9 2.8 + - - +
123A GLU* 3.0 31.8 + - - +
124A CYS* 3.0 26.3 + - - -
201A ARG* 5.9 5.1 + - - +
202A GLY* 4.1 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 6.5 0.2 - - - -
17A PRO 4.5 6.7 - - - +
18A LEU* 3.8 27.1 - - + -
120A THR* 1.3 74.4 - - - +
122A ALA* 1.3 57.2 + - - +
124A CYS* 3.9 6.9 - - + +
125A GLN* 3.0 60.6 + - - +
173A LEU* 4.4 7.9 - - + +
174A HIS 5.3 0.9 - - - +
175A ASP* 3.9 34.8 - - + +
202A GLY 4.9 0.6 + - - -
203A TYR* 5.5 1.6 - - + -
543A ARG* 3.9 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A THR* 3.2 4.1 + - - +
121A MET* 1.3 78.1 - - - +
123A GLU* 1.3 59.7 + - + +
125A GLN* 3.4 9.4 + - - +
126A PHE* 2.9 28.6 + - - +
201A ARG 4.7 1.3 - - - +
202A GLY* 3.6 23.0 + - - +
203A TYR 4.0 13.2 - - - +
204A PHE 5.0 0.2 - - - -
205A GLY* 4.2 16.2 - - - +
543A ARG* 4.2 3.6 - - - +
546A SER* 3.9 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 3.8 41.4 - - + +
89A VAL 5.3 1.7 + - - +
90A LYS* 3.6 26.5 + - - +
119A LEU* 4.2 6.1 - - + +
120A THR* 3.0 33.8 + - - +
122A ALA* 1.3 77.0 - - + +
124A CYS* 1.3 62.1 + - - +
126A PHE* 3.4 8.8 + - + +
127A ILE* 2.9 34.9 + - - +
201A ARG* 3.5 23.7 + - - +
206A GLU* 5.1 3.5 - - - +
546A SER* 5.7 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.1 18.4 - - + -
79A MET* 3.5 34.7 - - + +
119A LEU* 3.7 29.8 - - - -
120A THR 3.0 26.1 + - - +
121A MET* 3.9 9.0 - - + +
122A ALA 3.3 0.2 - - - -
123A GLU* 1.3 76.7 - - - +
125A GLN* 1.3 61.6 + - - +
127A ILE* 3.4 1.4 + - - -
128A ILE* 3.2 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.6 34.6 + - + +
19A VAL* 4.4 6.1 - - + +
121A MET* 3.0 46.8 + - + +
122A ALA* 3.9 5.2 - - - +
124A CYS* 1.3 75.1 - - - +
126A PHE* 1.3 62.3 + - - +
128A ILE* 3.6 1.7 + - - +
129A LYS 3.2 17.3 + - - -
172A PRO* 3.7 21.4 - - + +
173A LEU 3.0 25.6 + - - +
543A ARG* 3.6 21.8 + - - -
545A PHE* 3.5 17.4 - - + -
546A SER 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 3.6 33.2 - - + -
88A LEU* 4.7 13.7 - - + -
122A ALA 2.9 18.8 + - - +
123A GLU* 3.6 8.1 - - + +
125A GLN* 1.3 77.1 - - - +
127A ILE* 1.3 58.4 + - + +
129A LYS* 3.5 5.8 + - + +
130A HIS* 3.0 37.2 + - + +
277A MET* 5.5 3.6 - - + -
545A PHE* 4.9 6.0 - - + -
546A SER* 3.3 34.5 - - - +
547A GLU* 5.8 1.8 - - + -
548A PRO* 3.7 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG* 5.4 0.7 - - - +
79A MET* 3.9 23.3 - - + +
82A GLY* 3.8 25.8 - - - +
83A ALA* 3.8 29.2 - - + +
86A VAL* 4.0 20.6 - - + -
88A LEU* 4.0 15.7 - - + -
119A LEU* 4.4 6.7 - - + -
123A GLU 2.9 22.8 + - - +
124A CYS 3.9 3.6 - - - +
125A GLN 3.3 0.4 - - - -
126A PHE* 1.3 76.6 - - + +
128A ILE* 1.3 59.1 + - + +
130A HIS* 3.1 7.4 + - - +
131A GLU* 2.8 36.8 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
18A LEU* 3.8 31.2 - - + -
19A VAL* 3.8 23.6 - - + -
50A LEU* 4.6 11.6 - - + +
72A VAL* 3.9 22.7 - - + +
73A GLY* 3.8 27.6 - - - +
74A ALA* 4.1 2.5 - - + +
79A MET* 3.9 17.0 - - + -
124A CYS 3.2 13.7 + - - +
125A GLN 4.2 3.4 - - - +
127A ILE* 1.3 76.5 - - + +
129A LYS* 1.3 62.6 + - - +
131A GLU* 3.3 6.9 + - - +
132A LEU* 3.1 26.7 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
19A VAL* 4.9 1.5 - - - +
125A GLN 3.2 17.8 + - - +
126A PHE* 4.0 6.5 - - + +
128A ILE* 1.3 77.6 - - - +
130A HIS* 1.3 57.5 + - - +
132A LEU* 3.4 5.3 + - + -
133A GLU* 3.0 31.9 + - + +
158A LEU* 4.0 25.1 - - + -
162A LEU* 5.9 4.8 - - - +
170A VAL* 4.1 15.8 + - + +
545A PHE* 3.7 47.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ALA* 4.9 7.2 + - + +
86A VAL* 3.6 34.6 - - + +
126A PHE* 3.0 31.7 + - + +
127A ILE 3.1 4.5 + - - +
129A LYS* 1.3 77.9 - - - +
131A GLU* 1.3 68.6 + - - +
133A GLU* 3.7 6.1 - - - +
134A ASN* 3.1 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS* 3.3 24.2 + - - -
48A ALA* 4.8 6.6 - - + +
50A LEU* 4.5 17.9 - - + -
78A ARG* 3.3 26.6 + - - +
82A GLY* 3.9 16.8 - - - +
85A ALA* 4.1 15.1 - - - +
127A ILE* 2.8 27.9 + - + +
128A ILE* 3.3 6.0 + - - +
130A HIS* 1.3 84.4 - - - +
132A LEU* 1.3 66.5 + - - +
134A ASN* 3.5 25.4 - - - +
135A LEU* 3.9 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 4.7 13.9 - - + -
21A ILE* 4.0 26.9 - - + -
35A LEU* 6.4 0.4 - - + -
39A ILE* 4.3 20.6 - - + -
48A ALA* 5.4 0.4 - - + -
50A LEU* 4.4 15.9 - - + -
72A VAL* 4.9 4.9 - - + -
128A ILE* 3.1 24.6 + - + +
129A LYS* 3.9 6.3 - - + +
131A GLU* 1.3 75.9 - - - +
133A GLU* 1.3 64.1 + - - +
135A LEU* 3.5 34.2 - - + +
156A SER* 4.5 0.3 + - - -
158A LEU* 3.7 41.5 - - + +
170A VAL* 5.2 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LYS* 3.0 23.9 + - - +
130A HIS* 3.7 9.9 - - - +
131A GLU 3.3 0.2 - - - -
132A LEU* 1.3 77.2 - - - +
134A ASN* 1.3 63.0 + - - +
135A LEU 3.0 6.7 + - - -
136A ARG* 5.2 1.2 - - - +
156A SER* 3.3 27.5 + - - -
158A LEU* 4.9 5.5 - - - +
159A ARG* 5.1 13.6 + - - +
283A GLU* 5.0 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS* 5.5 4.5 - - - -
130A HIS* 3.1 42.6 + - + +
131A GLU* 3.5 18.4 - - - +
132A LEU 3.4 0.2 - - - -
133A GLU* 1.3 78.1 - - - +
135A LEU* 1.3 59.9 + - - +
136A ARG* 3.9 29.8 + - - +
283A GLU* 4.6 6.4 - - - +
636B LYS* 4.6 16.0 - - - +
----------------------------------------------------------
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