Contacts of the helix formed by residues 56 - 67 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54F GLY* 4.4 0.2 - - - -
55F GLY* 1.3 75.4 - - - +
57F GLY* 1.3 67.8 + - - +
58F GLN 3.3 0.9 - - - -
59F PRO* 3.1 4.7 - - - +
60F LEU* 3.1 38.4 + - + +
119F PRO* 4.2 17.7 - - + +
160F ILE* 5.1 8.1 - - + -
266F SER* 6.1 0.2 - - - +
267F ALA 4.0 7.2 - - - +
268F THR* 3.8 32.7 - - + +
271F MET* 3.4 34.3 - - + -
272F ALA* 4.0 4.9 - - - +
275F ALA* 5.5 0.2 - - + -
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Residues in contact with GLY 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ILE* 4.6 1.7 - - - +
51F GLY 3.4 24.7 + - - -
52F ALA* 3.2 11.9 - - - +
54F GLY* 3.5 5.0 + - - -
56F ILE* 1.3 80.2 - - - +
58F GLN* 1.3 56.6 + - - +
60F LEU* 3.5 5.8 - - - +
61F ALA* 2.8 30.8 + - - +
119F PRO* 4.3 10.8 - - - +
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Residues in contact with GLN 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261E LYS* 5.1 5.7 + - - -
268E THR* 4.4 6.6 + - - -
269E LEU* 3.8 26.5 - - + +
52F ALA 3.0 18.6 + - - +
53F ALA* 2.7 23.4 + - - +
54F GLY 3.2 9.6 + - - +
57F GLY* 1.3 72.3 - - - +
59F PRO* 1.3 76.5 - - + +
61F ALA* 3.0 6.2 + - - +
62F MET* 2.9 22.5 + - - +
80F ASN* 5.7 2.0 - - - +
84F VAL* 3.6 27.4 - - + +
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Residues in contact with PRO 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E PRO* 5.2 6.1 - - + -
62E MET* 4.0 17.0 - - + +
269E LEU* 4.3 12.6 - - + -
55F GLY 3.1 21.1 - - - +
56F ILE 3.1 11.7 - - - +
58F GLN* 1.3 92.5 - - + +
60F LEU* 1.3 62.5 + - - +
62F MET* 3.1 6.3 + - + +
63F LEU* 3.0 26.3 + - - +
268F THR 5.1 0.9 - - - +
269F LEU* 3.9 21.8 - - + -
272F ALA* 3.6 19.7 - - + -
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Residues in contact with LEU 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ILE* 4.4 9.6 - - + -
56F ILE* 3.1 27.0 + - + +
57F GLY 3.5 4.3 - - - +
59F PRO* 1.3 80.0 - - - +
61F ALA* 1.3 56.9 + - - +
63F LEU* 3.2 3.3 + - - +
64F MET* 2.9 40.1 + - + +
117F ILE* 3.8 26.5 - - + -
119F PRO* 4.4 9.4 - - + -
160F ILE* 4.1 7.0 - - + -
272F ALA* 3.6 10.7 - - + +
275F ALA* 3.5 28.0 - - + -
276F VAL* 3.5 24.0 - - + +
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Residues in contact with ALA 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ILE* 3.4 14.1 - - + -
52F ALA* 4.5 3.8 - - + +
57F GLY 2.8 20.7 + - - +
58F GLN* 3.0 8.3 + - - +
60F LEU* 1.3 71.0 - - - +
62F MET* 1.3 65.9 + - - +
64F MET* 3.2 2.8 + - - +
65F LYS* 3.0 23.6 + - - +
73F LEU* 3.8 4.2 - - - +
75F LEU* 3.7 25.6 - - + -
84F VAL* 4.9 0.4 - - + -
88F ILE* 3.4 18.2 - - + -
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Residues in contact with MET 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E PRO* 4.0 13.9 - - + +
62E MET* 3.6 30.1 - - + -
63E LEU* 3.5 35.9 - - + -
269E LEU* 3.4 41.7 - - + +
272E ALA* 4.3 3.6 - - - -
273E TYR* 4.2 3.8 - - - -
58F GLN 2.9 12.4 + - - +
59F PRO* 3.4 7.4 - - + +
61F ALA* 1.3 76.4 - - - +
63F LEU* 1.3 64.7 + - + +
65F LYS* 3.2 18.5 + - - +
66F MET* 3.4 11.8 + - - +
88F ILE* 3.5 9.1 - - - +
91F MET* 3.8 19.0 - - + +
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Residues in contact with LEU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E MET* 3.7 29.4 - - + -
63E LEU* 3.7 30.1 - - + -
66E MET* 4.0 21.3 - - + -
59F PRO 3.0 14.5 + - - +
60F LEU 3.6 1.1 - - - +
62F MET* 1.3 79.2 - - + +
64F MET* 1.3 57.6 + - - +
66F MET* 3.0 27.7 + - + +
67F ASN* 3.3 10.4 + - - +
272F ALA 4.2 1.1 - - - -
273F TYR* 4.0 15.0 - - - +
276F VAL* 3.4 42.8 - - + +
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Residues in contact with MET 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F VAL* 4.2 17.3 - - + -
49F ILE* 3.9 16.6 - - + -
60F LEU* 2.9 33.7 + - + +
61F ALA 3.7 4.3 - - - +
63F LEU* 1.3 70.7 - - - +
65F LYS* 1.3 61.3 + - - +
66F MET 3.0 6.1 - - - -
67F ASN* 3.2 16.7 + - + +
70F VAL* 3.4 49.6 - - + +
73F LEU* 4.2 10.1 - - + -
115F LEU* 5.1 0.2 - - + -
117F ILE* 3.9 19.1 - - + -
276F VAL* 4.1 17.3 - - - +
279F ALA* 4.0 15.7 - - + -
283F LEU* 4.2 10.8 - - + -
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Residues in contact with LYS 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F ALA 3.0 12.5 + - - +
62F MET 3.3 11.9 - - - +
63F LEU 3.2 0.2 - - - -
64F MET* 1.3 78.0 - - - +
66F MET* 1.3 57.6 + - - +
67F ASN 3.8 1.0 + - - +
73F LEU* 3.9 8.0 - - + +
88F ILE* 3.5 42.6 - - + -
89F SER 4.5 3.5 + - - -
91F MET* 3.3 34.2 + - + -
93F THR* 2.5 57.0 + - - +
95F ALA* 2.7 41.1 + - + +
97F VAL* 4.2 19.1 - - + +
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Residues in contact with MET 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E LEU* 4.1 31.4 - - + -
273E TYR* 3.8 31.2 - - + -
276E VAL* 6.1 2.9 - - + -
62F MET* 3.4 21.5 - - - +
63F LEU* 3.0 18.3 + - + +
64F MET 3.0 0.6 - - - -
65F LYS* 1.3 78.8 - - - +
67F ASN* 1.3 62.5 + - - +
68F PRO* 3.1 10.2 - - - +
91F MET* 3.4 16.4 - - + -
93F THR* 4.1 11.7 - - + +
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Residues in contact with ASN 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F LEU 3.3 9.4 + - - +
64F MET* 3.2 15.6 + - + +
65F LYS 4.7 2.1 - - - +
66F MET* 1.3 75.1 - - - +
68F PRO* 1.3 63.7 - - - +
69F LEU* 2.7 40.7 + - - +
70F VAL* 2.9 47.2 + - + +
95F ALA* 5.0 1.2 + - - +
276F VAL* 5.3 4.1 - - + +
280F ASP* 3.0 41.4 + - - +
283F LEU* 4.0 6.0 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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