Contacts of the helix formed by residues 48 - 59 (chain A) in PDB entry 2KT0
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 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A SER* 4.7 10.3 + - - -
46A TYR 3.7 1.2 + - - -
47A LEU* 1.3 77.0 - - - +
49A LEU* 1.3 75.1 + - - +
50A GLN* 3.2 5.8 + - - +
51A GLN* 3.4 29.9 - - - -
52A MET* 3.1 23.6 + - - +
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Residues in contact with LEU 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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48A SER* 1.3 81.5 + - - +
50A GLN* 1.3 57.0 + - - +
52A MET* 3.0 29.4 - - + +
53A GLN* 4.5 2.4 + - - +
63A TYR* 3.4 31.4 - - - +
67A LYS* 3.9 12.1 - - - +
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Residues in contact with GLN 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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1A SER* 4.4 26.6 + - - +
3A GLN* 4.7 12.5 + - - +
48A SER* 3.2 3.1 + - - +
49A LEU* 1.3 80.8 - - - +
51A GLN* 1.3 60.6 + - + +
52A MET 3.1 0.2 - - - -
53A GLN* 2.8 47.8 + - - +
54A GLU* 2.7 41.3 + - - +
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Residues in contact with GLN 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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1A SER* 4.6 10.7 - - - -
2A LYS 3.9 20.3 + - - +
4A PRO* 5.4 4.6 - - + +
44A GLN* 3.2 30.5 + - - +
46A TYR 3.1 24.3 + - - +
47A LEU* 3.5 20.4 - - + +
48A SER* 3.2 32.0 + - - +
50A GLN* 1.3 77.3 - - - +
52A MET* 1.3 56.9 + - - +
54A GLU* 3.3 12.1 + - - +
55A LEU* 2.9 32.0 + - - +
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Residues in contact with MET 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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47A LEU* 4.5 15.8 - - + +
48A SER 3.1 18.5 + - - +
49A LEU* 3.0 33.0 - - + +
51A GLN* 1.3 78.4 - - - +
53A GLN* 1.3 56.5 + - - +
55A LEU* 4.4 1.8 - - - -
56A SER* 3.0 27.9 + - - -
63A TYR* 3.4 14.4 - - + -
66A VAL* 3.4 28.7 - - + +
67A LYS* 3.2 52.9 - - + +
70A PHE* 4.7 15.7 - - + -
71A GLN* 4.8 5.4 - - - +
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Residues in contact with GLN 53 (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 LEU 4.7 2.4 + - - -
50A GLN* 2.8 38.0 + - - +
52A MET* 1.3 77.8 - - - +
54A GLU* 1.3 79.5 + - - +
56A SER* 3.4 5.3 - - - -
57A ASN* 3.1 22.2 + - - +
63A TYR* 3.5 31.0 - - + -
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Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A LYS 5.2 0.2 - - - +
3A GLN* 4.0 24.1 - - + +
4A PRO* 4.9 8.7 - - + -
5A THR* 6.4 2.0 - - - -
50A GLN* 2.7 60.0 + - - +
51A GLN* 3.5 13.1 + - - +
53A GLN* 1.3 94.1 - - - +
55A LEU* 1.3 63.2 + - - +
57A ASN* 3.0 17.3 + - - +
58A ILE* 3.0 25.8 + - + +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A PRO* 6.5 1.8 - - + -
36A VAL* 4.7 14.6 - - + -
37A LEU* 3.5 31.9 - - + -
40A ARG* 6.0 4.7 - - + -
47A LEU* 3.8 28.7 - - + -
51A GLN 2.9 16.7 + - - +
52A MET* 3.8 5.6 - - - +
54A GLU* 1.3 76.3 - - - +
56A SER* 1.3 64.4 + - - +
58A ILE* 3.1 13.6 + - + -
59A LEU* 3.0 53.1 + - + +
66A VAL* 4.0 13.5 - - + -
69A TRP* 6.3 0.7 - - + -
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Residues in contact with SER 56 (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 MET 3.0 19.3 + - - -
53A GLN* 3.4 9.0 - - - -
55A LEU* 1.3 77.9 - - - +
57A ASN* 1.3 60.9 + - - +
59A LEU 3.6 0.2 + - - -
60A ASN* 3.1 3.3 + - - -
61A LEU* 2.6 53.5 + - - +
62A SER 3.1 0.2 - - - -
63A TYR* 3.0 24.6 + - - +
66A VAL* 3.6 20.8 - - - +
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Residues in contact with ASN 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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53A GLN 3.1 11.6 + - - +
54A GLU* 3.0 11.9 + - - +
56A SER* 1.3 76.1 - - - +
58A ILE* 1.3 64.9 + - + +
60A ASN* 3.4 11.9 + - - +
61A LEU 5.1 0.4 - - - -
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Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A PRO* 3.3 30.3 - - + +
5A THR* 3.8 23.1 - - - +
54A GLU* 3.0 26.6 + - + +
55A LEU* 3.1 15.9 + - + +
57A ASN* 1.3 82.0 - - + +
59A LEU* 1.3 70.8 + - + +
60A ASN* 3.2 4.2 + - - +
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Residues in contact with LEU 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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32A THR* 6.1 2.9 - - + -
33A GLN* 3.5 37.5 - - + +
36A VAL* 5.6 8.7 - - + -
37A LEU* 6.0 1.8 - - + -
55A LEU* 3.0 49.2 + - + +
58A ILE* 1.3 89.5 - - + +
60A ASN* 1.3 71.3 + - - +
61A LEU* 3.1 30.0 + - + +
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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