Contacts of the helix formed by residues 120 - 131 (chain A) in PDB entry 6DZT
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 120 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ARG* 3.6 37.5 - - - +
118A THR* 4.0 23.1 - - + -
119A ILE* 1.3 75.1 - - - +
121A PRO* 1.3 69.6 - - + +
122A LYS* 3.2 18.8 - - + -
123A ASP* 2.6 32.5 + - - +
124A ILE* 3.1 10.0 + - - +
47B SER* 4.1 11.7 - - - +
50B ILE* 3.5 8.5 - - - +
71I A 4.0 13.7 - - - -
72I C 3.9 22.7 - - - +
81J C 6.0 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A MET* 1.3 88.9 - - + +
122A LYS* 1.3 55.8 + - - +
124A ILE* 3.3 2.6 + - + +
125A GLN* 2.9 39.4 + - - +
47B SER* 4.7 3.4 - - - +
49B LEU* 3.6 47.1 - - + +
50B ILE* 3.9 14.1 - - + -
53B GLU* 4.0 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ARG* 3.4 26.9 - - - +
120A MET* 4.1 22.1 - - + -
121A PRO* 1.3 76.3 - - - +
123A ASP* 1.3 62.9 + - - +
125A GLN* 3.8 12.7 - - - +
126A LEU* 2.9 29.1 + - - +
113E HIS* 3.5 29.3 + - + +
115E LYS* 5.2 9.4 - - - +
72I C 4.5 10.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR* 3.7 24.4 + - + +
110A CYS* 3.7 9.9 - - + +
111A ALA* 4.0 7.4 - - - -
116A ARG* 2.7 43.3 + - - -
119A ILE* 3.4 3.1 - - - -
120A MET* 2.6 31.6 + - - +
122A LYS* 1.3 74.6 - - - +
124A ILE* 1.3 64.7 + - - +
126A LEU* 3.4 1.6 + - - +
127A ALA* 3.0 25.3 + - - +
113E HIS* 2.7 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 4.5 11.4 - - + -
104A PHE* 4.2 11.9 - - + -
107A THR* 3.6 26.0 - - + +
120A MET 3.1 9.3 + - - +
121A PRO 3.3 6.9 + - - +
123A ASP* 1.3 75.6 - - - +
125A GLN* 1.3 58.3 + - - +
127A ALA* 3.4 1.9 + - - +
128A ARG* 2.9 34.4 + - - +
50B ILE* 3.7 20.6 - - + -
53B GLU* 3.7 30.7 - - + +
54B THR* 3.7 22.2 - - - +
57B VAL* 4.2 15.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
121A PRO* 2.9 28.5 + - - +
122A LYS* 3.9 10.6 - - - +
124A ILE* 1.3 77.7 - - - +
126A LEU* 1.3 55.7 + - - +
128A ARG* 4.5 0.2 - - - -
129A ARG* 3.0 25.1 + - - +
134A ARG* 3.4 51.2 + - - +
53B GLU* 3.2 33.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
110A CYS* 3.8 20.6 - - - -
122A LYS 2.9 19.3 + - - +
123A ASP 3.8 3.8 - - - +
124A ILE 3.3 0.2 - - - -
125A GLN* 1.3 74.5 - - - +
127A ALA* 1.3 64.8 + - - +
129A ARG* 3.4 7.0 + - + +
130A ILE* 3.0 44.6 + - + +
109E LEU* 3.7 40.6 - - + +
110E CYS* 4.4 11.2 - - - -
113E HIS* 3.6 35.7 - - + +
126E LEU* 4.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 4.3 6.7 - - + -
106A ASP* 3.9 27.6 - - + -
107A THR* 4.0 13.5 - - - +
110A CYS* 4.0 8.9 - - - -
123A ASP 3.0 17.4 + - - +
124A ILE 3.8 3.6 - - - +
126A LEU* 1.3 76.7 - - - +
128A ARG* 1.3 57.5 + - - +
130A ILE 3.4 0.2 + - - -
131A ARG* 3.0 35.9 + - - +
130E ILE* 3.6 9.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
99A TYR* 3.8 7.5 + - - -
103A LEU* 3.7 17.5 - - + -
124A ILE* 2.9 23.0 + - - +
127A ALA* 1.3 77.7 - - - +
129A ARG* 1.3 57.0 + - - +
131A ARG* 3.7 3.0 + - - -
132A GLY 3.2 5.7 + - - -
133A GLU* 2.8 75.2 + - - +
134A ARG* 3.3 30.0 + - + +
53B GLU* 5.2 2.9 + - - -
56B GLY 5.7 0.4 - - - -
57B VAL* 3.7 41.4 + - - +
60B VAL* 3.9 27.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLN 3.0 18.4 + - - +
126A LEU* 3.8 10.5 - - - +
128A ARG* 1.3 75.3 - - - +
130A ILE* 1.3 65.5 + - - +
132A GLY* 3.8 8.4 + - - +
134A ARG* 3.7 45.3 + - + +
110C ASN* 5.6 4.6 - - - +
112C GLN* 4.9 9.1 + - - +
106E ASP* 4.4 6.4 - - - +
109E LEU* 3.5 45.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 3.0 37.3 + - + +
127A ALA* 5.2 0.2 - - - -
129A ARG* 1.3 76.6 - - - +
131A ARG* 1.3 65.0 + - - +
132A GLY* 3.2 1.5 + - - -
106E ASP* 4.2 27.9 - - + +
109E LEU* 4.6 8.7 - - + -
110E CYS* 3.6 30.5 - - - -
127E ALA* 3.7 12.1 - - - +
130E ILE* 3.8 24.9 - - + -
131E ARG* 3.5 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A TYR* 4.0 10.5 + - - -
102A GLY* 3.3 13.9 + - - -
103A LEU* 3.7 29.8 - - - +
106A ASP* 2.4 36.9 + - - -
127A ALA 3.0 25.9 + - - +
128A ARG* 4.0 5.2 - - - +
130A ILE* 1.3 76.2 - - - +
132A GLY* 1.3 57.7 + - - +
133A GLU* 3.5 25.1 + - - +
95B ARG* 3.6 25.1 - - - +
130E ILE* 3.5 24.6 + - + +
131E ARG* 5.2 3.8 - - - +
----------------------------------------------------------
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