Contacts of the helix formed by residues 76 - 88 (chain M) in PDB entry 3LUE
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 GLY 76 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73M PHE 3.0 18.2 + - - -
74M ARG 3.2 1.4 + - - -
75M ASN* 1.3 77.1 + - - +
77M LEU* 1.3 58.0 + - - +
78M LYS 3.6 1.6 - - - -
79M LEU* 3.3 11.3 + - - +
80M MET* 2.9 37.0 + - - +
106M ASN* 4.6 1.8 - - - -
107M VAL* 3.7 21.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75M ASN* 2.9 41.0 + - + +
76M GLY* 1.3 71.6 - - - +
78M LYS* 1.3 62.2 + - + +
79M LEU 3.1 0.2 - - - -
80M MET* 3.1 7.7 + - - +
81M LEU* 2.9 27.2 + - - +
94M PRO* 3.8 32.1 - - + -
95M ASP 5.1 1.8 - - - +
106M ASN* 4.1 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 78 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M LEU* 3.6 9.7 - - + +
64M THR* 2.8 31.3 + - + +
65M GLN 2.8 29.5 + - - +
66M ILE* 3.9 13.6 - - + +
72M ASP* 4.1 14.9 + - + +
73M PHE* 3.6 17.4 - - + -
75M ASN* 4.3 2.3 + - - +
77M LEU* 1.3 78.0 - - + +
79M LEU* 1.3 59.8 + - - +
81M LEU* 3.6 12.3 - - + -
82M LEU* 2.8 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73M PHE* 3.6 24.3 - - + +
76M GLY* 3.3 15.9 + - - +
77M LEU 3.1 0.4 - - - -
78M LYS* 1.3 78.4 - - - +
80M MET* 1.3 62.2 + - - +
82M LEU* 3.4 5.4 + - + +
83M LEU* 3.2 25.3 + - + +
107M VAL* 4.7 8.5 - - + +
110M ALA* 3.7 23.8 - - + -
114M ILE* 5.6 0.2 - - + -
129M ILE* 4.5 11.9 - - + -
140M MET* 3.5 42.4 - - + -
141M ILE* 4.3 9.6 - - + -
144M ILE* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 80 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76M GLY 2.9 26.3 + - - +
77M LEU* 3.5 5.4 - - - +
79M LEU* 1.3 75.4 - - - +
81M LEU* 1.3 65.0 + - - +
83M LEU* 3.2 5.1 + - - +
84M GLU* 3.1 31.9 + - - +
91M LEU* 3.9 25.1 - - + +
92M PRO 3.1 27.8 - - - +
94M PRO* 4.3 19.3 - - + -
106M ASN* 3.5 36.1 - - - +
109M LYS* 3.8 24.2 - - + -
110M ALA* 4.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M LEU* 4.3 4.3 - - + -
62M ALA* 3.9 25.8 - - + +
64M THR* 3.9 29.6 - - + -
77M LEU 2.9 16.4 + - - +
78M LYS* 3.6 13.0 - - + +
79M LEU 3.3 0.2 - - - -
80M MET* 1.3 77.0 - - - +
82M LEU* 1.3 61.1 + - - +
84M GLU* 3.3 19.6 + - + +
85M VAL* 3.0 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M TRP* 4.1 15.7 - - + -
55M CYS* 3.7 38.8 - - + +
58M HIS* 3.8 28.0 - - + -
59M LEU* 3.6 12.7 - - + +
73M PHE* 4.3 9.4 - - + -
78M LYS 2.8 22.2 + - - +
79M LEU* 3.5 9.6 - - + +
81M LEU* 1.3 74.4 - - - +
83M LEU* 1.3 58.7 + - + +
85M VAL* 3.3 3.7 + - + +
86M ILE* 3.1 42.2 + - + +
141M ILE* 4.3 10.1 - - + -
144M ILE* 4.9 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79M LEU* 3.2 15.3 + - + +
80M MET 3.2 7.1 + - - +
82M LEU* 1.3 75.3 - - + +
84M GLU* 1.3 62.7 + - - +
86M ILE* 3.7 4.0 - - + +
87M SER* 2.8 31.5 + - - -
91M LEU* 4.0 15.3 - - + -
110M ALA* 3.6 40.4 - - + +
113M PHE* 4.1 10.9 - - + -
114M ILE* 4.0 12.8 - - + -
144M ILE* 3.8 30.1 - - + -
148M PHE* 3.9 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80M MET* 3.1 19.3 + - - +
81M LEU* 3.8 23.4 - - + +
83M LEU* 1.3 75.6 - - - +
85M VAL* 1.3 60.1 + - + +
87M SER* 4.0 1.3 - - - -
88M GLY* 2.8 30.7 + - - -
89M GLU 3.3 21.1 + - - +
90M ARG* 3.4 38.0 + - - +
91M LEU* 3.0 37.5 + - + +
92M PRO 5.0 0.7 - - - +
93M ARG* 3.5 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M HIS* 3.6 43.1 - - + +
59M LEU* 5.0 1.1 - - - -
61M LYS* 4.6 14.1 - - + +
62M ALA* 3.9 28.7 - - + +
81M LEU* 3.0 20.1 + - + +
82M LEU* 3.5 10.5 - - - +
83M LEU 3.3 0.2 - - - -
84M GLU* 1.3 80.7 - - - +
86M ILE* 1.3 63.6 + - + +
88M GLY* 3.7 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M TRP* 4.1 9.4 - - + -
58M HIS* 3.5 46.4 - - + +
82M LEU* 3.1 24.0 + - + +
83M LEU* 3.7 11.0 - - + +
85M VAL* 1.3 75.9 - - - +
87M SER* 1.3 62.3 + - - +
144M ILE* 3.5 26.2 - - + -
148M PHE* 3.4 43.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83M LEU 2.8 22.8 + - - -
84M GLU* 3.8 1.0 + - - -
86M ILE* 1.3 77.7 - - - +
88M GLY* 1.3 60.1 + - - +
89M GLU* 3.0 36.4 + - - +
113M PHE* 3.7 11.6 - - - -
148M PHE* 3.8 27.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 88 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84M GLU 2.8 14.3 + - - -
85M VAL 3.7 5.0 + - - -
86M ILE 3.5 1.6 - - - -
87M SER* 1.3 78.3 - - - +
89M GLU* 1.3 62.2 + - - +
90M ARG* 5.2 3.3 - - - -
----------------------------------------------------------
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