Contacts of the helix formed by residues 67 - 84 (chain B) in PDB entry 3NIE
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 67 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG 4.4 3.4 + - - +
64B MET 3.6 4.2 - - - +
65B PHE 4.1 1.6 - - - -
66B GLU* 1.3 79.3 - - - +
68B LEU* 1.3 63.7 + - - +
69B ILE* 3.0 21.5 + - - +
70B ASP* 3.4 22.4 + - + +
71B CYS* 2.9 24.9 + - - +
214B THR* 2.6 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 3.6 22.2 - - + +
66B GLU 5.5 0.9 - - - +
67B ASP* 1.3 73.6 + - - +
69B ILE* 1.3 61.3 + - + +
71B CYS* 3.5 8.6 - - + +
72B LYS* 3.1 26.3 + - - +
396B LEU 4.8 10.1 - - - +
397B SER* 5.4 1.1 - - - -
398B GLU* 4.2 34.8 - - + +
401B LEU* 4.0 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ASP* 3.0 11.9 + - - +
68B LEU* 1.3 75.9 - - + +
70B ASP* 1.3 68.2 + - - +
72B LYS* 3.4 7.0 + - + +
73B ARG* 3.2 19.1 + - - +
76B ARG* 5.3 2.3 + - - +
395B VAL* 6.2 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TYR* 3.3 30.4 + - + -
63B ARG 6.1 0.7 - - - +
64B MET* 4.8 2.7 - - - +
67B ASP* 3.4 20.5 + - + +
69B ILE* 1.3 80.8 - - - +
71B CYS* 1.3 62.1 + - - +
73B ARG* 3.0 24.4 - - - +
74B ILE* 3.2 16.0 + - + +
214B THR* 2.9 18.4 + - - +
216B HIS* 2.8 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B MET* 3.1 26.2 + - - +
65B PHE* 3.4 34.5 - - - -
67B ASP 2.9 14.0 + - - +
68B LEU* 3.5 14.4 - - + +
69B ILE 3.2 0.2 - - - -
70B ASP* 1.3 78.0 - - - +
72B LYS* 1.3 61.2 + - - +
74B ILE* 3.3 6.6 + - - +
75B LEU 3.2 15.9 + - - -
401B LEU* 3.6 15.0 - - + -
405B PHE* 3.4 26.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU 3.1 14.0 + - - +
69B ILE* 3.8 6.3 - - - +
70B ASP 3.3 0.2 - - - -
71B CYS* 1.3 76.1 - - - +
73B ARG* 1.3 60.0 + - - +
75B LEU* 3.2 3.9 + - + +
76B ARG* 2.9 48.2 + - - +
390B PHE* 4.7 16.6 - - + -
392B ASP 5.9 2.5 - - - +
394B MET 5.9 2.7 - - - +
396B LEU* 5.3 5.2 - - + -
401B LEU* 4.2 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TYR* 3.2 60.3 - - - +
61B VAL* 6.4 0.4 - - - +
69B ILE 3.2 12.2 + - - +
70B ASP* 3.0 15.7 + - - +
72B LYS* 1.3 76.5 - - - +
74B ILE* 1.3 62.1 + - - +
76B ARG* 3.1 10.3 + - - +
77B GLU* 2.9 41.6 + - - -
156B ASP* 5.5 2.2 + - - -
174B ASP* 3.9 7.3 + - - -
176B GLY* 3.4 43.4 - - - +
177B LEU* 4.9 17.7 - - + +
430B ANP 3.3 38.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TYR* 5.5 6.7 - - + -
61B VAL* 2.9 44.0 - - + -
64B MET* 4.0 20.0 - - + -
70B ASP* 3.2 16.4 + - + +
71B CYS 3.3 6.0 + - - +
73B ARG* 1.3 94.9 - - - +
75B LEU* 1.3 60.5 + - - +
77B GLU* 3.5 9.7 + - + +
78B ILE* 3.2 23.0 + - - +
107B LEU* 4.3 13.9 - - + -
109B ILE* 4.4 13.9 - - + -
405B PHE* 3.9 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B CYS 3.2 7.3 + - - +
72B LYS* 3.2 11.2 + - + +
73B ARG 3.1 0.6 - - - -
74B ILE* 1.3 76.5 - - - +
76B ARG* 1.3 60.8 + - - +
78B ILE* 3.7 3.8 - - + +
79B THR* 2.8 44.6 + - + +
390B PHE* 3.7 25.1 - - + -
396B LEU* 4.6 0.9 - - + -
401B LEU* 4.0 21.8 - - + +
404B ILE* 3.5 44.0 - - + +
405B PHE* 3.7 41.0 - - + +
408B GLU* 4.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ILE* 5.3 2.4 + - - +
72B LYS* 2.9 30.0 + - - +
73B ARG* 3.1 20.5 + - - +
75B LEU* 1.3 74.5 - - - +
77B GLU* 1.3 66.4 + - - +
79B THR* 3.7 4.9 - - - -
80B ILE* 3.2 45.3 + - + +
175B PHE 4.0 6.1 - - - +
176B GLY 2.9 24.4 + - - +
177B LEU* 4.4 11.9 - - - +
178B ALA 3.6 16.8 + - - +
179B ARG* 3.7 25.4 - - - +
388B LEU* 4.6 9.4 - - + -
390B PHE* 4.5 21.2 - - + -
392B ASP* 5.3 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LYS* 2.6 41.9 + - - +
61B VAL* 6.0 0.7 - - - +
73B ARG* 2.9 31.1 + - - +
74B ILE* 3.7 13.8 - - - +
75B LEU 3.3 0.2 - - - -
76B ARG* 1.3 79.6 - - - +
78B ILE* 1.3 66.0 + - + +
80B ILE* 4.1 0.9 - - - +
81B LEU* 3.2 39.1 + - + +
109B ILE* 4.5 11.3 - - - +
111B LEU* 5.0 3.8 - - - +
174B ASP* 4.3 12.1 + - - +
175B PHE* 4.0 12.0 - - - +
176B GLY* 3.9 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 3.2 13.6 + - + +
75B LEU* 3.7 7.2 - - + +
77B GLU* 1.3 79.1 - - + +
79B THR* 1.3 72.8 + - + +
81B LEU* 4.4 4.9 - - + -
82B ASN* 3.0 24.6 + - - +
92B LEU* 3.3 9.4 - - + +
95B LEU* 4.2 27.1 - - + -
107B LEU* 3.9 10.8 - - + -
109B ILE* 3.4 41.3 - - + -
405B PHE* 3.8 31.6 - - + +
408B GLU* 4.2 10.0 - - + +
409B ILE* 5.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 2.8 43.9 + - + +
76B ARG* 3.6 8.8 + - - -
78B ILE* 1.3 77.2 - - + +
80B ILE* 1.3 66.0 + - - +
82B ASN 3.2 5.9 + - - -
83B ARG* 2.7 38.6 + - - +
388B LEU* 3.9 8.1 - - - +
389B PRO* 4.1 19.1 - - + -
390B PHE* 3.9 9.0 - - + -
408B GLU* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ARG* 3.2 28.7 + - + +
79B THR* 1.3 76.8 + - - +
81B LEU* 1.3 70.9 + - - +
82B ASN 2.9 0.7 - - - -
83B ARG* 2.5 19.4 + - - -
84B LEU* 3.2 27.6 + - + -
152B ILE* 4.4 21.1 - - + -
175B PHE* 3.7 28.9 - - + +
178B ALA* 3.5 32.1 - - + -
386B ILE* 4.9 3.8 - - + -
388B LEU* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLU* 3.2 36.6 + - + +
78B ILE* 3.9 5.2 - - - +
80B ILE* 1.3 81.7 - - - +
82B ASN* 1.3 60.1 + - - +
83B ARG 3.2 0.7 + - - -
84B LEU* 3.3 21.8 + - - +
89B ILE* 4.3 1.6 - - + -
90B ILE* 3.1 41.5 - - + +
91B ARG* 5.6 0.5 - - - -
92B LEU* 4.1 22.6 + - + +
109B ILE* 5.2 1.8 - - + -
111B LEU* 3.3 31.6 - - + -
173B CYS* 4.9 0.7 - - + -
174B ASP 5.5 2.9 - - - +
175B PHE* 3.8 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ILE 3.0 20.9 + - - +
79B THR 3.2 8.5 - - - +
80B ILE 2.7 4.6 + - - -
81B LEU* 1.3 73.9 - - - +
83B ARG* 1.3 63.3 + - - +
84B LEU 3.6 2.1 + - - +
85B LYS* 5.6 5.5 + - - +
92B LEU* 3.6 14.2 - - + +
95B LEU* 5.0 0.6 - - - +
408B GLU* 2.7 25.9 + - - +
411B SER* 3.4 23.7 + - - -
412B PHE* 3.6 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B THR* 2.7 39.9 + - - +
80B ILE 2.5 13.7 + - - +
82B ASN* 1.3 81.6 - - - +
84B LEU* 1.3 57.5 + - - +
85B LYS* 4.3 3.2 + - - +
383B THR* 5.4 0.2 + - - -
386B ILE* 2.9 38.8 - - + +
387B ILE 3.5 28.7 + - - +
388B LEU* 4.8 4.9 - - - -
389B PRO* 3.5 26.8 - - - +
408B GLU* 2.6 41.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 3.2 26.8 + - + +
81B LEU 3.3 13.2 + - - +
82B ASN 4.9 0.9 - - - -
83B ARG* 1.3 76.5 + - - +
85B LYS* 1.3 70.9 + - - +
86B SER 4.1 0.9 - - - -
89B ILE* 3.8 24.7 - - + -
90B ILE 5.8 0.2 - - - +
91B ARG* 5.6 5.9 - - - +
146B PHE* 4.0 12.3 - - + -
147B ILE* 5.1 4.7 - - + -
150B SER* 3.6 28.5 - - - +
152B ILE* 5.0 5.6 - - + -
175B PHE* 3.8 33.0 - - + -
383B THR* 5.8 0.2 - - - -
386B ILE* 3.7 21.8 - - + -
----------------------------------------------------------
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