Contacts of the helix formed by residues 47 - 51 (chain A) in PDB entry 1K89
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 LEU 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A TYR* 3.3 0.6 + - - -
42A TYR* 3.1 50.6 + - + +
45A VAL* 3.1 7.2 - - + -
46A ALA* 1.3 77.9 - - - +
48A LEU* 1.3 65.4 + - + +
50A ARG* 3.3 13.3 + - - +
51A MET* 3.0 32.5 + - + +
435A PHE* 4.0 11.4 - - + -
439A ALA* 3.7 29.8 - - + -
442A MET* 3.8 41.1 - - + -
443A MET* 4.7 8.3 - - - -
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Residues in contact with LEU 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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3A TYR* 3.1 35.0 + - + +
4A VAL* 4.0 36.1 - - + -
7A VAL* 3.9 16.6 - - + -
29A LEU* 4.4 26.2 - - + -
32A LEU* 5.3 0.7 - - + -
36A VAL* 4.4 8.3 - - + -
42A TYR* 5.9 1.6 - - + -
47A LEU* 1.3 78.4 - - + +
49A GLU* 1.3 65.1 - - - +
51A MET* 3.3 9.2 + - + +
52A VAL* 3.2 29.6 + - - +
435A PHE* 3.9 31.6 - - + -
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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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3A TYR* 2.6 33.7 + - - -
6A ARG* 3.1 34.4 + - - +
7A VAL* 4.1 12.6 - - + -
10A GLU* 4.5 12.3 - - - +
43A GLU 5.2 0.9 - - - +
46A ALA* 3.1 26.0 - - + +
48A LEU* 1.3 75.2 - - - +
50A ARG* 1.3 63.3 + - + +
52A VAL* 3.5 17.9 - - - +
53A ILE* 3.8 16.3 - - - +
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Residues in contact with ARG 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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45A VAL* 2.9 40.3 + - - +
46A ALA* 3.0 17.6 + - + +
47A LEU* 3.5 13.5 - - - +
49A GLU* 1.3 79.5 - - - +
51A MET* 1.3 62.4 + - - +
53A ILE* 3.1 25.3 + - - +
442A MET* 3.9 29.4 + - + +
443A MET* 5.3 0.8 - - - -
446A GLY 3.3 15.2 + - - -
447A ILE* 3.1 29.4 - - - +
449A TRP* 2.8 55.6 + - - +
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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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29A LEU* 5.8 2.9 - - + -
47A LEU* 3.0 31.7 + - + +
48A LEU* 3.3 11.8 + - + +
50A ARG* 1.3 77.0 - - - +
52A VAL* 1.3 64.1 + - + +
53A ILE 3.1 1.4 - - - +
81A PHE* 3.3 20.3 - - - +
82A ASN* 4.7 11.7 + - - +
108A PHE* 4.0 10.8 - - + -
112A PHE* 3.9 30.5 - - + -
435A PHE* 3.7 29.4 - - + -
438A ILE* 4.4 21.8 - - + -
439A ALA 5.5 1.1 - - - -
442A MET* 3.9 21.3 - - - +
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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