Contacts of the helix formed by residues 56 - 67 (chain H) in PDB entry 1SMK
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 ILE 56 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H GLY* 4.4 0.2 - - - -
55H GLY* 1.3 76.7 - - - +
57H GLY* 1.3 67.3 + - - +
59H PRO* 3.0 19.1 - - - +
60H LEU* 3.0 18.2 + - + +
119H PRO* 4.4 25.4 - - + +
160H ILE* 5.2 4.7 - - + -
266H SER* 5.9 0.7 - - - +
267H ALA 4.2 7.4 - - - +
268H THR* 4.1 19.3 - - - +
271H MET* 3.6 38.1 - - + +
272H ALA* 3.9 17.0 - - - +
275H ALA* 5.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 57 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H ILE* 4.5 1.8 - - - +
51H GLY 3.5 23.8 + - - -
52H ALA* 3.1 11.8 - - - +
54H GLY* 3.6 5.1 + - - -
55H GLY 3.5 0.6 - - - -
56H ILE* 1.3 79.5 - - - +
58H GLN* 1.3 56.8 + - - +
60H LEU* 3.5 5.8 - - - +
61H ALA* 2.8 30.5 + - - +
119H PRO* 4.3 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 58 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261G LYS* 4.9 5.4 + - - -
268G THR* 4.2 8.8 + - - -
269G LEU* 3.7 33.3 - - + +
52H ALA 3.1 18.9 + - - +
53H ALA* 2.8 20.8 + - - +
54H GLY 3.2 10.8 + - - +
57H GLY* 1.3 72.1 - - - +
59H PRO* 1.3 75.0 - - + +
61H ALA* 3.0 5.7 + - - +
62H MET 2.9 19.1 + - - -
80H ASN* 5.9 1.0 - - - +
84H VAL* 3.7 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G PRO* 5.0 7.2 - - + -
62G MET* 4.1 15.9 - - + -
269G LEU* 4.1 10.5 - - + -
55H GLY 3.0 26.9 - - - +
56H ILE* 3.0 15.7 - - - +
58H GLN* 1.3 90.3 - - + +
60H LEU* 1.3 59.9 + - - +
62H MET* 3.4 7.2 + - + +
63H LEU* 3.0 27.2 + - - +
268H THR* 4.1 8.7 - - + -
269H LEU* 4.3 9.2 - - + -
272H ALA* 3.5 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H ILE* 3.9 14.4 - - + -
56H ILE* 3.0 21.1 + - + +
57H GLY 3.5 3.6 - - - +
59H PRO* 1.3 78.1 - - - +
61H ALA* 1.3 63.2 + - - +
63H LEU* 3.1 4.9 + - - +
64H MET* 2.9 27.5 + - + +
117H ILE* 3.5 31.0 - - + -
119H PRO* 4.3 17.5 - - + -
160H ILE* 4.1 7.9 - - + -
272H ALA* 3.7 17.7 - - + +
275H ALA* 3.7 17.0 - - + -
276H VAL* 3.2 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H ILE* 3.5 13.4 - - + +
52H ALA* 4.7 2.9 - - + +
57H GLY 2.8 21.9 + - - +
58H GLN* 3.4 5.8 - - - +
60H LEU* 1.3 73.8 - - - +
62H MET* 1.3 63.5 + - - +
64H MET 3.1 1.2 + - - -
65H LYS* 3.0 20.4 + - - +
73H LEU* 3.6 8.1 - - - +
75H LEU* 3.6 25.6 - - + -
84H VAL* 4.9 0.4 - - + -
88H ILE* 3.2 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 62 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G PRO* 4.0 20.4 - - + -
62G MET* 3.5 32.1 - - + -
63G LEU* 3.9 31.9 - - + -
269G LEU* 3.3 44.4 - - + +
273G TYR* 4.3 2.7 - - - -
58H GLN 2.9 12.2 + - - +
59H PRO* 3.6 8.1 - - + +
60H LEU 3.2 0.2 - - - -
61H ALA* 1.3 77.4 - - - +
63H LEU* 1.3 64.8 + - + +
65H LYS* 3.3 12.0 + - - +
66H MET* 3.3 17.8 + - - +
88H ILE* 3.4 10.6 - - - +
91H MET* 3.7 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G MET* 3.3 29.6 - - + -
63G LEU* 3.6 30.3 - - + -
66G MET* 4.0 20.0 - - + -
59H PRO 3.0 10.0 + - - +
60H LEU 3.6 1.6 - - - +
62H MET* 1.3 77.6 - - + +
64H MET* 1.3 62.6 + - - +
66H MET* 3.1 24.7 + - + +
67H ASN* 3.3 10.9 + - - +
272H ALA 4.2 0.7 - - - +
273H TYR* 4.0 17.5 - - - +
276H VAL* 3.2 45.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H VAL* 4.1 13.7 - - + -
49H ILE* 3.8 17.0 - - + -
60H LEU* 2.9 19.0 + - + +
61H ALA 3.7 7.2 - - - +
63H LEU* 1.3 71.0 - - - +
65H LYS* 1.3 66.5 + - - +
66H MET 3.0 1.8 - - - -
67H ASN* 2.9 29.8 + - - +
70H VAL* 3.9 30.9 - - + +
73H LEU* 3.8 20.9 - - + -
115H LEU* 4.5 0.7 - - + -
117H ILE* 3.5 28.9 - - + -
276H VAL* 4.3 19.5 - - - -
279H ALA* 3.7 17.9 - - + -
283H LEU* 4.4 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G THR* 6.1 0.2 - - - +
61H ALA 3.0 8.6 + - - +
62H MET 3.4 10.8 - - - +
64H MET* 1.3 76.0 - - - +
66H MET* 1.3 57.3 + - - +
67H ASN 3.6 1.6 + - - +
73H LEU* 3.6 7.5 - - + +
88H ILE* 3.4 47.1 - - + +
89H SER* 4.6 3.6 - - - +
91H MET* 3.1 29.1 + - + -
93H THR* 2.5 56.7 + - - +
94H GLY 4.6 0.2 + - - -
95H ALA* 2.9 42.7 + - + +
97H VAL* 4.0 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 66 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G LEU* 4.1 23.8 - - + -
273G TYR* 3.8 30.3 - - + -
276G VAL* 6.2 1.8 - - + -
62H MET* 3.3 22.0 - - - +
63H LEU* 3.1 28.7 + - + +
64H MET 3.0 0.8 - - - -
65H LYS* 1.3 77.6 - - - +
67H ASN* 1.3 60.8 + - - +
68H PRO* 3.2 10.2 - - - +
91H MET* 3.4 16.4 - - + -
93H THR* 4.2 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 67 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H LEU 3.3 7.7 + - - +
64H MET* 2.9 27.1 + - - +
65H LYS 4.4 3.2 - - - +
66H MET* 1.3 76.6 - - - +
68H PRO* 1.3 62.8 - - - +
69H LEU* 2.8 41.6 + - - +
70H VAL* 3.0 41.1 + - + +
94H GLY* 5.8 0.6 - - - -
95H ALA* 4.7 1.2 + - - +
276H VAL* 5.0 5.8 - - + +
280H ASP* 3.3 38.5 + - - +
283H LEU* 4.3 2.8 - - - +
----------------------------------------------------------
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