Contacts of the helix formed by residues 117 - 128 (chain A) in PDB entry 6LTJ
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 MET 117 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ARG* 3.4 31.0 - - - +
115A THR* 3.7 25.6 - - - -
116A ILE* 1.3 75.6 - - - +
118A PRO* 1.3 75.9 - - + +
119A LYS* 3.2 24.7 - - + +
120A ASP* 2.5 26.3 + - - +
121A ILE* 3.9 2.1 + - - +
47B SER* 4.3 12.6 - - - +
49B LEU* 5.9 4.3 - - + -
50B ILE* 3.5 7.2 - - - +
84X C 6.1 0.2 - - - +
74Y A 4.7 4.9 - - - +
75Y C 3.5 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A MET* 1.3 87.1 - - + +
119A LYS* 1.3 60.0 + - + +
121A ILE* 2.9 22.3 + - + +
122A GLN* 2.9 22.6 + - - +
47B SER* 4.8 0.4 - - - +
49B LEU* 3.7 49.4 - - + +
50B ILE* 3.9 14.8 - - + -
53B GLU* 3.3 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ARG* 3.8 28.7 - - - +
117A MET* 3.9 23.2 - - + +
118A PRO* 1.3 75.1 - - + +
120A ASP* 1.3 62.2 + - - +
122A GLN* 3.5 19.0 - - + +
123A LEU* 2.9 30.8 + - - +
113E HIS* 3.8 15.6 + - + +
115E LYS* 5.2 13.9 - - - +
75Y C 4.0 19.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A THR* 3.7 25.3 - - - +
107A CYS* 4.0 8.1 - - + -
108A ALA* 3.9 10.5 - - - +
113A ARG* 2.3 31.7 + - - -
116A ILE* 3.2 8.4 - - + -
117A MET 2.5 35.1 + - - +
119A LYS* 1.3 77.6 - - - +
121A ILE* 1.3 56.1 + - - +
123A LEU* 3.7 1.0 - - - +
124A ALA* 2.9 31.5 + - - +
113E HIS* 3.0 17.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 4.3 14.3 - - + +
101A PHE* 4.4 10.5 - - + -
104A THR* 3.7 21.8 - - + +
116A ILE* 5.5 0.4 - - + -
117A MET 4.2 7.4 - - - +
118A PRO* 2.9 10.0 + - + +
120A ASP* 1.3 77.1 - - - +
122A GLN* 1.3 57.8 + - - +
124A ALA* 3.9 1.0 - - - +
125A ARG* 2.9 34.9 + - - +
50B ILE* 3.7 25.8 - - + -
53B GLU* 4.1 17.9 - - + +
54B THR* 3.9 21.3 - - - +
57B VAL* 3.9 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PRO* 2.9 26.8 + - - +
119A LYS* 3.5 25.0 - - + +
121A ILE* 1.3 77.6 - - - +
123A LEU* 1.3 59.7 + - - +
126A ARG* 2.9 30.1 + - - +
131A ARG* 3.7 33.1 + - - +
53B GLU* 2.9 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A CYS* 3.7 21.8 - - + -
119A LYS 2.9 20.0 + - - +
120A ASP 3.7 2.7 - - - +
121A ILE 3.2 0.2 - - - -
122A GLN* 1.3 77.3 - - - +
124A ALA* 1.3 57.7 + - - +
126A ARG* 3.1 4.1 + - + +
127A ILE* 2.9 50.2 + - + +
109E LEU* 4.0 33.0 - - + +
110E CYS* 4.9 6.1 - - - -
113E HIS* 3.4 39.0 - - + +
126E LEU* 5.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 4.5 5.2 - - + -
103A ASP* 4.0 23.6 - - + -
104A THR* 4.0 10.8 - - + -
107A CYS* 3.9 17.0 - - - -
120A ASP 2.9 16.9 + - - +
121A ILE 4.0 2.9 - - - +
123A LEU* 1.3 76.9 - - - +
125A ARG* 1.3 58.6 + - - +
127A ILE* 4.0 1.0 - - - -
128A ARG* 3.0 36.4 + - - +
130E ILE* 4.0 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 2.8 29.1 + - - -
100A LEU* 3.8 16.6 - - + -
121A ILE* 2.9 21.7 + - - +
124A ALA* 1.3 78.0 - - - +
126A ARG* 1.3 60.1 + - - +
128A ARG* 3.8 2.9 + - - +
129A GLY 3.3 1.0 + - - -
130A GLU* 2.8 72.0 + - + +
131A ARG* 3.0 48.4 + - + +
57B VAL* 3.7 28.8 - - - +
60B VAL* 3.9 24.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLN 2.9 19.8 + - - +
123A LEU* 3.1 7.2 + - + +
125A ARG* 1.3 76.3 - - - +
127A ILE* 1.3 64.1 + - - +
129A GLY* 3.2 16.3 + - - -
131A ARG* 3.4 57.1 - - + +
106E ASP* 5.3 2.1 - - - +
109E LEU* 3.7 28.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
123A LEU* 2.9 37.1 + - + +
126A ARG* 1.3 77.8 - - - +
128A ARG* 1.3 61.1 + - - +
129A GLY* 3.1 1.7 + - - -
106E ASP* 4.5 24.7 - - + +
109E LEU* 5.0 6.3 - - + -
110E CYS* 3.6 31.2 - - - -
127E ALA* 4.0 8.3 - - - +
130E ILE* 3.8 39.3 - - + -
131E ARG* 3.8 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 4.2 6.7 + - - -
99A GLY* 4.5 4.4 - - - -
100A LEU* 3.4 43.9 - - - +
103A ASP* 3.2 27.8 + - - -
124A ALA* 3.0 24.8 + - - +
125A ARG 4.3 0.9 - - - +
126A ARG 3.4 0.2 - - - -
127A ILE* 1.3 75.2 - - - +
129A GLY* 1.3 59.5 + - - +
130A GLU* 3.1 38.8 + - - +
95B ARG* 4.0 23.4 - - - +
130E ILE* 3.7 25.6 + - + +
131E ARG* 5.2 4.0 - - - +
----------------------------------------------------------
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