Contacts of the helix formed by residues 50 - 59 (chain J) in PDB entry 1XK4
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 50 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38J LEU* 4.9 0.2 - - - -
47J ARG 2.9 14.1 + - - -
48J LYS 3.1 2.4 - - - -
49J LYS* 1.3 81.9 - - - +
51J ALA* 1.3 59.8 + - - -
52J ASP 3.4 3.1 - - - -
53J VAL* 3.4 3.2 + - - -
54J TRP* 3.1 31.3 + - - -
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Residues in contact with ALA 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J ARG* 5.2 4.3 - - + +
34J LEU* 4.2 3.4 - - + +
35J LYS* 3.8 47.3 - - + +
38J LEU* 3.7 17.6 - - + +
47J ARG 4.7 0.8 + - - -
50J GLY* 1.3 68.7 - - - -
52J ASP* 1.3 65.4 + - - +
54J TRP* 3.4 1.2 + - - +
55J PHE* 2.8 30.9 + - - +
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Residues in contact with ASP 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J ARG* 3.3 41.1 + - - +
50J GLY 3.4 0.6 - - - -
51J ALA* 1.3 79.2 - - - +
53J VAL* 1.3 66.2 + - + +
55J PHE* 3.3 2.5 + - - +
56J LYS* 3.0 24.8 + - - +
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Residues in contact with VAL 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49J LYS* 3.5 46.9 - - + +
50J GLY* 3.4 2.8 + - - -
51J ALA 3.3 0.4 - - - -
52J ASP* 1.3 75.6 - - + +
54J TRP* 1.3 65.5 + - - +
56J LYS* 3.5 6.2 + - - +
57J GLU* 3.1 24.3 + - + +
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Residues in contact with TRP 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J LEU* 4.2 4.5 - - + -
38J LEU* 3.9 27.1 - - + -
46J ILE* 2.9 46.9 + - + +
47J ARG 5.2 0.7 - - - -
49J LYS* 3.3 34.8 - - + +
50J GLY 3.1 26.8 + - - +
51J ALA 3.9 3.1 - - - +
53J VAL* 1.3 75.7 - - - +
55J PHE* 1.3 64.6 + - - +
57J GLU* 3.1 24.3 + - - +
58J LEU* 2.8 52.6 + - + +
74J LEU* 3.7 35.0 - - + -
77J LYS* 4.0 27.4 - - + -
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Residues in contact with PHE 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J VAL 3.9 2.5 - - - -
30J TYR 3.8 5.4 - - - -
31J ARG* 3.5 71.6 - - + +
34J LEU* 3.6 22.6 - - + +
51J ALA 2.8 18.5 + - - +
52J ASP* 3.3 4.7 + - - +
54J TRP* 1.3 77.9 - - - +
56J LYS* 1.3 58.9 + - - +
58J LEU* 3.8 1.9 - - - +
59J ASP* 2.9 46.7 + - + +
64J GLY* 3.5 33.2 - - - -
65J ALA* 3.7 4.9 - - - -
66J VAL* 3.8 17.3 - - + -
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Residues in contact with LYS 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I LYS* 5.2 5.4 + - - -
31J ARG* 5.9 1.3 - - - +
52J ASP 3.0 15.8 + - - +
53J VAL* 3.9 6.3 - - - +
55J PHE* 1.3 80.3 - - - +
57J GLU* 1.3 64.5 + - - +
59J ASP* 3.7 13.5 + - - +
62J THR* 6.0 0.9 - - - +
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Residues in contact with GLU 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60I ILE* 6.3 0.4 - - + -
77I LYS* 5.6 0.5 + - - -
49J LYS* 2.9 33.4 + - - +
53J VAL* 3.1 18.7 + - + +
54J TRP* 3.5 16.5 - - + +
56J LYS* 1.3 78.1 - - - +
58J LEU* 1.3 63.0 + - + +
60J ILE* 3.5 18.7 - - - +
73J ILE* 4.9 5.8 - - + +
77J LYS* 2.6 42.2 + - - +
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Residues in contact with LEU 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J LEU* 4.1 28.5 - - + -
54J TRP* 2.8 42.7 + - + +
55J PHE 4.0 0.4 - - - +
57J GLU* 1.3 73.0 - - + +
59J ASP* 1.3 59.6 + - - +
60J ILE* 2.9 14.3 + - - +
66J VAL* 3.9 24.2 - - + -
70J GLU* 3.1 29.1 - - - +
71J PHE* 5.4 0.9 - - - -
73J ILE* 3.7 22.9 - - + -
74J LEU* 3.7 42.8 - - + +
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Residues in contact with ASP 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I LYS* 4.2 2.1 + - - -
55J PHE* 2.9 32.2 + - + +
56J LYS* 3.7 10.6 + - - +
57J GLU 3.6 1.4 - - - -
58J LEU* 1.3 73.9 - - - +
60J ILE* 1.3 61.2 + - - +
61J ASN* 3.2 3.5 - - - +
62J THR* 3.1 22.5 + - + +
63J ASP* 3.0 8.7 + - - +
64J GLY* 2.7 28.9 + - - -
65J ALA 2.9 14.3 - - - +
66J VAL* 4.5 1.1 - - + +
70J GLU* 3.7 2.7 - - - -
2521J CA 2.3 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