Contacts of the helix formed by residues 56 - 66 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D GLY 3.2 0.4 - - - -
55D GLY* 1.3 76.1 - - - +
57D GLY* 1.3 61.4 + - - +
59D PRO* 3.2 5.9 - - - +
60D LEU* 2.9 39.1 + - + +
119D PRO* 4.1 25.8 - - + +
160D ILE* 4.8 12.6 - - + -
267D ALA 3.9 17.5 - - - +
268D THR* 4.1 6.5 - - - +
271D MET* 3.3 39.0 - - + -
272D ALA* 3.8 14.7 - - - +
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Residues in contact with GLY 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ILE* 4.7 1.2 - - - +
51D GLY 3.3 24.3 + - - -
52D ALA* 2.9 12.0 - - - -
54D GLY* 3.1 4.8 + - - -
56D ILE* 1.3 79.6 - - - +
58D GLN* 1.3 51.4 + - - +
60D LEU* 3.2 6.0 + - - +
61D ALA* 2.6 37.6 + - - +
119D PRO* 4.4 9.6 - - - +
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Residues in contact with GLN 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C LYS* 5.2 6.1 + - - -
268C THR* 4.9 6.8 - - - +
269C LEU* 3.4 34.2 - - + +
52D ALA 2.8 17.2 + - - +
53D ALA* 3.0 20.7 + - - +
54D GLY 2.9 15.8 + - - +
55D GLY* 5.7 0.2 - - - -
57D GLY* 1.3 71.2 - - - -
59D PRO* 1.3 70.4 - - + +
61D ALA* 3.1 3.7 + - - +
62D MET* 2.9 19.4 + - - +
80D ASN* 5.4 4.0 - - - +
84D VAL* 3.5 29.1 - - + +
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Residues in contact with PRO 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C PRO* 4.8 6.7 - - + -
62C MET* 4.0 16.6 - - + +
269C LEU* 4.3 6.3 - - + -
55D GLY* 2.9 29.2 - - - +
56D ILE* 3.2 11.9 - - - +
58D GLN* 1.3 90.7 - - + +
60D LEU* 1.3 59.1 + - - +
62D MET* 3.5 8.8 + - + +
63D LEU* 3.1 28.1 + - - +
268D THR* 4.2 11.0 - - + +
269D LEU* 4.2 12.1 - - + -
272D ALA* 3.8 16.8 - - + -
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Residues in contact with LEU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ILE* 4.1 11.0 - - + -
56D ILE* 2.9 22.9 + - + +
57D GLY 3.4 3.8 - - - +
59D PRO* 1.3 75.7 - - - +
61D ALA* 1.3 66.4 + - - +
63D LEU* 3.1 3.1 + - - +
64D MET* 2.9 32.1 + - + +
117D ILE* 3.5 30.7 - - + -
119D PRO* 3.5 21.5 - - + -
160D ILE* 4.3 1.8 - - + -
272D ALA* 3.5 13.9 - - + +
275D ALA* 3.9 14.4 - - + -
276D VAL* 3.1 36.1 - - + +
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Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ILE* 3.5 13.9 - - + +
52D ALA* 4.5 3.8 - - + +
57D GLY 2.6 22.1 + - - +
58D GLN* 3.5 4.3 - - - +
60D LEU* 1.3 74.5 - - - +
62D MET* 1.3 62.9 + - - +
64D MET* 3.1 2.8 + - - +
65D LYS* 2.9 24.6 + - - +
73D LEU* 3.7 3.3 - - - +
75D LEU* 3.5 23.8 - - + -
88D ILE* 3.3 24.7 - - + -
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Residues in contact with MET 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C PRO* 3.9 13.9 - - + -
62C MET* 3.4 33.0 - - + -
63C LEU* 3.6 34.1 - - + -
269C LEU* 3.3 45.1 - - + +
272C ALA* 4.1 5.2 - - - -
273C TYR* 4.4 0.9 - - - -
58D GLN 2.9 12.5 + - - +
59D PRO* 3.7 6.1 - - + +
60D LEU 3.2 0.2 - - - -
61D ALA* 1.3 79.1 - - - +
63D LEU* 1.3 61.7 + - + +
65D LYS* 3.4 3.8 + - - -
66D MET* 3.3 24.5 + - - +
88D ILE* 3.8 6.7 - - - +
91D MET* 3.5 21.3 - - + +
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Residues in contact with LEU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C MET* 3.6 28.7 - - + -
63C LEU* 3.7 28.0 - - + -
66C MET* 4.2 20.0 - - + -
59D PRO 3.1 10.3 + - - +
60D LEU 3.1 4.0 + - - +
62D MET* 1.3 77.7 - - + +
64D MET* 1.3 65.2 + - - +
66D MET* 3.1 23.2 + - + +
67D ASN* 3.3 10.9 + - - +
272D ALA 4.0 2.0 - - - +
273D TYR* 4.0 13.7 - - - +
276D VAL* 3.3 44.9 - - + +
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Residues in contact with MET 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D VAL* 3.8 24.0 - - + -
49D ILE* 3.8 18.4 - - + -
60D LEU* 2.9 21.3 + - + +
61D ALA 3.1 6.5 + - - +
63D LEU* 1.3 71.7 - - - +
65D LYS* 1.3 58.3 + - - +
66D MET 2.9 5.4 - - - -
67D ASN* 2.9 30.2 + - + +
70D VAL* 3.7 37.5 - - + +
73D LEU* 4.1 16.2 - - + -
115D LEU* 4.5 0.4 - - + -
117D ILE* 3.8 11.4 - - + -
276D VAL* 4.2 19.5 - - - +
279D ALA* 3.9 22.7 - - + -
283D LEU* 4.4 8.1 - - + -
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Residues in contact with LYS 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ALA 2.9 15.5 + - - +
62D MET 3.6 7.0 - - - +
63D LEU 3.3 0.2 - - - -
64D MET* 1.3 76.6 - - - +
66D MET* 1.3 56.0 + - - +
67D ASN 3.3 1.1 + - - +
73D LEU* 3.7 8.2 - - + +
88D ILE* 3.6 37.2 - - + -
89D SER* 4.6 3.3 + - - +
91D MET* 3.2 31.3 + - + -
93D THR* 2.5 58.3 + - - +
95D ALA* 2.7 46.1 + - + +
97D VAL* 4.1 21.3 - - + +
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Residues in contact with MET 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C LEU* 4.0 31.6 - - + -
273C TYR* 3.8 30.5 - - + -
276C VAL* 6.5 0.4 - - + -
62D MET* 3.3 21.3 - - - +
63D LEU* 3.1 20.6 + - + +
64D MET 2.9 0.6 - - - -
65D LYS* 1.3 78.4 - - - +
67D ASN* 1.3 60.9 + - - +
68D PRO* 3.2 10.6 - - - +
91D MET* 3.4 16.8 - - + -
93D THR* 4.2 10.8 - - + +
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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