Contacts of the helix formed by residues 53 - 65 (chain I) in PDB entry 6NMY
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 LEU 53 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I ILE* 4.0 22.4 - - + +
50I GLU* 3.3 29.9 + - + +
51I ASN 2.9 1.8 + - - -
52I ASN* 1.3 83.8 - - + +
54I ARG* 1.3 62.9 + - - +
55I ARG 3.5 2.0 - - - -
56I PRO* 3.3 13.6 - - + +
57I ASN* 3.0 33.5 + - - +
92I PRO* 4.2 17.7 - - + -
93I THR 4.4 1.8 - - - +
94I ARG* 4.0 36.6 - - + +
95I HIS 4.2 4.7 - - - +
96I PRO* 4.0 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 54 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I LEU 3.6 16.2 + - - -
49I MET* 3.8 12.3 + - - +
50I GLU 4.1 5.9 + - - -
51I ASN* 2.9 27.6 + - - +
52I ASN 3.4 1.0 - - - -
53I LEU* 1.3 77.7 - - - +
55I ARG* 1.3 65.7 + - - +
57I ASN* 3.6 0.9 - - - +
58I LEU 3.0 19.4 + - - -
85I LEU* 3.5 20.2 - - + +
86I PRO* 4.3 26.9 - - + +
88I ALA* 6.3 0.4 - - + -
114I TYR* 3.2 60.1 + - - -
117I THR* 2.9 37.0 + - - -
118I LEU* 3.8 17.7 - - - +
120I ASN* 5.6 0.6 - - - +
178M GLN* 4.6 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I ASN 4.9 0.6 + - - -
54I ARG* 1.3 78.7 - - - +
56I PRO* 1.3 68.8 - - + +
58I LEU* 3.4 3.3 + - - +
59I GLU* 3.1 41.7 + - + +
82I LEU* 3.5 37.4 + - + +
85I LEU* 3.6 17.2 + - + +
86I PRO 5.3 4.0 + - - -
87I LEU* 4.3 23.4 - - - +
88I ALA* 5.0 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 56 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I ASN 4.1 7.0 - - - +
53I LEU* 3.3 36.1 - - + +
55I ARG* 1.3 93.0 - - + +
57I ASN* 1.3 60.9 + - - +
59I GLU* 2.9 12.3 + - + +
60I ALA* 2.9 20.1 + - - +
63I ARG* 5.3 0.9 + - - -
92I PRO* 4.8 16.4 - - + -
96I PRO* 4.1 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 57 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I ILE* 3.1 27.6 + - - +
48I LEU* 3.7 16.8 + - - +
53I LEU* 3.0 30.6 + - - +
54I ARG 3.6 3.6 - - - +
56I PRO* 1.3 75.3 - - - +
58I LEU* 1.3 62.6 + - - +
60I ALA* 2.9 15.4 + - - +
61I PHE* 3.1 19.8 + - + -
96I PRO* 3.5 6.6 - - - +
97I ILE* 3.1 42.3 + - + +
114I TYR* 3.8 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54I ARG 3.0 13.1 + - - +
55I ARG 3.6 9.0 - - - +
57I ASN* 1.3 75.2 - - - +
59I GLU* 1.3 72.0 + - - +
61I PHE* 2.9 22.6 + - + +
62I ASN* 2.9 33.3 + - - +
78I LEU* 3.9 35.0 - - + +
81I LEU* 4.2 13.0 - - + +
82I LEU* 4.1 22.0 - - + +
85I LEU* 4.0 27.1 - - + -
114I TYR* 3.9 11.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I ARG* 3.1 32.1 - - + +
56I PRO* 2.9 10.4 + - + +
58I LEU* 1.3 86.7 - - - +
60I ALA* 1.3 60.3 + - - +
62I ASN* 3.7 17.3 + - - +
63I ARG* 3.4 30.1 + - - +
82I LEU* 4.8 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I PRO 2.9 10.9 + - - +
57I ASN* 2.9 10.5 + - - +
59I GLU* 1.3 74.5 - - - +
61I PHE* 1.3 66.4 + - - +
63I ARG* 2.9 37.0 + - - +
64I ALA* 3.1 12.6 + - - +
96I PRO* 5.5 3.1 - - + -
97I ILE* 3.7 34.1 - - + +
99I ILE* 4.1 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 61 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I LEU* 4.1 11.7 - - + -
57I ASN 3.1 28.1 + - - -
58I LEU* 2.9 12.1 + - + +
60I ALA* 1.3 74.6 - - - +
62I ASN* 1.3 58.3 + - - +
63I ARG 2.9 0.7 + - - -
64I ALA 2.9 0.7 + - - -
65I VAL* 2.8 34.4 + - - +
78I LEU* 3.9 19.1 - - + -
97I ILE* 4.6 3.8 - - + -
99I ILE* 3.5 22.9 - - + -
107I PHE* 3.5 25.7 - + + -
110I LYS* 3.8 15.5 - - + -
111I LEU* 3.5 53.4 - - + -
114I TYR* 4.1 21.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 62 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I LEU* 2.9 48.5 + - - +
59I GLU* 3.8 20.4 + - - +
60I ALA 3.3 0.2 - - - -
61I PHE* 1.3 74.4 - - - +
63I ARG* 1.3 57.1 + - - +
65I VAL* 3.5 12.6 - - - +
66I LYS* 3.1 24.6 - - - +
75I GLU* 4.5 1.7 - - - +
78I LEU* 3.4 32.9 + - - +
79I LYS* 3.6 18.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I PRO 5.3 0.8 + - - -
59I GLU* 3.4 12.7 + - - +
60I ALA* 2.9 40.8 + - - +
62I ASN* 1.3 79.1 - - - +
64I ALA* 1.3 60.0 + - - +
66I LYS* 2.9 30.0 + - + +
67I SER* 3.9 3.1 + - - -
96I PRO* 6.1 3.2 - - - +
97I ILE 5.7 0.6 + - - -
101I ASP* 5.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60I ALA 3.1 4.6 + - - +
61I PHE 2.9 5.2 + - - +
63I ARG* 1.3 77.2 - - - +
65I VAL* 1.3 57.9 + - - +
66I LYS 3.0 0.2 - - - -
67I SER* 2.9 31.4 + - - -
68I LEU* 3.7 11.7 - - + +
99I ILE* 4.0 41.5 - - + +
100I LYS 4.8 6.3 - - - +
101I ASP* 4.2 4.7 - - - +
107I PHE* 4.0 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I PHE 2.8 18.4 + - - +
62I ASN* 3.5 19.3 - - - +
64I ALA* 1.3 75.9 - - - +
66I LYS* 1.3 63.9 + - + +
67I SER 3.2 0.6 + - - -
68I LEU* 3.6 24.8 + - + +
71I ALA* 3.9 19.0 - - + +
74I ILE* 4.0 15.7 - - + -
75I GLU* 3.8 51.0 - - + +
78I LEU* 4.4 3.8 - - + -
107I PHE* 4.0 12.2 - - + -
----------------------------------------------------------
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