Contacts of the helix formed by residues 53 - 58 (chain A) in PDB entry 1LIK
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 ARG 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A GLU* 5.2 5.3 + - - -
37A PHE* 3.3 26.8 - - + -
49A PRO 4.8 0.6 + - - -
50A GLU 4.4 5.7 + - - +
51A GLN 3.0 0.8 - - - -
52A MET* 1.3 77.2 - - - +
54A ILE* 1.3 57.9 + - - +
56A SER* 3.0 18.6 + - - +
57A THR* 2.3 46.8 + - + +
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Residues in contact with ILE 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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33A PHE* 4.2 13.2 - - + -
37A PHE* 3.0 50.0 - - + -
39A LEU* 5.0 5.6 - - + -
51A GLN* 2.8 26.9 + - + +
53A ARG* 1.3 76.8 - - - +
55A TYR* 1.3 118.2 + - + +
57A THR* 2.9 14.1 + - - -
58A LEU* 3.1 25.6 + - + +
128A ALA* 4.5 13.0 - - + -
130A LEU* 5.5 1.8 - - + -
139A CYS* 4.7 12.8 - - + -
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Residues in contact with TYR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 4.8 16.7 - - + +
47A ALA* 3.5 7.6 - - + +
52A MET* 3.7 30.3 - - + +
53A ARG 3.1 1.6 + - - -
54A ILE* 1.3 108.8 - - + +
56A SER* 1.3 60.4 + - - +
58A LEU* 4.0 10.3 - - + +
59A ASP* 5.0 2.8 + - - +
126A THR* 3.7 34.8 - - + +
128A ALA* 3.6 32.8 - - + -
139A CYS 3.0 21.3 + - - -
140A THR 3.2 22.0 - - - -
141A HIS* 4.0 14.6 - - + -
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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 4.6 3.1 + - - -
53A ARG* 3.0 12.8 + - - +
55A TYR* 1.3 76.0 - - - +
57A THR* 1.3 55.9 + - - +
58A LEU 2.5 17.4 + - - -
59A ASP* 3.0 23.1 + - - +
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Residues in contact with THR 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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33A PHE* 4.5 4.5 - - + -
36A GLU* 5.7 1.1 - - - +
37A PHE* 3.9 22.0 - - + -
53A ARG* 2.3 57.9 + - + +
54A ILE* 2.9 9.4 + - - -
56A SER* 1.3 70.9 - - - +
58A LEU* 1.3 55.2 + - - -
59A ASP 3.4 0.7 - - - -
60A GLN* 3.0 40.2 + - - +
61A PHE* 3.5 2.1 - - - -
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Residues in contact with LEU 58 (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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25A LEU* 4.1 34.8 - - + +
27A ALA* 4.3 17.5 - - + -
29A VAL* 4.8 2.9 - - + -
33A PHE* 3.3 37.7 - - + -
54A ILE* 3.1 22.2 + - + +
55A TYR* 4.0 10.5 - - - +
56A SER 2.5 6.3 + - - -
57A THR* 1.3 70.7 - - - +
59A ASP* 1.3 52.7 + - - +
60A GLN 3.1 2.7 - - - -
61A PHE* 2.8 40.6 + - + +
63A PRO* 3.3 16.2 - - + +
128A ALA* 4.8 7.9 - - + -
130A LEU* 3.9 15.0 - - + -
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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