Contacts of the helix formed by residues 69 - 86 (chain I) in PDB entry 6NRB
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 HIS 69 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I MET* 3.9 27.6 - - + +
10I ASP* 4.7 0.2 + - - -
17I ILE* 5.2 0.2 - - - +
20I GLN* 3.7 37.8 + - + +
21I ASN* 3.5 18.2 + - - +
24I ALA* 3.5 22.8 - - + +
67I VAL* 3.4 1.3 - - - +
68I GLU* 1.3 88.7 + - + +
70I PRO* 1.3 58.6 - - - +
72I ALA* 3.5 18.4 - - + +
73I LYS* 2.6 36.5 + - - +
14K THR* 4.0 24.1 + - - +
60L MET* 4.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 70 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I ASP* 3.0 30.7 - - - +
21I ASN* 3.1 25.4 - - - +
68I GLU 3.9 0.2 - - - -
69I HIS* 1.3 82.7 - - - +
71I ALA* 1.3 56.2 + - - +
73I LYS* 3.2 17.8 + - + +
74I VAL* 2.9 32.7 + - - +
524I ILE* 3.5 21.3 - - + -
58L ASP* 3.1 33.4 - - + +
60L MET* 4.1 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ASN* 3.4 38.6 - - + +
25I ALA* 4.2 4.0 - - + +
69I HIS 3.3 0.4 - - - -
70I PRO* 1.3 78.2 - - - +
72I ALA* 1.3 64.4 + - - +
74I VAL* 3.2 22.5 - - - +
75I LEU* 3.3 13.3 + - - +
101I LEU* 3.6 27.8 - - + +
524I ILE* 3.4 8.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ASN 4.9 1.4 + - - -
24I ALA* 4.6 1.8 - - + -
25I ALA 5.0 1.5 - - - +
28I ILE* 3.5 32.5 - - + +
67I VAL* 3.3 30.7 - - + +
69I HIS* 3.3 30.1 + - + +
70I PRO 3.3 0.2 - - - -
71I ALA* 1.3 75.1 - - - +
73I LYS* 1.3 64.6 + - - +
75I LEU* 3.8 3.6 - - - +
76I CYS* 3.4 14.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67I VAL* 3.6 18.0 - - + +
69I HIS 2.6 20.2 + - - +
70I PRO* 3.2 19.9 - - - +
72I ALA* 1.3 73.7 - - - +
74I VAL* 1.3 85.3 + - - +
75I LEU 3.2 1.2 + - - -
76I CYS* 3.4 10.6 + - - +
77I GLU* 3.5 29.3 + - - +
523I THR* 5.6 2.0 - - - +
58L ASP* 4.5 12.5 + - - -
60L MET* 3.9 15.7 - - + -
70L ILE* 3.7 34.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I PRO 2.9 19.6 + - - +
71I ALA* 3.2 23.1 - - - +
73I LYS* 1.3 94.0 - - - +
75I LEU* 1.3 61.1 + - - +
77I GLU* 4.0 6.9 + - - +
78I LEU* 3.0 37.0 + - + +
101I LEU* 3.9 16.6 - - + -
520I ALA* 3.9 19.5 - - + +
523I THR* 4.2 25.4 - - + -
524I ILE* 4.9 9.6 - - + -
58L ASP* 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I ALA* 3.7 12.3 - - + +
28I ILE* 3.5 29.6 - - + -
29I ALA* 3.6 20.2 - - + +
62I LEU* 3.8 2.2 - - + +
71I ALA 3.3 17.0 + - - +
72I ALA 4.0 4.9 - - - +
73I LYS 3.1 1.4 - - - -
74I VAL* 1.3 78.5 - - + +
76I CYS* 1.3 64.9 + - - +
78I LEU* 3.3 4.8 + - + -
79I ALA* 3.0 22.0 + - - +
94I VAL* 3.5 41.5 - - + +
97I ALA* 3.6 21.8 - - + -
98I ALA 4.8 2.5 - - - +
101I LEU* 5.9 1.6 - - + -
520I ALA* 5.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 76 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I ILE* 4.5 2.9 - - - -
62I LEU* 3.5 49.6 - - + +
65I LEU* 4.6 2.9 - - - -
67I VAL* 3.4 40.8 - - + -
72I ALA 3.4 6.1 + - - +
73I LYS 3.4 4.4 + - - +
75I LEU* 1.3 79.0 - - - +
77I GLU* 1.3 59.3 + - + +
79I ALA* 3.3 3.3 + - - +
80I ASP* 2.8 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I LYS* 3.5 27.9 + - + +
74I VAL* 4.4 6.6 - - - +
75I LEU 3.4 0.4 - - - -
76I CYS* 1.3 77.6 - - + +
78I LEU* 1.3 57.3 + - + +
80I ASP* 4.0 8.7 - - - +
81I LEU* 2.2 48.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74I VAL* 3.0 32.2 + - + +
75I LEU* 3.7 5.8 - - + +
76I CYS 3.2 0.2 - - - -
77I GLU* 1.3 78.6 - - + +
79I ALA* 1.3 64.3 + - - +
81I LEU* 5.7 0.9 - - + -
82I GLN* 3.1 28.4 + - - +
93I VAL* 3.4 18.1 - - + +
97I ALA* 4.2 2.2 - - + -
516I PHE* 3.0 42.6 - - + +
519I GLU* 3.4 31.2 - - + +
520I ALA* 3.3 33.0 - - + +
523I THR* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I GLY 3.8 15.5 - - - +
59I ALA* 3.2 10.0 - - - +
62I LEU* 3.8 6.7 - - + -
75I LEU 3.0 11.0 + - - +
76I CYS 3.5 7.6 - - - +
78I LEU* 1.3 75.5 - - - +
80I ASP* 1.3 58.4 + - - +
83I ASP* 3.1 26.0 + - - +
90I THR* 3.3 28.4 - - - +
93I VAL* 3.7 6.1 - - - +
94I VAL* 3.7 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 80 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I ALA* 3.0 30.2 - - - +
62I LEU* 4.4 0.9 - - - +
63I LYS* 3.2 42.9 + - - +
76I CYS* 2.8 26.9 + - - +
77I GLU* 3.5 8.5 + - - +
79I ALA* 1.3 77.0 - - - +
81I LEU* 1.3 55.0 + - - +
83I ASP* 3.1 7.3 + - - +
84I LYS* 2.5 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I GLU* 2.2 37.2 + - + +
78I LEU* 5.7 0.9 - - + -
80I ASP* 1.3 68.6 - - - +
82I GLN* 1.3 51.5 + - - +
84I LYS* 3.2 38.3 + - + +
85I GLU* 2.6 43.7 + - - +
516I PHE* 3.4 25.1 - - + -
519I GLU* 4.0 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 82 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I LEU 3.1 21.1 + - - +
81I LEU* 1.3 73.0 - - - +
83I ASP* 1.3 60.8 + - - +
85I GLU* 3.4 13.5 - - - +
86I VAL* 2.8 27.9 + - - +
87I GLY 3.2 2.6 + - - -
88I ASP 2.8 26.8 + - - +
89I GLY* 3.5 15.5 - - - +
93I VAL* 4.5 1.3 - - + -
509I VAL 3.6 10.9 + - - -
512I LYS* 3.1 10.1 - - - +
513I SER* 3.0 31.0 + - - +
516I PHE* 3.0 40.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 83 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I ASP* 4.3 3.6 - - - +
59I ALA* 3.2 17.9 - - + +
63I LYS* 4.0 15.1 + - - +
79I ALA 3.1 19.5 + - - +
80I ASP* 3.1 8.5 - - - +
82I GLN* 1.3 76.8 - - - +
84I LYS* 1.3 62.8 + - - +
86I VAL 3.1 6.4 - - - +
87I GLY* 3.0 31.3 + - - +
90I THR* 3.4 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I ASP 2.5 17.3 + - - +
81I LEU* 3.2 36.3 + - + +
83I ASP* 1.3 72.4 - - - +
85I GLU* 1.3 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I LEU* 2.6 37.4 + - - +
82I GLN* 3.2 19.1 - - - +
83I ASP 3.1 0.2 - - - -
84I LYS* 1.3 79.9 + - - +
86I VAL* 1.3 64.4 + - - +
512I LYS* 2.9 36.3 + - + +
515I LYS* 6.1 2.7 - - - -
516I PHE* 3.4 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I GLN* 2.8 13.7 + - - +
83I ASP* 3.1 9.4 - - - +
85I GLU* 1.3 80.2 - - - +
87I GLY* 1.3 55.9 + - - +
88I ASP* 3.3 23.8 - - - +
401I ARG* 6.4 0.9 - - - -
508I ILE* 4.8 3.4 - - + -
509I VAL* 3.5 35.2 - - + -
512I LYS* 3.6 28.7 - - + -
----------------------------------------------------------
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