Contacts of the helix formed by residues 63 - 76 (chain B) in PDB entry 4LGD
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 63 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLU 3.1 8.3 + - - +
62B SER* 1.3 76.1 - - - +
64B LEU* 1.3 65.8 + - - +
65B GLN* 3.3 3.6 - - + +
66B GLU* 3.5 21.4 + - + +
67B ILE* 3.7 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B VAL* 4.9 2.0 - - + -
59B PRO 4.5 4.5 - - - +
60B VAL* 3.3 55.4 + - + +
62B SER 3.3 2.1 + - - +
63B ASP* 1.3 69.5 - - - +
65B GLN* 1.3 57.0 + - - +
66B GLU 3.0 2.5 - - - -
67B ILE* 2.8 15.2 + - + +
68B ILE* 2.7 54.5 + - + +
95B LEU* 4.0 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ASP* 3.3 2.0 - - + -
64B LEU* 1.3 78.9 - - - +
66B GLU* 1.3 63.0 + - - +
68B ILE* 3.9 10.4 - - - +
69B LYS* 3.1 47.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 5.8 9.6 - - + +
63B ASP* 3.5 21.4 + - + +
64B LEU 3.0 0.8 - - - -
65B GLN* 1.3 83.0 + - - +
67B ILE* 1.3 66.0 + - + +
69B LYS* 3.4 26.6 + - - +
70B GLU* 3.2 26.8 + - - +
167B VAL* 4.2 5.7 - - - +
173B ASP* 5.4 4.8 - - - +
177B LYS* 2.6 47.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 3.9 41.5 - - + -
56B LYS* 5.2 5.8 - - - +
58B VAL* 4.3 22.7 - - + -
59B PRO 6.0 1.1 - - - +
62B SER 5.0 3.6 - - - +
63B ASP 4.2 9.6 - - - +
64B LEU* 2.8 17.5 + - + +
66B GLU* 1.3 76.7 - - + +
68B ILE* 1.3 59.4 + - - +
70B GLU* 3.1 20.0 + - - +
71B ILE* 2.8 33.8 + - + +
95B LEU* 4.6 6.7 - - + -
97B ILE* 4.2 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 2.7 56.5 + - + +
65B GLN* 4.1 8.1 - - + +
67B ILE* 1.3 71.4 - - + +
69B LYS* 1.3 64.7 + - - +
71B ILE* 3.4 10.8 + - + +
72B SER* 3.2 24.5 + - - -
95B LEU* 5.0 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLN* 3.1 36.4 + - + +
66B GLU* 3.6 24.6 + - - +
68B ILE* 1.3 77.2 - - - +
70B GLU* 1.3 58.7 + - - +
72B SER* 2.6 21.9 + - - +
73B ILE* 3.4 15.1 - - + +
167B VAL* 4.1 26.3 - - + +
168B ALA 5.4 1.5 + - - +
173B ASP* 4.0 18.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 5.7 5.5 - - - -
66B GLU* 3.2 17.1 + - - +
67B ILE* 3.1 25.9 + - + +
69B LYS* 1.3 74.7 - - - +
71B ILE* 1.3 67.7 + - + +
73B ILE* 2.9 29.2 + - + +
74B MET* 3.4 11.9 + - + +
164B ASP* 4.2 20.0 - - - +
165B PHE* 3.5 27.5 - - + +
167B VAL* 4.7 12.3 - - + +
177B LYS* 5.9 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 2.8 24.5 + - + +
68B ILE* 3.8 12.1 - - + +
70B GLU* 1.3 75.5 - - - +
72B SER* 1.3 67.8 + - - +
74B MET* 3.0 21.8 + - + +
75B GLN* 3.0 14.3 + - - +
85B TYR* 3.6 34.7 - - + +
88B SER* 5.0 2.9 - - - +
95B LEU* 4.3 11.9 - - + -
97B ILE* 3.6 47.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 3.2 12.4 + - - -
69B LYS* 2.6 28.6 + - - +
71B ILE* 1.3 82.1 - - - +
73B ILE* 1.3 60.1 + - - +
75B GLN* 4.0 9.0 - - - +
76B GLN* 3.3 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LYS* 3.4 19.1 - - + +
70B GLU* 2.9 17.5 + - + +
72B SER* 1.3 76.4 + - - +
74B MET* 1.3 66.1 + - + +
76B GLN* 3.2 28.8 + - - +
77B CYS* 3.5 9.0 - - - -
142B LYS* 3.7 14.8 - - - +
165B PHE* 3.4 38.6 - - + -
166B GLY 3.9 20.2 - - - +
167B VAL* 4.1 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLU* 3.8 16.2 - - + +
71B ILE* 3.0 10.3 + - - +
73B ILE* 1.3 76.5 - - - +
75B GLN* 1.3 61.6 + - - +
77B CYS* 3.4 23.0 + - - +
82B VAL* 4.1 8.3 - - + -
83B VAL* 3.5 31.8 - - + +
85B TYR* 4.2 24.2 + - + +
162B LEU 4.1 18.2 - - - +
163B ALA* 4.5 5.8 - - + -
164B ASP* 4.7 3.4 - - - +
165B PHE* 3.8 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 3.0 15.5 + - - +
72B SER* 4.0 8.6 - - - +
73B ILE 3.2 0.2 - - - -
74B MET* 1.3 75.6 - - - +
76B GLN* 1.3 55.8 + - - +
77B CYS 3.2 12.2 + - - +
85B TYR* 3.1 49.1 + - + +
86B TYR 4.7 8.3 + - - -
87B GLY* 4.8 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B SER 3.3 12.6 + - - +
73B ILE* 3.2 25.2 - - - +
75B GLN* 1.3 76.9 - - - +
77B CYS* 1.3 59.1 + - - +
78B ASP* 4.3 0.7 + - - -
136B TYR* 4.5 4.3 + - - -
140B MET* 4.6 12.6 - - - +
142B LYS* 3.7 30.1 + - + +
----------------------------------------------------------
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