Contacts of the helix formed by residues 42 - 53 (chain A) in PDB entry 1MK0
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 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A TYR* 4.2 8.5 - - - -
40A HIS* 2.9 21.0 + - - -
41A SER* 1.3 80.2 + - - +
43A ILE* 1.3 56.6 + - - +
44A LYS* 3.3 4.7 + - - +
45A LEU* 3.1 19.3 + - - +
46A GLN* 2.9 28.1 + - - +
89A TYR 2.7 28.3 + - - -
91A ILE* 3.7 13.1 - - - +
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Residues in contact with ILE 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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40A HIS 4.7 1.7 + - - -
41A SER 3.8 3.8 + - - -
42A SER* 1.3 72.1 - - - +
44A LYS* 1.3 71.6 + - + +
46A GLN* 3.6 8.6 - - + +
47A ARG* 2.8 67.5 + - + +
91A ILE* 4.4 9.9 - - + +
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Residues in contact with LYS 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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42A SER* 3.1 4.0 - - - +
43A ILE* 1.3 86.8 - - + +
45A LEU* 1.3 65.3 + - - +
47A ARG* 3.4 12.5 + - - +
48A SER* 3.1 18.7 + - - -
85A LYS 2.7 29.7 + - - -
88A GLY 3.0 18.5 + - - +
89A TYR* 3.5 27.1 - - + -
90A ASN 2.8 26.2 + - - -
91A ILE* 4.1 10.7 - - + +
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Residues in contact with LEU 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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8A ILE* 5.0 10.1 - - + -
17A TYR* 4.4 18.8 - - + -
31A HIS* 4.8 4.3 - - - +
35A LEU* 4.0 20.2 - - + -
40A HIS* 3.7 29.8 - - + +
42A SER* 3.1 21.2 + - - +
44A LYS* 1.3 73.2 - - - +
46A GLN* 1.3 61.1 + - - +
48A SER* 3.3 2.6 + - - -
49A PHE* 2.9 30.7 + - - +
56A PHE* 3.6 37.9 - - + -
89A TYR* 3.7 26.4 - - + -
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Residues in contact with GLN 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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35A LEU* 2.9 37.0 + - + +
38A GLY* 3.2 24.3 - - - +
39A CYS 3.4 0.2 + - - -
40A HIS* 3.0 36.8 + - + +
42A SER 2.9 17.5 + - - +
43A ILE* 3.6 10.3 - - + +
45A LEU* 1.3 77.6 - - - +
47A ARG* 1.3 58.0 + - + +
49A PHE* 3.3 2.5 + - - -
50A ASN* 2.8 64.9 + - - +
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Residues in contact with ARG 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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43A ILE* 2.8 60.4 + - + +
44A LYS* 3.7 11.2 - - - +
45A LEU 3.3 0.2 - - - -
46A GLN* 1.3 78.1 - - + +
48A SER* 1.3 62.5 + - - +
50A ASN* 3.2 11.2 + - - +
51A LYS* 3.2 34.2 + - - +
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Residues in contact with SER 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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10A ASN* 3.0 28.8 + - - -
13A ASN* 5.1 0.5 + - - -
44A LYS 3.1 10.8 + - - -
45A LEU 3.7 7.2 - - - -
47A ARG* 1.3 79.7 - - - +
49A PHE* 1.3 59.1 + - - +
51A LYS* 3.1 5.2 + - - -
52A HIS* 2.9 43.1 + - - +
56A PHE* 3.6 7.8 - - - -
89A TYR* 3.3 19.2 + - - -
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Residues in contact with PHE 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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32A PHE* 4.3 10.1 - + + -
35A LEU* 3.6 58.1 - - + -
36A GLU* 3.7 28.3 - - + -
45A LEU 2.9 17.7 + - - +
46A GLN* 3.7 6.1 - - - +
48A SER* 1.3 74.2 - - - +
50A ASN* 1.3 67.2 + - - +
53A GLY* 2.7 45.4 + - - +
54A ASN* 3.6 27.6 - - + -
56A PHE* 4.4 7.8 - + + -
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Residues in contact with ASN 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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35A LEU 4.6 0.9 - - - +
38A GLY* 5.4 0.7 - - - -
46A GLN* 2.8 55.7 + - - +
47A ARG* 3.6 10.6 - - - +
48A SER 3.2 0.4 - - - -
49A PHE* 1.3 81.7 - - - +
51A LYS* 1.3 60.9 + - + +
53A GLY 5.0 0.2 + - - -
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Residues in contact with LYS 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 ARG* 3.2 18.6 + - - +
48A SER* 3.1 10.1 + - - +
50A ASN* 1.3 81.7 - - + +
52A HIS* 1.3 82.6 + - + +
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Residues in contact with HIS 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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10A ASN* 4.2 6.6 + - - -
12A LEU* 3.6 26.0 - - + +
13A ASN* 5.5 4.2 + - - -
48A SER* 2.9 36.6 + - - +
51A LYS* 1.3 103.4 + - + +
53A GLY* 1.3 63.4 + - - +
54A ASN 3.8 0.3 + - - -
55A VAL* 3.6 33.7 - - + +
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Residues in contact with GLY 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 PHE* 2.7 43.5 + - - -
50A ASN 4.7 0.2 - - - -
51A LYS 3.9 0.2 - - - -
52A HIS* 1.3 76.5 - - - +
54A ASN* 1.3 58.3 + - - -
55A VAL* 3.0 10.0 + - - +
56A PHE* 3.5 15.6 - - - -
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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