Contacts of the helix formed by residues 78 - 92 (chain B) 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 ASN 78 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 4.4 15.8 - - - +
69B TYR* 2.7 43.7 + - - +
70B PRO* 3.6 14.3 + - + +
76B VAL* 3.5 10.2 - - - +
77B THR* 1.3 84.8 + - - +
79B TRP* 1.3 60.4 + - - +
80B ASP* 3.9 3.8 + - - +
81B ASP* 3.0 8.5 + - - +
82B MET* 3.1 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 3.7 42.2 + - + -
77B THR 4.1 5.1 + - - -
78B ASN* 1.3 74.5 - - - +
80B ASP* 1.3 65.1 + - - +
82B MET* 3.6 5.0 + - + +
83B GLU* 3.0 29.5 + - - +
86B TRP* 4.1 20.6 - + - -
115B ASN* 4.1 34.4 - - + +
118B LYS* 3.4 46.1 - - + +
119B MET* 4.2 13.0 - - + -
122B ILE* 3.5 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU 4.4 10.6 - - - +
68B LYS* 5.2 0.9 - - - -
69B TYR* 1.3 66.7 - - + +
78B ASN* 3.6 4.0 + - - +
79B TRP* 1.3 77.3 - - - +
81B ASP* 1.3 48.0 - - - +
83B GLU* 4.0 13.2 - - + +
84B LYS* 5.0 0.2 - - - -
118B LYS* 5.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 1.7 52.2 - - + +
67B LEU* 3.2 30.5 - - - +
69B TYR* 0.4 442.1 + - + +
78B ASN* 2.9 9.3 + - - +
80B ASP* 1.3 65.3 - - - +
82B MET* 1.3 51.9 + - - +
84B LYS* 3.4 0.5 - - - +
85B ILE* 3.1 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASN* 3.2 27.1 - - - +
17B CYS* 4.7 0.2 - - - -
69B TYR* 2.3 2.2 - - - -
70B PRO* 3.8 6.8 - - + +
71B ILE* 3.4 38.6 - - + -
76B VAL* 3.5 24.2 - - + -
78B ASN 3.1 20.1 + - - +
79B TRP* 3.9 7.9 - - + +
80B ASP 3.4 0.2 - - - -
81B ASP* 1.3 73.5 - - - +
83B GLU* 1.3 61.7 + - - +
85B ILE* 2.8 43.2 + - + +
86B TRP* 3.1 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B TYR* 2.9 20.5 - - + +
79B TRP 3.0 21.5 + - - +
80B ASP* 3.3 11.0 - - - +
82B MET* 1.3 73.7 - - - +
84B LYS* 1.3 64.3 + - - +
86B TRP* 3.3 9.7 + - - +
87B HIS* 3.1 20.8 + - - +
118B LYS* 4.5 5.9 + - - -
122B ILE* 3.9 37.1 - - + +
126B THR* 3.9 22.0 + - - +
127B PHE* 4.0 6.7 - - + -
120M LYS* 5.4 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 2.7 26.4 - - + +
35B VAL* 2.6 20.4 + - - +
67B LEU 2.9 5.0 - - - -
68B LYS* 0.4 253.8 + - + +
69B TYR* 0.8 212.6 - - + +
81B ASP 3.4 0.2 - - - +
83B GLU* 1.3 65.3 - - - +
85B ILE* 1.3 62.4 + - - +
86B TRP 3.2 0.3 + - - -
87B HIS 3.3 0.5 + - - -
88B HIS* 3.0 19.8 + - - +
120M LYS* 4.6 0.2 - - + -
122M VAL* 3.4 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B CYS* 3.9 16.4 - - - -
31B PHE* 4.0 12.6 - - + -
32B PRO 5.1 2.0 - - - +
33B SER* 4.2 30.3 - - - +
34B ILE* 5.1 11.7 - - + +
69B TYR* 4.8 0.9 - - + -
70B PRO* 3.6 27.1 - - + -
71B ILE* 5.0 0.2 - - + -
81B ASP 3.1 9.8 + - - +
82B MET* 2.8 34.9 + - + +
84B LYS* 1.3 75.7 - - - +
86B TRP* 1.3 61.8 + - + +
88B HIS* 3.2 9.0 + - - +
89B THR* 2.8 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 3.7 22.1 - - + +
12B ASN* 2.9 37.9 + - - -
76B VAL* 5.6 1.3 - - + -
79B TRP* 4.1 17.9 - + - -
82B MET* 3.1 47.4 + - + +
83B GLU* 3.8 6.1 - - - +
85B ILE* 1.3 76.8 - - + +
87B HIS* 1.3 64.6 + - - +
89B THR* 2.8 29.2 + - - -
90B PHE* 3.1 14.9 + + + -
105B LEU* 4.4 11.0 - - + -
119B MET* 4.2 26.5 - - + -
122B ILE* 4.1 20.4 - - + -
123B MET* 3.5 28.5 - - + -
127B PHE* 3.9 12.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B TYR 4.6 2.5 - - - +
83B GLU 3.1 13.1 + - - +
84B LYS* 3.4 10.5 - - - +
86B TRP* 1.3 72.1 - - - +
88B HIS* 1.3 57.4 + - - +
90B PHE* 4.5 0.4 - - - -
91B TYR* 2.9 78.6 + + + +
92B ASN* 5.4 2.7 - - - -
127B PHE* 3.7 18.1 - - + -
118M GLY 5.6 0.7 - - - -
119M VAL* 4.5 8.5 - - + -
120M LYS* 4.0 44.5 + - + +
122M VAL* 4.2 7.0 - - + -
143M THR* 4.2 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 4.2 22.2 - + - +
84B LYS 3.0 12.6 + - - +
85B ILE* 3.3 9.9 - - - +
87B HIS* 1.3 72.2 - - - +
89B THR* 1.3 58.3 + - - +
92B ASN* 3.0 46.8 + - + +
93B GLU* 2.7 63.8 + - - +
122M VAL* 4.3 17.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 3.9 21.6 - - + +
17B CYS* 5.7 0.2 - - - -
19B ALA* 3.7 31.2 - - + -
31B PHE* 3.5 16.9 - - + -
85B ILE* 2.8 17.9 + - - +
86B TRP* 2.8 27.7 + - - -
88B HIS* 1.3 72.8 - - - +
90B PHE* 1.3 57.8 + - + +
93B GLU* 3.3 8.4 + - - +
94B LEU* 2.7 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 3.3 35.2 - - + -
10B VAL* 4.5 17.3 - - + -
86B TRP* 3.1 30.7 + + + -
87B HIS* 4.1 2.2 - - - +
89B THR* 1.3 77.2 - - + +
91B TYR* 1.3 61.7 + + + +
94B LEU* 4.8 0.7 - - + -
95B ARG 2.8 31.4 + - - -
96B VAL* 2.8 22.8 + - + +
98B PRO* 3.6 32.3 - - + -
103B VAL* 4.0 17.3 - - + -
105B LEU* 5.6 0.2 - - + -
123B MET* 4.0 30.5 - - + -
127B PHE* 4.2 18.6 - + + -
142M TRP* 3.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B HIS* 2.9 71.1 + + + +
90B PHE* 1.3 65.1 - - + +
92B ASN* 1.3 64.8 + - - +
96B VAL 4.0 0.7 - - - -
98B PRO* 3.7 25.4 - - + +
99B GLU* 4.8 3.6 + - - -
127B PHE* 4.1 20.8 + + - -
142M TRP* 1.2 86.5 - - + +
143M THR* 4.6 6.3 - - - +
146M LEU* 1.0 129.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B HIS* 5.4 2.3 - - - -
88B HIS* 3.0 44.6 + - + +
91B TYR* 1.3 95.0 + - - +
93B GLU* 1.3 72.2 + - - +
95B ARG* 3.5 17.7 - - - +
43M TRP* 4.6 5.4 - - - -
47M GLN* 4.3 4.2 + - - +
122M VAL* 5.0 5.9 + - - +
124M ILE* 4.2 13.7 - - - +
139M GLY* 2.7 45.4 + - - -
142M TRP* 3.7 0.9 - - - -
143M THR* 3.3 9.8 + - - -
----------------------------------------------------------
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