Contacts of the helix formed by residues 113 - 132 (chain A) in PDB entry 2RFJ
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 113 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A THR* 6.0 0.6 - - + +
109A ASN* 3.7 10.7 - - + +
110A LYS* 2.9 46.6 + - - +
111A PRO 3.3 0.6 - - - -
112A GLY* 1.3 80.5 + - - +
114A ASP* 1.3 66.3 - - - +
115A ILE* 4.3 7.2 - - + +
116A VAL* 3.0 19.6 + - + +
117A LEU* 3.1 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLY 4.5 1.8 - - - +
113A ASP* 1.3 73.2 - - - +
115A ILE* 1.3 63.5 + - - +
117A LEU* 3.3 15.7 + - - +
118A MET* 3.0 31.0 + - + +
20B MET* 3.1 49.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PRO* 4.0 19.3 - - + +
52A PHE* 3.7 24.0 - - + -
68A THR* 3.6 43.1 - - + +
69A ILE* 4.0 17.3 - - + +
72A ASN* 6.3 2.9 - - + +
105A CYS* 4.0 8.1 - - - -
109A ASN* 3.8 23.8 - - + +
113A ASP* 4.3 5.4 - - + +
114A ASP* 1.3 78.4 - - - +
116A VAL* 1.3 58.8 + - + +
118A MET* 3.5 4.2 + - - +
119A ALA* 2.9 28.6 + - - +
20B MET* 4.0 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A CYS* 4.1 16.4 - - - +
106A TYR* 3.9 20.2 - - + -
109A ASN* 3.7 26.0 - - + +
110A LYS 3.3 22.7 - - - +
111A PRO* 3.8 20.9 - - + +
113A ASP* 3.0 10.2 + - + +
115A ILE* 1.3 75.0 - - - +
117A LEU* 1.3 59.2 + - - +
119A ALA* 3.4 1.9 + - - +
120A GLN* 2.9 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 5.1 1.6 - - - -
111A PRO 4.2 13.5 - - - +
112A GLY* 3.7 17.0 - - - +
113A ASP 3.1 15.7 + - - +
114A ASP* 3.9 17.0 - - - +
116A VAL* 1.3 75.7 - - - +
118A MET* 1.3 62.7 + - + +
120A GLN* 3.4 19.3 + - - +
121A ALA* 3.1 21.8 + - - +
124A LYS* 5.1 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 3.7 49.3 - - + +
50A TRP* 3.7 16.6 - - + +
51A PRO* 3.9 19.1 - - + -
52A PHE* 4.4 6.5 - - + -
114A ASP* 3.0 23.6 + - + +
115A ILE* 3.7 5.8 - - - +
117A LEU* 1.3 75.2 - - + +
119A ALA* 1.3 63.2 + - - +
121A ALA* 3.3 3.5 + - - +
122A LEU* 3.1 26.3 + - - +
20B MET* 4.0 25.4 - - - +
21B ASN 3.5 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 3.6 18.3 - - + -
102A PHE* 3.6 11.5 - - + -
105A CYS* 3.6 23.6 - - + -
106A TYR* 3.5 15.3 - - + +
115A ILE 2.9 18.1 + - - +
116A VAL 3.7 4.0 - - - +
118A MET* 1.3 75.8 - - - +
120A GLN* 1.3 52.2 + - - +
122A LEU* 3.3 5.9 + - - +
123A GLU* 2.7 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 3.4 23.4 - - + +
111A PRO 5.0 1.7 + - - +
116A VAL* 2.9 32.7 + - - +
117A LEU* 3.6 25.4 - - - +
118A MET 3.2 0.2 - - - -
119A ALA* 1.3 76.1 - - - +
121A ALA* 1.3 57.5 + - - +
123A GLU* 3.3 4.2 + - - +
124A LYS* 3.0 43.1 + - - +
108C TYR* 4.5 22.8 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
46A HIS* 4.8 10.5 + - + +
48A PHE* 4.0 23.6 - - + -
117A LEU 3.1 13.1 + - - +
118A MET 3.3 7.4 + - - +
120A GLN* 1.3 74.8 - - - +
122A LEU* 1.3 61.8 + - - +
124A LYS* 3.4 21.1 + - - +
125A LEU* 3.2 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.9 29.5 - - + +
46A HIS* 3.6 39.3 - - + +
48A PHE* 3.5 26.9 - - + +
49A SER* 3.8 8.5 - - - -
52A PHE* 3.5 28.7 - - + -
76A LEU* 5.3 3.6 - - + -
101A MET* 5.6 1.8 - - + -
102A PHE* 4.2 12.3 - - + -
118A MET 3.1 11.6 + - - +
119A ALA* 3.6 6.5 - - - +
121A ALA* 1.3 75.6 - - - +
123A GLU* 1.3 57.2 + - - +
125A LEU* 3.3 6.7 + - + +
126A PHE* 2.8 29.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
102A PHE* 3.8 20.1 - - + -
106A TYR* 2.5 39.3 + - - +
119A ALA 2.7 20.6 + - - +
120A GLN* 3.6 7.8 - - - +
122A LEU* 1.3 71.4 - - - +
124A LYS* 1.3 59.6 + - - +
126A PHE* 3.5 1.4 - - + +
127A MET* 3.0 43.1 + - + +
67C TYR* 2.6 38.9 + - + +
71C LYS* 4.5 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU 5.1 1.0 + - - -
120A GLN* 3.0 23.5 + - - +
121A ALA* 3.7 33.0 - - - +
122A LEU 3.3 0.4 - - - -
123A GLU* 1.3 74.5 - - - +
125A LEU* 1.3 57.7 + - - +
127A MET* 3.5 17.0 + - + +
128A GLN* 3.0 48.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASP* 3.7 30.5 - - + +
43A LEU* 3.9 17.3 - - + -
46A HIS* 3.8 26.7 - - + -
121A ALA 3.2 10.2 + - - +
122A LEU* 3.3 9.1 + - + +
124A LYS* 1.3 79.7 - - - +
126A PHE* 1.3 63.3 + - - +
128A GLN* 3.4 15.1 + - + +
129A LYS* 3.0 48.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
35A LEU* 5.2 0.2 - - + -
39A VAL* 3.5 27.1 - - + +
43A LEU* 4.0 14.5 - - + +
95A ILE* 3.9 15.3 - - + -
98A PHE* 3.6 46.9 - + + -
102A PHE* 4.0 13.7 - + + -
122A LEU 2.8 18.1 + - - +
123A GLU* 3.5 7.2 - - - +
125A LEU* 1.3 77.3 - - - +
127A MET* 1.3 67.4 + - + +
129A LYS* 3.9 1.4 - - - +
130A LEU* 2.8 55.9 + - + +
67C TYR* 3.7 31.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLU* 3.0 38.2 + - + +
124A LYS* 4.0 18.6 - - + +
126A PHE* 1.3 75.0 - - + +
128A GLN* 1.3 65.8 + - + +
130A LEU* 3.8 7.5 - - + +
131A SER* 3.0 26.7 + - - -
64C PRO* 5.7 0.5 - - - +
67C TYR* 3.8 33.0 - - + -
68C THR* 5.9 1.3 - - - -
71C LYS* 3.8 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LYS* 3.0 35.4 + - - +
125A LEU* 3.7 17.0 - - + +
126A PHE 3.3 0.2 - - - -
127A MET* 1.3 76.4 - - + +
129A LYS* 1.3 64.4 - - + +
131A SER* 3.2 20.2 - - - -
132A GLN* 3.3 24.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
34A TYR* 2.5 29.8 + - - +
38A VAL* 4.5 10.3 - - + +
39A VAL* 4.1 20.6 - - + -
42A ASP* 3.2 35.1 + - + +
43A LEU* 5.8 0.7 - - + -
125A LEU* 3.0 36.9 + - + +
126A PHE 4.0 2.0 - - - +
128A GLN* 1.3 75.7 - - - +
130A LEU* 1.3 65.3 + - - +
132A GLN* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 4.8 2.2 - - - -
35A LEU* 4.2 4.9 - - + -
39A VAL* 4.4 2.7 - - + +
95A ILE* 3.6 24.0 - - + -
126A PHE* 2.8 52.4 + - + +
127A MET* 3.8 6.7 - - - +
129A LYS* 1.3 72.2 - - - +
131A SER* 1.3 62.3 + - - +
133A MET* 3.1 39.0 + - + +
63C LEU* 4.1 16.2 - - + +
64C PRO* 3.6 30.4 - - + +
67C TYR* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A MET 3.0 15.9 + - - -
128A GLN* 3.2 15.7 - - - -
130A LEU* 1.3 76.4 - - - +
132A GLN* 1.3 61.6 + - - +
133A MET 3.3 4.0 + - - +
64C PRO* 4.1 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 3.6 15.5 + - - +
128A GLN* 3.4 24.8 + - - +
129A LYS* 3.0 25.6 + - - +
131A SER* 1.3 79.3 - - - +
133A MET* 1.3 65.0 + - - +
134A PRO* 3.4 7.1 - - - +
----------------------------------------------------------
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