Contacts of the helix formed by residues 40 - 52 (chain A) in PDB entry 1SK1
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 SER 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PRO* 1.3 75.0 - - - +
41A ARG* 1.3 60.4 + - - +
42A ASP* 3.7 5.3 + - - +
43A GLU* 2.8 43.6 + - - +
44A LEU* 2.8 27.2 + - - +
86A LEU* 3.8 2.5 - - - -
403A CS 3.6 8.2 - - - -
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Residues in contact with ARG 41 (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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40A SER* 1.3 73.4 - - - +
42A ASP* 1.3 68.1 + - - +
44A LEU* 3.2 2.4 + - - +
45A VAL* 2.8 43.5 + - + +
79A ASP* 2.7 41.6 + - - +
82A ILE* 3.7 12.1 - - + +
83A ASP* 2.9 40.4 + - - -
86A LEU* 3.4 26.8 - - + +
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Residues in contact with ASP 42 (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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40A SER* 3.3 5.8 + - - +
41A ARG* 1.3 83.4 - - - +
43A GLU* 1.3 59.5 - - + +
45A VAL* 3.3 8.6 + - - +
46A LYS* 3.0 29.7 + - - +
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Residues in contact with GLU 43 (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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7A TYR* 4.9 9.6 + - - +
39A PRO* 3.2 11.7 - - + +
40A SER* 2.8 49.7 + - - +
42A ASP* 1.3 78.0 - - + +
44A LEU* 1.3 56.6 + - - +
46A LYS* 3.3 6.9 + - - +
47A LEU* 2.9 34.9 + - + +
403A CS 3.2 15.0 - - - -
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Residues in contact with LEU 44 (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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39A PRO* 4.0 17.4 - - + +
40A SER 2.8 21.1 + - - +
41A ARG* 3.7 4.0 - - - +
43A GLU* 1.3 72.7 - - - +
45A VAL* 1.3 62.9 + - - +
47A LEU* 3.3 14.2 + - + +
48A ILE* 3.0 31.5 + - + +
58A LEU* 4.0 25.6 - - + -
82A ILE* 4.2 11.9 - - + +
85A MET* 3.8 32.3 - - + -
86A LEU* 4.0 22.0 - - + -
92A ILE* 4.5 14.1 - - + -
96A ILE* 5.3 0.9 - - + -
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Residues in contact with VAL 45 (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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41A ARG* 2.8 45.9 + - + +
42A ASP* 3.6 8.1 - - - +
44A LEU* 1.3 75.9 - - - +
46A LYS* 1.3 64.6 + - - +
48A ILE* 3.4 8.9 + - - +
49A ALA* 3.0 24.1 + - + +
79A ASP* 5.5 0.4 - - - +
82A ILE* 4.3 18.2 - - + -
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Residues in contact with LYS 46 (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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42A ASP 3.0 14.4 + - - +
43A GLU* 3.6 10.3 - - - +
45A VAL* 1.3 76.4 - - - +
47A LEU* 1.3 68.5 + - + +
49A ALA* 3.2 5.9 + - + +
50A ASP* 2.9 46.8 + - - +
98A VAL* 6.1 3.0 - - - +
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Residues in contact with LEU 47 (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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7A TYR* 3.9 33.9 - - + +
39A PRO* 4.3 18.2 - - + -
43A GLU* 2.9 24.5 + - + +
44A LEU* 3.6 10.1 - - + +
46A LYS* 1.3 74.3 - - + +
48A ILE* 1.3 58.5 + - - +
50A ASP* 3.2 6.5 + - - +
51A MET* 2.8 46.5 + - + +
96A ILE* 4.2 16.2 - - + -
98A VAL* 3.7 30.1 - - + -
103A THR* 4.1 9.9 - - + +
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Residues in contact with ILE 48 (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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44A LEU* 3.0 37.4 + - + +
45A VAL* 3.8 5.6 - - - +
46A LYS 3.2 0.2 - - - -
47A LEU* 1.3 75.7 - - - +
49A ALA* 1.3 65.7 + - - +
51A MET* 3.2 18.8 + - + +
52A GLY* 3.4 7.4 + - - -
53A ILE* 3.6 24.5 + - + +
54A SER 4.5 0.9 - - - +
55A VAL* 4.1 28.9 - - + +
58A LEU* 3.6 29.4 - - + -
82A ILE* 4.1 24.5 - - + -
85A MET* 4.9 1.8 - - - -
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Residues in contact with ALA 49 (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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45A VAL* 3.0 20.0 + - + +
46A LYS* 3.7 6.5 - - + +
48A ILE* 1.3 78.6 - - - +
50A ASP* 1.3 69.6 + - - +
52A GLY* 3.3 11.4 + - - -
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Residues in contact with ASP 50 (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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46A LYS* 2.9 50.8 + - - +
47A LEU* 3.9 2.6 - - - +
49A ALA* 1.3 81.5 - - - +
51A MET* 1.3 60.9 + - - +
52A GLY* 3.2 1.2 + - - -
102A GLY* 6.1 0.7 - - - -
103A THR* 3.7 35.7 + - - +
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Residues in contact with MET 51 (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 LEU* 2.8 34.5 + - + +
48A ILE* 3.2 13.4 + - + +
50A ASP* 1.3 75.3 - - - +
52A GLY* 1.3 62.9 + - - +
53A ILE* 3.3 22.8 + - + +
58A LEU* 4.0 28.9 - - + -
96A ILE* 4.0 21.1 - - + -
103A THR* 3.5 29.8 - - + +
104A ARG* 3.9 9.8 - - - -
105A LEU* 3.5 36.5 + - - +
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Residues in contact with GLY 52 (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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48A ILE 3.4 1.9 + - - -
49A ALA 3.3 10.7 + - - -
50A ASP 3.1 6.2 + - - -
51A MET* 1.3 77.7 - - - +
53A ILE* 1.3 61.8 + - - +
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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