Contacts of the helix formed by residues 56 - 67 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLY* 1.3 74.8 - - - +
57A GLY* 1.3 67.5 + - - +
59A PRO* 3.2 8.6 - - - +
60A LEU* 3.1 28.0 + - + +
119A PRO* 3.9 26.0 - - + +
160A ILE* 5.1 8.1 - - + -
266A SER* 6.1 0.4 - - - +
267A ALA 4.0 9.0 - - - +
268A THR* 3.7 26.9 - - + +
271A MET* 3.5 35.0 - - + -
272A ALA* 3.8 5.7 - - - +
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Residues in contact with GLY 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 4.7 1.9 - - - +
51A GLY 3.4 24.2 + - - -
52A ALA* 3.3 10.2 - - - +
54A GLY* 3.3 5.7 + - - -
56A ILE* 1.3 79.0 - - - +
58A GLN* 1.3 51.0 + - - +
60A LEU* 3.1 9.1 + - - +
61A ALA* 2.7 36.2 + - - +
119A PRO* 4.3 9.2 - - - +
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Residues in contact with GLN 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA 3.4 15.3 - - - +
53A ALA* 2.9 23.1 + - - +
54A GLY 3.1 11.5 + - - +
55A GLY* 5.7 0.2 - - - -
57A GLY* 1.3 72.4 - - - +
59A PRO* 1.3 74.6 - - + +
61A ALA* 2.9 13.8 + - - +
62A MET 2.9 10.4 + - - -
80A ASN* 6.0 1.2 - - - +
84A VAL* 3.7 22.7 - - + +
261B LYS* 5.1 5.5 + - - -
268B THR* 4.4 7.3 + - - -
269B LEU* 3.7 33.7 - - + +
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Residues in contact with PRO 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLY 3.0 26.5 - - - +
56A ILE* 3.2 14.8 - - - +
58A GLN* 1.3 89.6 - - + +
60A LEU* 1.3 58.4 + - - -
62A MET* 3.5 8.2 + - + +
63A LEU* 3.2 29.3 + - - +
268A THR 4.4 2.0 - - - +
269A LEU* 4.1 21.5 - - + -
272A ALA* 3.6 17.9 - - + -
59B PRO* 5.0 5.8 - - + -
62B MET* 4.1 17.1 - - + +
269B LEU* 4.4 6.9 - - + -
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 3.9 15.9 - - + -
56A ILE* 3.1 28.9 + - + +
57A GLY* 3.1 5.6 + - - +
58A GLN 2.9 0.4 - - - -
59A PRO* 1.3 76.0 - - - +
61A ALA* 1.3 59.4 + - - +
63A LEU* 3.3 2.6 + - - +
64A MET* 3.0 37.0 + - + +
117A ILE* 3.9 22.9 - - + -
119A PRO* 4.6 7.2 - - + -
160A ILE* 4.1 7.0 - - + -
272A ALA* 3.6 9.4 - - + +
275A ALA* 3.6 27.4 - - + -
276A VAL* 3.4 24.7 - - + +
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 3.5 13.4 - - + +
52A ALA* 4.6 5.2 - - + +
57A GLY 2.7 19.2 + - - +
58A GLN* 2.9 4.2 + - - +
60A LEU* 1.3 71.0 - - - +
62A MET* 1.3 67.5 + - - +
64A MET 3.3 0.4 + - - +
65A LYS* 2.9 25.3 + - - +
73A LEU* 3.7 4.3 - - - +
75A LEU* 3.6 26.0 - - + -
88A ILE* 3.2 24.6 - - + +
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Residues in contact with MET 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLN 2.9 12.0 + - - +
59A PRO* 3.7 5.2 - - + +
61A ALA* 1.3 79.5 - - - +
63A LEU* 1.3 67.9 + - + +
65A LYS* 3.4 2.8 + - - +
66A MET* 3.2 27.0 + - - +
88A ILE* 3.9 8.8 - - - +
91A MET* 3.5 24.9 - - + +
59B PRO* 4.1 15.7 - - + -
62B MET* 3.4 33.2 - - + -
63B LEU* 3.5 35.0 - - + -
269B LEU* 3.6 40.8 - - + +
272B ALA* 4.3 0.7 - - - -
273B TYR* 4.5 0.7 - - - -
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PRO 3.2 13.8 + - - +
60A LEU 3.8 0.2 - - - +
61A ALA 3.2 0.2 - - - -
62A MET* 1.3 79.8 - - + +
64A MET* 1.3 63.3 + - - +
66A MET* 3.2 19.7 + - + +
67A ASN* 3.3 11.3 + - - +
272A ALA 4.1 2.0 - - - +
273A TYR* 4.0 15.0 - - - +
276A VAL* 3.5 39.0 - - + +
62B MET* 3.5 31.6 - - + -
63B LEU* 3.7 30.3 - - + -
66B MET* 3.9 20.9 - - + -
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Residues in contact with MET 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 3.7 24.9 - - + -
49A ILE* 3.8 10.5 - - + -
60A LEU* 3.0 32.6 + - + +
61A ALA 3.3 4.7 + - - +
63A LEU* 1.3 72.7 - - - +
65A LYS* 1.3 58.8 + - - +
66A MET 3.0 4.9 - - - -
67A ASN* 2.9 30.1 + - + +
70A VAL* 3.4 39.8 - - + +
73A LEU* 4.1 17.7 - - + -
117A ILE* 3.9 14.8 - - + -
276A VAL* 4.0 20.6 - - - -
279A ALA* 4.0 10.1 - - + -
283A LEU* 4.0 11.4 - - + -
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA 2.9 17.5 + - - +
62A MET 3.5 6.5 - - - +
63A LEU 3.3 0.2 - - - -
64A MET* 1.3 76.8 - - - +
66A MET* 1.3 56.1 + - - +
67A ASN 4.5 0.9 - - - +
73A LEU* 3.7 10.4 - - + +
88A ILE* 3.4 44.6 - - + +
89A SER* 4.5 3.6 + - - +
91A MET* 3.1 27.4 + - + -
93A THR* 2.5 58.5 + - - +
95A ALA* 2.6 41.3 + - + +
96A VAL* 5.1 0.2 - - - +
97A VAL* 4.2 18.2 - - + +
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Residues in contact with MET 66 (chain A).
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* 3.2 22.7 - - - +
63A LEU* 3.2 18.4 + - + +
64A MET 3.0 0.8 - - - -
65A LYS* 1.3 78.8 - - - +
67A ASN* 1.3 62.2 + - - +
68A PRO* 3.2 11.1 - - - +
91A MET* 3.4 15.7 - - + -
93A THR* 4.2 10.2 - - + +
63B LEU* 3.9 32.5 - - + -
273B TYR* 3.8 30.5 - - + -
276B VAL* 6.3 1.6 - - + -
277B LYS* 6.1 0.9 - - + -
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Residues in contact with ASN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU 3.3 9.4 + - - +
64A MET* 2.9 23.8 + - + +
65A LYS 4.5 2.6 - - - +
66A MET* 1.3 75.8 - - - +
68A PRO* 1.3 64.8 - - - +
69A LEU* 2.9 39.4 + - - +
70A VAL* 3.0 36.8 + - + +
95A ALA* 4.8 2.1 + - - +
276A VAL* 4.7 5.7 - - - +
280A ASP* 2.9 40.1 + - - +
283A LEU* 4.4 4.1 - - - +
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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