Contacts of the helix formed by residues 76 - 88 (chain K) 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 K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73K PHE 3.0 17.4 + - - -
74K ARG 3.2 1.6 + - - -
75K ASN* 1.3 77.7 + - - +
77K LEU* 1.3 57.7 + - - +
78K LYS 3.6 1.6 - - - -
79K LEU* 3.4 10.9 - - - +
80K MET* 2.9 38.1 + - - +
106K ASN* 4.6 2.2 - - - -
107K VAL* 3.7 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75K ASN* 2.9 40.8 + - + +
76K GLY* 1.3 70.7 - - - +
78K LYS* 1.3 61.9 + - + +
80K MET* 3.1 7.7 + - - +
81K LEU* 2.9 27.1 + - - +
94K PRO* 3.8 31.6 - - + -
95K ASP 5.1 2.0 - - - +
106K ASN* 4.1 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 78 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59K LEU* 3.6 9.1 - - + +
64K THR* 2.8 30.5 + - + +
65K GLN 2.8 29.2 + - - +
66K ILE* 3.9 13.6 - - + +
72K ASP* 4.1 14.8 + - + +
73K PHE* 3.6 17.9 - - + -
75K ASN* 4.3 2.5 + - - +
77K LEU* 1.3 76.9 - - + +
79K LEU* 1.3 59.5 + - - +
81K LEU* 3.6 11.7 - - + -
82K LEU* 2.8 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73K PHE* 3.6 23.6 - - + +
76K GLY* 3.4 16.3 - - - +
77K LEU 3.1 0.2 - - - -
78K LYS* 1.3 79.0 - - - +
80K MET* 1.3 62.9 + - - +
82K LEU* 3.4 5.8 + - + +
83K LEU* 3.2 24.8 + - + +
107K VAL* 4.7 7.9 - - + -
110K ALA* 3.7 23.3 - - + -
111K LEU* 5.4 0.2 - - + -
129K ILE* 4.5 11.9 - - + -
140K MET* 3.5 44.2 - - + -
141K ILE* 4.3 9.2 - - + -
144K ILE* 3.9 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 80 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76K GLY 2.9 25.8 + - - +
77K LEU* 3.5 5.6 - - - +
79K LEU* 1.3 73.9 - - - +
81K LEU* 1.3 64.9 + - - +
83K LEU* 3.2 4.7 + - - +
84K GLU* 3.1 30.9 + - - +
91K LEU* 4.0 25.6 - - + +
92K PRO 3.1 27.4 - - - +
94K PRO* 4.3 18.4 - - + -
106K ASN* 3.5 36.8 - - - +
109K LYS* 3.8 23.8 - - + -
110K ALA* 4.1 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59K LEU* 4.3 3.6 - - + -
62K ALA* 3.9 26.2 - - + +
64K THR* 3.9 30.1 - - + -
77K LEU 2.9 16.4 + - - +
78K LYS* 3.6 12.8 - - + +
80K MET* 1.3 77.0 - - - +
82K LEU* 1.3 61.7 + - - +
84K GLU* 3.3 19.8 + - + +
85K VAL* 3.0 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54K TRP* 4.1 15.3 - - + -
55K CYS* 3.7 39.3 - - + +
58K HIS* 3.8 27.8 - - + -
59K LEU* 3.6 14.5 - - + +
73K PHE* 4.3 9.4 - - + -
78K LYS 2.8 21.7 + - - +
79K LEU* 3.5 9.4 - - + +
81K LEU* 1.3 74.0 - - - +
83K LEU* 1.3 57.3 + - + +
85K VAL* 3.3 4.1 + - + +
86K ILE* 3.1 42.5 + - + +
141K ILE* 4.3 9.6 - - + -
144K ILE* 4.9 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K LEU* 3.2 15.5 + - + +
80K MET 3.2 6.7 + - - +
82K LEU* 1.3 76.0 - - + +
84K GLU* 1.3 63.6 + - - +
86K ILE* 3.7 3.9 - - + +
87K SER* 2.8 31.1 + - - -
91K LEU* 4.0 15.0 - - + -
110K ALA* 3.6 40.6 - - + +
113K PHE* 4.1 11.0 - - + -
114K ILE* 4.0 13.0 - - + -
144K ILE* 3.8 30.5 - - + -
148K PHE* 3.9 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80K MET* 3.1 19.9 + - - +
81K LEU* 3.8 22.6 - - + +
83K LEU* 1.3 76.7 - - - +
85K VAL* 1.3 58.2 + - + +
87K SER* 4.0 1.1 - - - -
88K GLY* 2.8 30.5 + - - -
89K GLU 3.3 21.6 + - - +
90K ARG* 3.4 36.7 + - - +
91K LEU* 3.0 36.8 + - + +
92K PRO 5.0 0.5 - - - +
93K ARG* 3.5 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58K HIS* 3.6 42.2 - - + +
59K LEU* 5.0 1.6 - - - -
61K LYS* 4.6 14.6 - - + +
62K ALA* 3.9 28.3 - - + +
81K LEU* 3.0 19.5 + - + +
82K LEU* 3.5 9.9 - - - +
83K LEU 3.3 0.2 - - - -
84K GLU* 1.3 79.0 - - + +
86K ILE* 1.3 63.7 + - + +
87K SER 3.5 0.2 + - - -
88K GLY* 3.7 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54K TRP* 4.1 10.3 - - + -
58K HIS* 3.5 45.8 - - + +
82K LEU* 3.3 22.7 - - + +
83K LEU* 3.7 11.4 - - + +
85K VAL* 1.3 75.9 - - - +
87K SER* 1.3 61.4 + - - +
144K ILE* 3.5 26.0 - - + -
148K PHE* 3.4 44.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83K LEU 2.8 21.6 + - - -
84K GLU* 3.8 1.0 + - - -
86K ILE* 1.3 78.6 - - - +
88K GLY* 1.3 60.9 + - - +
89K GLU* 3.0 37.6 + - - +
113K PHE* 3.7 11.7 - - - -
148K PHE* 3.8 27.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 88 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84K GLU 2.8 13.5 + - - -
85K VAL 3.7 4.8 + - - -
86K ILE 3.5 1.8 - - - -
87K SER* 1.3 79.5 - - - +
89K GLU* 1.3 61.0 + - - +
90K 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