Contacts of the helix formed by residues 46 - 57 (chain A) in PDB entry 3KMP
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 GLY 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A LYS 3.3 0.8 + - - -
45A LYS* 1.3 72.4 - - - +
47A ALA* 1.3 55.1 - - - +
49A GLU* 2.8 29.8 + - - +
50A GLU* 2.8 34.3 + - - +
53A LYS* 5.4 0.7 + - - -
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Residues in contact with ALA 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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41A LEU* 3.7 31.4 - - + +
44A LYS* 3.2 28.7 + - + +
45A LYS 3.3 2.6 + - - -
46A GLY* 1.3 76.0 - - - +
48A MET* 1.3 58.9 + - - +
50A GLU* 3.1 6.3 + - - +
51A LEU* 2.8 32.2 + - - +
65A VAL* 4.2 12.2 - - + +
66A THR 6.2 0.2 - - - +
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Residues in contact with MET 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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38A VAL* 3.7 39.5 - - + -
41A LEU* 3.6 42.7 + - + +
42A LYS* 4.0 11.9 - - + +
44A LYS 4.5 0.4 + - - +
47A ALA* 1.3 77.9 - - - +
49A GLU* 1.3 71.9 + - + +
51A LEU* 3.5 8.3 + - + +
52A GLU* 3.0 36.4 + - - +
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Residues in contact with GLU 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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44A LYS 4.9 0.3 - - - +
45A LYS* 5.5 3.5 - - - +
46A GLY* 2.8 37.9 + - - +
48A MET* 1.3 82.6 + - - +
50A GLU* 1.3 57.2 + - - +
52A GLU* 3.3 8.4 + - - +
53A LYS* 2.8 50.9 + - - +
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Residues in contact with GLU 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 GLY 2.8 20.2 + - - +
47A ALA* 3.5 5.4 - - - +
49A GLU* 1.3 76.9 - - - +
51A LEU* 1.3 56.3 + - - +
53A LYS* 3.0 31.0 + - - +
54A ALA* 2.9 27.4 + - - +
62A SER* 3.5 10.3 - - - -
63A ASN* 2.6 54.3 + - + +
64A CYS 4.6 1.6 - - - +
65A VAL* 3.9 18.8 - - + -
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Residues in contact with LEU 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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37A LEU* 4.1 6.3 - - + -
38A VAL* 6.4 1.6 - - + -
41A LEU* 3.9 22.2 - - + -
47A ALA 2.8 19.0 + - - +
48A MET* 3.9 8.5 - - - +
50A GLU* 1.3 73.1 - - - +
52A GLU* 1.3 63.5 + - - +
54A ALA* 3.2 5.0 + - + +
55A LEU* 3.0 46.1 + - + +
65A VAL* 4.0 15.4 - - + +
92A TRP* 4.0 27.6 - - + -
122A ILE* 4.7 10.1 - - + -
123A ASN* 4.8 3.1 - - - -
124A PRO* 4.0 26.5 - - + -
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Residues in contact with GLU 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 MET* 3.0 28.3 + - - +
49A GLU* 3.5 7.6 - - - +
51A LEU* 1.3 75.7 - - - +
53A LYS* 1.3 55.6 + - - +
55A LEU* 3.9 9.0 - - + +
56A SER* 2.6 41.4 + - - +
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Residues in contact with LYS 53 (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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46A GLY* 5.4 0.6 + - - -
49A GLU* 2.8 38.1 + - - +
50A GLU* 3.0 33.5 + - - +
52A GLU* 1.3 75.3 - - - +
54A ALA* 1.3 59.5 + - - +
56A SER* 3.1 5.7 + - - -
57A CYS* 2.8 40.8 + - - +
60A GLN 6.0 0.2 - - - -
62A SER* 5.3 3.1 - - - -
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Residues in contact with ALA 54 (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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50A GLU 2.9 12.4 + - - +
51A LEU* 3.2 12.8 + - + +
53A LYS* 1.3 78.9 - - - +
55A LEU* 1.3 61.6 + - + +
56A SER 3.5 0.2 + - - -
57A CYS 4.7 3.4 - - - -
58A PRO* 3.7 15.1 - - - +
60A GLN 5.5 0.4 - - - -
62A SER* 3.5 26.9 - - - +
123A ASN* 3.8 23.8 - - - +
124A PRO* 5.3 0.2 - - + -
125A TYR* 3.4 22.9 - - + -
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Residues in contact with LEU 55 (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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51A LEU* 3.0 35.7 + - + +
52A GLU* 4.0 7.9 - - + +
54A ALA* 1.3 77.2 - - - +
56A SER* 1.3 61.5 + - - +
58A PRO* 3.9 12.4 - - - +
92A TRP* 3.7 58.6 - - + +
124A PRO* 3.9 15.9 - - + -
125A TYR* 3.9 21.8 + - + +
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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 GLU* 2.6 26.4 + - - +
53A LYS* 3.1 9.5 + - - -
55A LEU* 1.3 78.9 - - - +
57A CYS* 1.3 69.9 + - - +
58A PRO* 3.3 10.5 - - - +
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Residues in contact with CYS 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 LYS* 2.8 19.3 + - - +
54A ALA 3.9 4.2 - - - +
56A SER* 1.3 94.1 - - - +
58A PRO* 1.3 66.7 - - - +
59A GLY 3.2 2.5 - - - -
60A GLN* 3.2 56.3 + - + +
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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