Contacts of the helix formed by residues 111 - 127 (chain A) in PDB entry 3LRA
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 SER 111 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PRO* 4.7 11.3 - - - -
3A VAL* 3.8 25.7 + - - +
53A GLN* 5.8 1.3 - - - -
112A LEU* 1.3 70.4 + - - +
113A HIS* 3.4 8.7 - - - +
114A SER* 3.2 18.6 + - - +
115A LEU* 3.0 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 3.6 30.7 - - + +
8A THR* 5.0 1.6 - - + -
41A PHE* 4.1 19.1 - - + -
46A PHE* 4.2 16.2 - - + -
50A ILE* 6.2 0.4 - - + -
83A LEU* 4.8 4.0 - - + -
106A MET* 3.5 38.1 - - + +
107A PHE* 3.6 32.5 - - + -
111A SER* 1.3 77.9 + - - +
113A HIS* 1.3 62.9 + - + +
115A LEU* 3.0 9.1 + - + +
116A VAL* 2.9 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 5.0 0.7 - - - +
80A TYR* 3.5 41.8 + + + -
83A LEU* 3.7 40.0 - - + +
84A ALA* 3.9 13.6 - - + +
106A MET 4.3 7.4 + - - -
107A PHE* 4.0 22.5 - + - -
111A SER 3.4 6.0 - - - +
112A LEU* 1.3 77.6 - - + +
114A SER* 1.3 63.3 + - - +
116A VAL* 3.4 2.4 + - - +
117A LYS* 3.0 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.5 34.1 - - - +
70A PHE* 4.0 14.2 - - - -
111A SER* 3.2 17.0 + - - -
113A HIS* 1.3 75.5 - - - +
115A LEU* 1.3 68.4 + - - +
117A LYS* 3.3 5.2 + - - +
118A ILE* 3.0 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 5.5 3.8 - - + -
46A PHE* 3.4 30.1 - - + -
49A LEU* 3.5 38.6 - - + +
50A ILE* 4.7 8.1 - - + +
53A GLN* 4.2 32.8 - - + +
111A SER 3.0 13.2 + - - +
112A LEU* 3.0 18.1 + - + +
114A SER* 1.3 78.9 - - - +
116A VAL* 1.3 58.9 + - - +
118A ILE* 3.1 12.3 + - + +
119A HIS 2.9 22.3 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
40A ILE* 4.1 11.7 - - + -
41A PHE* 4.7 8.1 - - + -
46A PHE* 3.8 23.1 - - + -
79A LEU* 3.3 34.1 - - + -
83A LEU* 3.6 27.8 - - + -
112A LEU* 2.9 26.9 + - + +
113A HIS 3.9 2.9 - - - +
115A LEU* 1.3 74.1 - - - +
117A LYS* 1.3 61.1 + - - +
119A HIS* 3.3 7.7 + - - +
120A GLU* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU 5.1 1.0 - - - +
70A PHE* 3.9 27.1 - - + -
74A GLY 4.3 3.3 - - - +
75A SER* 4.6 20.2 - - - +
76A ASP* 4.7 11.9 + - - +
79A LEU* 4.0 16.6 - - + -
80A TYR* 3.5 40.1 - - + +
113A HIS* 3.0 26.6 + - + +
114A SER* 3.3 5.4 + - - +
116A VAL* 1.3 72.5 - - - +
118A ILE* 1.3 65.7 + - - +
120A GLU* 3.2 6.8 + - - +
121A LYS* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 4.4 10.8 - - + -
60A LEU* 4.8 2.2 - - + -
66A LEU* 4.0 28.0 - - + -
69A LEU* 3.9 27.1 - - + -
70A PHE* 4.1 21.3 - - + -
114A SER* 3.0 21.2 + - - +
115A LEU* 3.3 15.0 - - + +
117A LYS* 1.3 76.8 - - - +
119A HIS* 1.3 56.5 + - - +
121A LYS* 3.1 7.6 + - - +
122A LEU* 2.9 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 3.7 23.2 - - + +
43A SER* 3.3 31.9 + - - -
45A LEU* 3.4 20.5 - - + +
46A PHE* 3.4 33.3 + + + -
49A LEU* 3.8 17.0 - - + +
115A LEU 2.9 10.1 + - - +
116A VAL* 3.4 9.6 - - - +
117A LYS 3.2 0.2 - - - -
118A ILE* 1.3 78.0 - - - +
120A GLU* 1.3 81.3 + - - +
122A LEU* 3.8 2.6 - - - -
123A HIS* 2.8 47.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
40A ILE* 3.0 30.4 - - - +
74A GLY* 4.0 12.0 - - - +
75A SER 5.7 0.4 - - - +
77A THR* 4.2 18.8 - - + +
79A LEU* 3.4 23.2 - - + +
116A VAL 3.0 15.7 + - - +
117A LYS* 3.2 10.5 + - - +
119A HIS* 1.3 89.8 + - - +
121A LYS* 1.3 60.3 + - - +
123A HIS* 4.0 14.8 - - - +
124A TYR* 3.4 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL 4.6 2.8 + - - -
69A LEU* 3.0 41.5 + - + +
71A GLN 2.4 33.7 + - - -
72A GLY* 3.8 5.7 - - - -
73A PRO* 3.0 28.2 - - - +
74A GLY 3.6 13.7 + - - +
117A LYS 3.0 12.5 + - - +
118A ILE* 3.1 10.1 + - - +
120A GLU* 1.3 76.7 - - - +
122A LEU* 1.3 64.4 + - - +
124A TYR* 3.3 16.0 + - - +
125A TYR* 3.3 43.7 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
45A LEU* 3.7 23.8 - - + -
49A LEU* 3.8 22.7 - - + -
69A LEU* 4.3 25.4 - - + -
118A ILE* 2.9 39.0 + - + +
121A LYS* 1.3 73.7 - - + +
123A HIS* 1.3 67.1 + - - +
125A TYR* 2.9 15.5 + - + +
126A GLU* 2.9 22.7 + - - +
244A VAL* 6.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER* 5.4 2.9 + - - -
45A LEU* 3.7 10.2 - - + +
119A HIS* 2.8 38.5 + - + +
120A GLU* 4.0 15.3 - - - +
122A LEU* 1.3 77.8 - - - +
124A TYR* 1.3 62.6 + - - +
126A GLU* 3.6 19.8 + - + +
127A LYS* 3.2 52.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PRO* 3.0 59.0 - - + +
74A GLY* 4.7 3.4 - - - -
120A GLU 3.4 12.7 + - - +
121A LYS* 3.3 11.6 + - - +
122A LEU 3.0 0.2 - - - -
123A HIS* 1.3 80.5 - - - +
125A TYR* 1.3 87.3 + + - +
127A LYS* 3.2 35.7 + - - +
128A GLN* 2.9 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 4.6 12.5 - - + +
73A PRO* 5.7 2.4 - - + +
121A LYS* 3.3 52.1 + - + -
122A LEU* 2.9 16.9 + - + +
124A TYR* 1.3 93.7 - + - +
126A GLU* 1.3 55.9 + - - +
127A LYS 3.0 1.8 - - - -
128A GLN* 2.6 45.6 + - + +
129A SER* 3.4 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 4.0 21.7 - - + +
122A LEU 2.9 14.8 + - - +
123A HIS* 3.6 26.4 + - + +
125A TYR* 1.3 75.2 - - - +
127A LYS* 1.3 58.6 + - + +
128A GLN 3.0 0.2 - - - -
129A SER* 2.9 34.7 + - - +
179A VAL* 6.1 1.4 - - - +
182A LYS* 5.0 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A HIS* 3.2 46.6 + - + +
124A TYR* 3.2 36.8 + - - +
125A TYR 2.9 1.0 + - - -
126A GLU* 1.3 79.3 - - + +
128A GLN* 1.3 58.8 + - + +
129A SER 3.2 3.5 + - - +
----------------------------------------------------------
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