Contacts of the helix formed by residues 56 - 67 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C GLY 3.2 0.4 - - - -
55C GLY* 1.3 73.2 - - - +
57C GLY* 1.3 68.4 + - - +
59C PRO* 3.1 5.5 - - - +
60C LEU* 3.0 36.1 + - + +
119C PRO* 3.7 33.9 - - + +
160C ILE* 4.7 7.4 - - + -
266C SER* 6.0 0.4 - - - +
267C ALA 3.7 17.9 - - - +
268C THR* 4.0 8.7 - - - +
271C MET* 3.7 24.2 - - + -
272C ALA* 3.9 9.4 - - - +
1313C CIT 3.4 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE* 4.6 2.0 - - - +
51C GLY 3.4 24.6 + - - -
52C ALA* 3.2 11.0 - - - +
54C GLY* 3.3 6.2 + - - -
56C ILE* 1.3 79.5 - - - +
58C GLN* 1.3 55.0 + - - +
60C LEU* 3.4 4.8 + - - +
61C ALA* 2.7 31.5 + - - +
119C PRO* 4.2 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ALA 3.4 15.3 - - - +
53C ALA* 2.9 22.3 + - - +
54C GLY 3.0 14.2 + - - +
57C GLY* 1.3 72.3 - - - +
59C PRO* 1.3 73.0 - - + +
61C ALA* 3.1 5.2 + - - +
62C MET* 2.9 22.0 + - - +
80C ASN* 5.7 2.0 - - - +
84C VAL* 3.5 27.2 - - + +
261D LYS* 4.7 7.1 + - - -
268D THR* 4.6 7.4 - - - +
269D LEU* 3.7 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C GLY 2.9 30.1 - - - +
56C ILE 3.1 13.5 - - - +
58C GLN* 1.3 87.4 - - + +
60C LEU* 1.3 54.6 + - - +
62C MET* 3.2 10.7 + - + +
63C LEU* 2.9 32.6 + - - +
268C THR* 4.0 12.1 - - + +
269C LEU* 4.1 9.0 - - + -
272C ALA* 3.7 18.2 - - + -
59D PRO* 4.8 7.4 - - + -
62D MET* 3.9 19.1 - - + -
269D LEU* 4.1 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE* 4.1 13.0 - - + -
56C ILE* 3.0 33.9 + - + +
57C GLY 3.5 2.5 - - - +
59C PRO* 1.3 76.2 - - - +
61C ALA* 1.3 60.1 + - - +
63C LEU* 3.2 2.1 + - - +
64C MET* 2.8 38.6 + - + +
117C ILE* 3.8 29.6 - - + -
119C PRO* 4.2 14.6 - - + -
160C ILE* 4.4 1.1 - - + -
272C ALA* 3.6 15.4 - - + +
275C ALA* 4.1 13.7 - - + -
276C VAL* 3.2 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE* 3.4 13.0 - - + -
52C ALA 4.6 3.8 - - - +
57C GLY 2.7 22.8 + - - +
58C GLN* 3.5 7.2 - - - +
60C LEU* 1.3 73.3 - - - +
62C MET* 1.3 65.0 + - - +
64C MET* 3.2 2.3 + - - +
65C LYS* 2.9 24.1 + - - +
73C LEU* 3.7 3.6 - - - +
75C LEU* 3.7 37.7 - - + -
84C VAL* 4.9 0.7 - - + -
88C ILE* 4.0 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLN 2.9 12.9 + - - +
59C PRO* 3.2 7.6 + - + +
61C ALA* 1.3 75.8 - - - +
63C LEU* 1.3 67.3 + - + +
65C LYS* 3.1 13.3 + - - +
66C MET* 3.3 21.5 + - - +
88C ILE* 3.5 16.3 - - + +
91C MET* 4.1 13.9 - - - -
59D PRO* 4.0 13.7 - - + -
62D MET* 3.4 33.0 - - + -
63D LEU* 3.6 31.6 - - + -
269D LEU* 3.3 35.0 - - + +
272D ALA* 4.2 7.0 - - - -
273D TYR* 4.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C PRO 2.9 17.3 + - - +
60C LEU 3.7 0.2 - - - +
62C MET* 1.3 76.7 - - + +
64C MET* 1.3 63.6 + - - +
66C MET* 3.0 24.0 + - + +
67C ASN* 3.2 10.9 + - - +
272C ALA 3.8 4.5 - - - +
273C TYR* 3.8 22.0 - - + -
276C VAL* 3.4 40.2 - - + +
62D MET* 3.6 22.9 - - + -
63D LEU* 3.7 30.5 - - + -
66D MET* 4.0 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C VAL* 3.7 29.6 - - + -
49C ILE* 4.1 7.0 - - + -
60C LEU* 2.8 35.0 + - + +
61C ALA 3.6 4.5 - - - +
63C LEU* 1.3 72.0 - - - +
65C LYS* 1.3 61.9 + - - +
67C ASN* 3.1 24.9 + - - +
70C VAL* 3.8 34.4 - - + +
73C LEU* 4.1 17.7 - - + -
115C LEU* 4.9 0.2 - - + -
117C ILE* 3.8 13.5 - - + -
276C VAL* 4.0 20.9 - - - -
279C ALA* 4.0 20.2 - - + -
283C LEU* 4.3 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ALA 2.9 12.0 + - - +
62C MET 3.3 10.1 - - - +
64C MET* 1.3 78.2 - - - +
66C MET* 1.3 58.0 + - - +
67C ASN 3.6 1.2 + - - +
73C LEU* 3.8 10.7 - - + +
88C ILE* 3.5 28.9 - - + -
89C SER* 4.6 3.5 + - - +
91C MET* 3.2 44.2 + - + -
93C THR* 2.7 50.6 + - - +
95C ALA* 2.5 48.1 + - + +
96C VAL* 4.9 0.2 - - - +
97C VAL* 4.0 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C MET* 3.4 22.0 - - - +
63C LEU* 3.0 19.4 + - + +
65C LYS* 1.3 76.2 - - - +
67C ASN* 1.3 65.0 + - - +
68C PRO* 3.2 10.2 - - - +
91C MET* 4.8 3.8 - - - -
93C THR* 4.1 14.2 - - + +
63D LEU* 4.2 30.3 - - + -
273D TYR* 3.9 37.9 - - + -
276D VAL* 6.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LEU 3.2 9.1 + - - +
64C MET* 3.1 24.4 + - - +
65C LYS 4.3 3.5 - - - +
66C MET* 1.3 75.5 - - - +
68C PRO* 1.3 69.1 - - - +
69C LEU* 2.6 43.5 + - - +
70C VAL* 3.1 30.7 + - + +
95C ALA* 4.8 1.4 + - - +
276C VAL* 5.0 5.3 - - + +
280C ASP* 3.1 38.3 + - - +
283C LEU* 4.5 4.5 - - - +
----------------------------------------------------------
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