Contacts of the helix formed by residues 56 - 67 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B GLY* 1.3 73.7 - - - +
57B GLY* 1.3 67.9 + - - +
59B PRO* 3.2 5.7 - - - +
60B LEU* 3.0 31.4 + - + +
119B PRO* 3.8 28.0 - - + +
160B ILE* 4.5 14.1 - - + -
267B ALA 4.1 5.8 - - - +
268B THR* 3.9 22.4 - - + +
271B MET* 3.3 37.2 - - + -
272B ALA* 3.8 12.7 - - - +
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Residues in contact with GLY 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ILE* 4.7 1.0 - - - +
51B GLY 3.4 24.4 + - - -
52B ALA* 3.0 13.0 - - - +
54B GLY* 3.5 5.2 + - - -
56B ILE* 1.3 79.8 - - - +
58B GLN* 1.3 57.2 + - - +
60B LEU* 3.6 6.8 - - - +
61B ALA* 2.7 32.4 + - - +
119B PRO* 4.3 8.6 - - - +
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Residues in contact with GLN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A LYS* 4.9 7.7 + - - +
268A THR* 4.3 7.1 + - - -
269A LEU* 3.7 37.2 - - + +
52B ALA 3.0 17.4 + - - +
53B ALA* 3.1 18.6 + - - +
54B GLY 3.1 15.9 + - - +
57B GLY* 1.3 72.7 - - - +
59B PRO* 1.3 71.9 - - + +
61B ALA* 3.0 6.8 + - - +
62B MET* 3.0 18.0 + - - +
80B ASN* 5.9 1.8 - - - +
84B VAL* 3.6 24.8 - - + +
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Residues in contact with PRO 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PRO* 5.0 5.6 - - + -
62A MET* 4.1 11.2 - - + -
269A LEU* 4.5 5.8 - - + -
55B GLY 2.9 30.1 - - - +
56B ILE* 3.2 10.3 - - - +
58B GLN* 1.3 90.5 - - + +
60B LEU* 1.3 59.3 + - - +
62B MET* 3.2 12.4 + - + +
63B LEU* 3.0 27.4 + - - +
268B THR 4.6 1.6 - - - +
269B LEU* 4.1 26.7 - - + -
272B ALA* 3.7 17.0 - - + -
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE* 3.9 22.7 - - + -
56B ILE* 3.0 20.4 + - + +
57B GLY* 3.6 2.5 - - - +
59B PRO* 1.3 77.9 - - - +
61B ALA* 1.3 58.1 + - - +
63B LEU* 3.4 1.0 + - - +
64B MET* 3.0 37.2 + - + +
117B ILE* 3.6 30.5 - - + -
119B PRO* 4.1 17.5 - - + -
272B ALA* 3.6 12.9 - - + +
275B ALA* 4.1 19.3 - - + -
276B VAL* 3.3 28.0 - - + +
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ILE* 3.6 11.9 - - + -
52B ALA* 4.5 3.4 - - + +
57B GLY 2.7 22.9 + - - +
58B GLN* 3.0 5.6 + - - +
60B LEU* 1.3 72.4 - - - +
62B MET* 1.3 63.6 + - - +
64B MET 3.3 0.5 + - - -
65B LYS* 3.0 23.2 + - - +
73B LEU* 3.7 4.9 - - - +
75B LEU* 3.5 25.1 - - + -
84B VAL* 4.7 0.4 - - + -
88B ILE* 3.2 24.3 - - + +
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Residues in contact with MET 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PRO* 4.1 18.6 - - + -
62A MET* 3.4 32.8 - - + -
63A LEU* 3.5 31.9 - - + -
269A LEU* 3.5 37.2 - - + +
272A ALA* 4.3 0.9 - - - -
273A TYR 4.3 0.9 - - - -
58B GLN 3.0 11.7 + - - +
59B PRO* 3.2 8.9 + - + +
61B ALA* 1.3 76.8 - - - +
63B LEU* 1.3 63.9 + - - +
65B LYS* 3.3 8.0 + - - +
66B MET* 3.2 24.3 + - - +
88B ILE* 3.5 8.0 - - - +
91B MET* 3.4 23.2 - - + +
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A MET* 3.5 27.8 - - + -
63A LEU* 3.7 29.2 - - + -
66A MET* 3.9 21.5 - - + -
59B PRO 3.0 16.1 + - - +
60B LEU 3.8 0.2 - - - +
62B MET* 1.3 75.1 - - + +
64B MET* 1.3 63.8 + - - +
66B MET* 3.1 22.4 + - + +
67B ASN* 3.2 11.4 + - - +
272B ALA 3.8 10.8 - - - +
273B TYR* 4.0 8.3 - - - -
276B VAL* 3.3 41.1 - - + +
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Residues in contact with MET 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 4.0 21.8 - - + -
49B ILE* 3.8 15.7 - - + -
60B LEU* 3.0 27.3 + - + +
61B ALA 3.9 4.0 - - - +
62B MET 3.3 0.4 - - - -
63B LEU* 1.3 73.1 - - - +
65B LYS* 1.3 67.0 + - - +
67B ASN* 2.9 27.5 + - + +
70B VAL* 3.5 36.4 - - + +
73B LEU* 4.0 17.9 - - + -
117B ILE* 3.9 13.0 - - + -
276B VAL* 4.0 23.6 - - - +
279B ALA* 4.0 12.6 - - + -
283B LEU* 4.1 11.0 - - + -
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Residues in contact with LYS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ALA 3.0 13.6 + - - +
62B MET 3.4 11.0 - - - +
63B LEU 3.2 0.2 - - - -
64B MET* 1.3 76.3 - - - +
66B MET* 1.3 56.7 + - - +
67B ASN 4.6 0.9 - - - +
73B LEU* 3.9 7.1 - - + +
88B ILE* 3.4 40.2 - - + -
89B SER* 4.4 4.3 - - - +
91B MET* 3.1 35.1 + - + -
93B THR* 2.6 57.9 + - - +
95B ALA* 2.6 43.4 + - + +
97B VAL* 4.1 16.2 - - + -
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Residues in contact with MET 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 3.9 32.5 - - + -
273A TYR* 3.8 31.0 - - + -
276A VAL* 6.4 1.3 - - + -
62B MET* 3.4 21.1 - - - +
63B LEU* 3.1 18.8 + - + +
64B MET 3.0 1.0 - - - -
65B LYS* 1.3 78.8 - - - +
67B ASN* 1.3 60.7 + - - +
68B PRO* 3.2 10.4 - - - +
91B MET* 3.5 15.0 - - + -
93B THR* 4.2 11.8 - - + +
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Residues in contact with ASN 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU 3.2 8.5 + - - +
64B MET* 2.9 22.0 + - + +
65B LYS 4.6 2.7 - - - +
66B MET* 1.3 76.4 - - - +
68B PRO* 1.3 66.0 - - - +
69B LEU* 2.7 40.9 + - - +
70B VAL* 2.9 42.6 + - + +
95B ALA* 4.8 0.7 + - - +
276B VAL* 5.0 6.9 - - + +
280B ASP* 2.9 40.2 + - - +
283B LEU* 4.5 3.4 - - - +
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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