Contacts of the helix formed by residues 67 - 87 (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 ASN 67 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J TYR* 3.2 9.6 - - - -
27J HIS* 3.7 13.5 - - + +
28J ALA* 5.5 0.2 - - - -
61J ASN* 5.4 0.6 + - - +
63J ASP* 5.8 1.6 + - - +
65J ALA 3.9 0.8 - - - -
66J VAL* 1.3 74.2 - - - +
68J PHE* 1.3 59.8 + - - +
69J GLN* 3.0 10.6 + - - +
70J GLU* 2.7 39.0 + - - +
71J PHE* 2.8 26.5 + - - +
68K THR* 5.6 7.6 - - + -
81K MET* 3.4 32.5 - - - +
85K ARG* 3.3 27.2 - - - +
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Residues in contact with PHE 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J ILE* 4.2 0.4 - - + -
13J ILE* 3.6 32.3 - - + -
16J TYR* 3.5 46.4 + + + -
27J HIS 4.6 0.8 + - - -
67J ASN* 1.3 77.0 - - - +
69J GLN* 1.3 64.5 + - - +
71J PHE* 3.0 32.4 + + - +
72J LEU* 3.0 33.9 + - + +
87L THR* 3.7 18.2 - - + -
88L TRP* 3.9 13.7 - + + -
91L HIS* 3.7 48.7 - + + +
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Residues in contact with GLN 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J ASN* 3.0 16.4 + - - +
68J PHE* 1.3 78.4 - - - +
70J GLU* 1.3 62.4 + - + +
72J LEU* 3.3 23.5 + - + +
73J ILE* 3.8 8.1 + - - +
81K MET* 4.0 21.0 + - + +
84K ALA* 5.5 4.2 - - - +
85K ARG* 2.7 51.0 + - - +
88L TRP* 3.7 29.2 - - + -
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Residues in contact with GLU 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58J LEU* 3.1 30.7 - - - +
60J ILE* 2.9 26.0 + - + -
61J ASN* 2.9 7.3 - - - +
65J ALA 3.1 3.5 - - - +
66J VAL* 3.2 7.6 - - + -
67J ASN* 2.7 42.3 + - - +
69J GLN* 1.3 75.9 - - + +
71J PHE* 1.3 64.3 + - - +
73J ILE* 3.0 29.3 + - + +
2521J CA 2.5 30.3 - - - -
81K MET* 3.2 21.6 - - + +
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Residues in contact with PHE 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J ILE* 3.7 25.6 - - + -
15J VAL* 4.3 13.9 - - + -
16J TYR* 3.6 28.3 - + + -
34J LEU* 5.7 2.2 - - + -
37J LEU* 3.9 24.7 - - + -
58J LEU* 5.4 0.7 - - + -
66J VAL* 3.7 11.6 - - + +
67J ASN 2.8 14.2 + - - +
68J PHE* 3.0 27.3 + + - +
70J GLU* 1.3 75.4 - - - +
72J LEU* 1.3 59.7 + - + +
74J LEU* 3.0 45.6 + - + +
75J VAL* 3.1 33.9 + - + +
8L LEU* 4.3 13.5 - - + -
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Residues in contact with LEU 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J ILE* 4.5 2.9 - - + -
68J PHE* 3.0 52.2 + - + +
69J GLN* 3.5 16.2 - - + +
70J GLU 3.1 0.6 - - - -
71J PHE* 1.3 74.3 - - - +
73J ILE* 1.3 65.0 + - - +
75J VAL* 3.8 21.1 - - + +
76J ILE* 2.9 31.8 + - + +
84L ALA* 3.9 34.8 - - + +
87L THR* 4.0 16.6 - - + -
88L TRP* 4.2 12.6 - - + +
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Residues in contact with ILE 73 (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* 3.8 40.6 - - + -
73I ILE* 4.7 11.7 - - + -
57J GLU* 4.9 5.2 - - + +
58J LEU* 3.7 18.4 - - + +
60J ILE* 3.8 34.5 - - + -
69J GLN 3.8 5.8 + - - +
70J GLU* 3.0 20.5 + - - +
72J LEU* 1.3 78.3 - - - +
74J LEU* 1.3 61.9 + - - +
76J ILE* 3.4 2.6 + - + +
77J LYS* 3.0 37.0 + - + +
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Residues in contact with LEU 74 (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* 4.8 2.9 - - + -
37J LEU* 3.9 28.0 - - + -
38J LEU* 3.9 20.6 - - + -
46J ILE* 4.2 0.9 - - + -
54J TRP* 3.7 39.0 - - + -
58J LEU* 3.7 24.8 - - + +
71J PHE* 3.0 24.5 + - + +
73J ILE* 1.3 77.2 - - - +
75J VAL* 1.3 58.2 + - + +
77J LYS* 3.2 1.0 + - - -
78J MET* 2.8 52.8 + - + +
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Residues in contact with VAL 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J ILE* 3.9 34.1 - - + -
71J PHE* 3.1 47.8 + - + +
72J LEU* 3.8 15.0 - - + +
73J ILE 3.3 0.2 - - - -
74J LEU* 1.3 75.2 - - - +
76J ILE* 1.3 60.6 + - + +
78J MET* 3.4 8.0 + - - +
79J GLY* 2.8 27.2 + - - -
8L LEU* 4.5 7.9 - - + -
12L ILE* 4.5 11.6 - - + +
15L ILE* 5.7 2.7 - - + -
80L ILE* 4.1 4.6 - - + +
84L ALA* 6.3 1.8 - - + -
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Residues in contact with ILE 76 (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* 3.8 20.0 - - + +
61I ASN* 3.7 34.8 - - + -
69I GLN* 5.9 1.3 - - - +
72J LEU* 2.9 24.9 + - + +
73J ILE* 3.7 4.0 - - + +
75J VAL* 1.3 76.2 - - + +
77J LYS* 1.3 57.5 + - - +
79J GLY 3.1 1.4 + - - -
80J VAL* 2.9 30.8 + - + +
80L ILE* 3.5 24.4 - - + +
81L MET* 4.0 22.2 - - + -
84L ALA* 3.7 29.8 - - + -
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Residues in contact with LYS 77 (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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56I LYS 5.3 4.9 + - - -
57I GLU* 5.1 3.4 + - - +
59I ASP 5.2 1.6 - - - -
60I ILE* 3.7 49.4 - - + +
62I THR* 5.9 3.6 - - - -
46J ILE* 4.6 3.5 - - + +
49J LYS* 5.2 2.2 - - - +
54J TRP* 4.0 23.1 - - + -
57J GLU* 2.6 32.0 + - - +
73J ILE* 3.0 19.2 + - + +
74J LEU 3.9 2.9 - - - +
76J ILE* 1.3 76.1 - - - +
78J MET* 1.3 59.0 + - - +
80J VAL* 3.5 6.0 + - - +
81J ALA* 2.9 30.8 + - - +
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Residues in contact with MET 78 (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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41J GLU 4.2 2.2 - - - +
42J SER* 3.9 28.5 - - - -
43J PRO* 4.1 12.8 - - + -
45J TYR* 4.8 1.4 + - - -
46J ILE* 3.8 26.7 - - + -
74J LEU* 2.8 40.9 + - + +
75J VAL* 3.7 2.2 - - - +
77J LYS* 1.3 77.7 - - - +
79J GLY* 1.3 56.6 + - - +
81J ALA* 3.9 0.7 - - - +
82J ALA* 3.0 31.2 + - - +
8L LEU* 3.7 31.2 - - + -
9L GLU* 4.9 4.3 - - + -
12L ILE* 3.5 27.7 - - + +
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Residues in contact with GLY 79 (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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75J VAL 2.8 18.7 + - - -
76J ILE 3.1 3.3 + - - -
78J MET* 1.3 73.4 - - - +
80J VAL* 1.3 56.8 + - - +
82J ALA* 3.2 2.4 + - - +
83J HIS* 2.9 26.5 + - - +
12L ILE* 4.0 19.5 - - - +
16L ILE* 4.2 0.7 - - - +
76L PHE* 3.4 17.2 - - - -
80L ILE* 3.7 11.4 - - - -
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Residues in contact with VAL 80 (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 5.4 0.7 - - - +
61I ASN* 4.0 17.7 - - - +
62I THR* 3.8 17.9 - - - +
76J ILE* 2.9 24.4 + - + +
77J LYS* 3.9 6.1 - - - +
79J GLY* 1.3 76.8 - - - +
81J ALA* 1.3 57.5 + - - +
83J HIS* 3.4 3.1 + - - +
84J LYS* 3.0 35.0 + - + +
76L PHE* 3.9 8.5 - - + -
77L GLU* 3.8 26.0 - - + +
80L ILE* 4.1 20.0 - - + -
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Residues in contact with ALA 81 (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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45J TYR* 3.6 27.4 - - + -
46J ILE* 4.2 9.2 - - + -
77J LYS 2.9 17.8 + - - +
78J MET 4.1 2.5 - - - +
80J VAL* 1.3 76.4 - - - +
82J ALA* 1.3 63.9 + - - +
84J LYS* 3.2 11.7 + - - +
85J LYS* 3.0 28.1 + - + +
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Residues in contact with ALA 82 (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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45J TYR* 3.5 17.6 + - - +
78J MET 3.0 18.6 + - - +
79J GLY 3.7 0.4 - - - +
81J ALA* 1.3 75.5 - - - +
83J HIS* 1.3 58.5 + - - +
85J LYS* 3.2 4.9 + - - +
86J SER* 2.9 30.0 + - - -
12L ILE* 3.7 12.8 - - + -
16L ILE* 3.5 20.0 - - + +
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Residues in contact with HIS 83 (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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79J GLY 2.9 17.2 + - - +
80J VAL 3.6 4.1 + - - +
82J ALA* 1.3 73.6 - - - +
84J LYS* 1.3 70.1 + - - +
86J SER* 3.2 20.0 + - - -
87J HIS* 3.4 23.4 + + - -
16L ILE* 3.5 20.8 - - + +
19L PHE* 4.5 5.0 - + - -
30L ASP* 2.8 42.9 + - - -
76L PHE* 3.5 52.8 - + + +
77L GLU* 4.8 10.5 + - - -
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Residues in contact with LYS 84 (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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80J VAL* 3.0 21.4 + - + +
81J ALA* 3.3 13.9 - - - +
83J HIS* 1.3 83.3 - - - +
85J LYS* 1.3 63.5 + - + +
87J HIS* 3.3 12.5 + - + +
88J GLU 3.1 28.2 + - - +
77L GLU* 5.3 7.9 - - - +
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Residues in contact with LYS 85 (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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45J TYR* 3.9 53.2 - - + +
48J LYS* 5.9 1.0 - - - +
81J ALA* 3.0 20.7 + - - +
82J ALA* 3.5 7.2 - - - +
83J HIS 3.2 0.2 - - - -
84J LYS* 1.3 77.7 - - + +
86J SER* 1.3 58.4 + - - +
87J HIS 3.0 0.2 - - - -
88J GLU* 2.9 30.0 + - - +
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Residues in contact with SER 86 (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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82J ALA 2.9 14.0 + - - -
83J HIS* 3.2 13.4 + - - -
85J LYS* 1.3 75.7 - - - +
87J HIS* 1.3 61.0 + - - +
88J GLU* 3.8 6.6 - - - +
16L ILE* 3.7 26.8 - - - +
17L ASN* 6.0 0.2 - - - -
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Residues in contact with HIS 87 (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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83J HIS* 3.4 28.2 + + - -
84J LYS* 3.3 10.4 + - + -
85J LYS 3.0 0.4 - - - -
86J SER* 1.3 81.7 + - - +
88J GLU* 1.3 79.8 + - + +
30L ASP* 3.1 36.0 + - + +
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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