Contacts of the helix formed by residues 67 - 87 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I TYR* 3.2 9.6 - - - -
27I HIS* 3.6 14.6 - - + +
28I ALA* 4.9 0.2 - - - +
61I ASN* 5.5 0.8 + - - +
63I ASP* 5.8 1.2 + - - -
65I ALA* 4.0 1.2 - - - +
66I VAL* 1.3 75.0 - - - +
68I PHE* 1.3 61.1 + - - +
69I GLN* 3.2 9.5 + - - +
70I GLU* 2.7 40.1 + - - +
71I PHE* 2.9 24.1 + - - +
68L THR* 5.5 7.6 - - + -
81L MET* 3.6 31.1 - - - +
85L ARG* 3.4 27.3 - - - +
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Residues in contact with PHE 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I ILE* 4.6 0.4 - - + -
13I ILE* 3.8 21.5 - - + -
16I TYR* 3.5 47.0 + + + -
27I HIS 4.6 0.4 + - - -
67I ASN* 1.3 78.0 - - - +
69I GLN* 1.3 64.6 + - - +
71I PHE* 3.1 22.9 + + - +
72I LEU* 3.0 42.7 + - + +
87K THR* 3.7 26.2 - - + -
88K TRP* 3.8 22.4 - + + -
91K HIS* 3.8 42.2 - + + +
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Residues in contact with GLN 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67I ASN* 3.2 14.1 - - - +
68I PHE* 1.3 79.6 - - - +
70I GLU* 1.3 64.0 + - + +
72I LEU* 3.2 26.3 + - + +
73I ILE* 3.7 8.0 + - - +
88K TRP* 3.8 28.3 - - + -
81L MET* 3.1 24.4 - - + +
84L ALA* 5.5 3.4 - - - +
85L ARG* 2.7 46.7 + - - +
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Residues in contact with GLU 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I LEU* 3.1 30.4 - - - +
60I ILE* 2.9 27.8 + - + +
61I ASN* 3.0 10.4 + - - +
65I ALA 3.2 3.6 - - - +
66I VAL* 3.2 7.9 - - + -
67I ASN* 2.7 48.2 + - - +
69I GLN* 1.3 75.7 - - + +
71I PHE* 1.3 67.1 + - - +
73I ILE* 3.0 29.3 + - - +
1521I CA 2.5 30.8 - - - -
81L MET* 4.5 4.0 - - - +
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Residues in contact with PHE 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I ILE* 3.5 29.8 - - + -
15I VAL* 4.2 17.0 - - + -
16I TYR* 3.6 27.6 - + + -
34I LEU* 5.8 1.8 - - + -
37I LEU* 3.9 28.7 - - + -
58I LEU* 5.2 0.7 - - + -
66I VAL* 3.6 11.3 - - + +
67I ASN 2.9 14.7 + - - +
68I PHE* 3.2 28.9 - + - +
70I GLU* 1.3 75.9 - - - +
72I LEU* 1.3 54.0 + - - -
74I LEU* 3.0 41.9 + - + +
75I VAL* 3.1 34.0 + - + +
8K LEU* 4.4 8.1 - - + -
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Residues in contact with LEU 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I ILE* 4.6 2.2 - - + -
68I PHE* 3.0 53.8 + - + +
69I GLN* 3.4 16.2 - - + +
70I GLU 3.1 0.8 - - - -
71I PHE* 1.3 75.6 - - - +
73I ILE* 1.3 58.2 + - - +
75I VAL* 3.6 22.4 - - + +
76I ILE* 2.9 35.0 + - + +
84K ALA* 3.9 33.4 - - + +
87K THR* 4.1 16.2 - - + -
88K TRP* 4.2 11.9 - - + -
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Residues in contact with ILE 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I GLU* 4.9 5.8 - - + +
58I LEU* 3.6 18.2 - - + +
60I ILE* 3.9 33.0 - - + -
69I GLN 4.1 6.5 - - - +
70I GLU* 3.0 21.1 + - - +
72I LEU* 1.3 79.0 - - - +
74I LEU* 1.3 63.2 + - - +
76I ILE* 3.3 4.1 + - + +
77I LYS* 3.0 36.1 + - + +
60J ILE* 3.9 36.7 - - + +
73J ILE* 4.7 12.6 - - + -
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Residues in contact with LEU 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I LEU* 4.6 3.6 - - + -
37I LEU* 3.9 21.1 - - + -
38I LEU* 3.9 24.0 - - + -
46I ILE* 4.3 0.7 - - + -
54I TRP* 3.8 41.5 - - + -
58I LEU* 3.6 27.5 - - + +
71I PHE* 3.0 23.2 + - + +
73I ILE* 1.3 80.3 - - - +
75I VAL* 1.3 56.4 + - - +
77I LYS 3.3 0.7 + - - -
78I MET* 2.9 58.1 + - + +
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Residues in contact with VAL 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I ILE* 3.8 33.7 - - + -
71I PHE* 3.1 48.5 + - + +
72I LEU* 3.6 17.0 - - + +
73I ILE 3.2 0.4 - - - -
74I LEU* 1.3 75.4 - - + +
76I ILE* 1.3 59.7 + - + +
78I MET* 3.8 7.0 - - - +
79I GLY* 2.9 26.5 + - - -
8K LEU* 4.6 6.7 - - + -
12K ILE* 4.4 12.0 - - + +
15K ILE* 5.7 1.8 - - + -
80K ILE* 4.9 7.6 - - + +
84K ALA* 6.3 2.0 - - + -
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Residues in contact with ILE 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I LEU* 2.9 24.0 + - + +
73I ILE* 3.6 4.5 - - + +
75I VAL* 1.3 78.8 - - + +
77I LYS* 1.3 56.3 + - - +
79I GLY* 3.3 1.0 + - - -
80I VAL* 2.9 30.9 + - + +
60J ILE* 3.9 22.4 - - + +
61J ASN* 3.8 33.4 - - + -
69J GLN* 6.0 1.1 - - - +
80K ILE* 4.1 24.2 - - + +
81K MET* 4.4 19.3 - - + -
84K ALA* 3.9 27.6 - - + -
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Residues in contact with LYS 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I ILE* 4.7 3.3 - - + +
49I LYS* 5.2 2.0 - - - +
54I TRP* 4.0 24.0 - - + -
57I GLU* 3.3 28.7 - - - +
73I ILE* 3.0 24.3 + - + +
74I LEU 3.9 2.9 - - - +
76I ILE* 1.3 75.7 - - - +
78I MET* 1.3 58.4 - - - +
80I VAL* 3.5 5.4 + - - +
81I ALA* 3.0 29.5 + - - +
56J LYS 5.2 4.8 + - - -
57J GLU 5.6 0.6 + - - -
59J ASP 4.2 4.0 + - - -
60J ILE* 3.0 52.1 + - + +
62J THR* 4.9 7.3 - - - +
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Residues in contact with MET 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I GLU 4.2 4.0 - - - +
42I SER* 4.0 25.1 - - - -
43I PRO* 4.2 11.9 - - + -
45I TYR* 4.5 1.9 + - - -
46I ILE* 3.9 24.0 - - + -
74I LEU* 2.9 46.8 + - + +
75I VAL* 3.8 2.0 - - - +
77I LYS* 1.3 76.6 - - - +
79I GLY* 1.3 56.3 + - - +
81I ALA* 3.4 2.3 + - - +
82I ALA* 2.9 31.2 + - - +
8K LEU* 3.6 29.8 - - + -
9K GLU* 5.0 4.0 - - + -
12K ILE* 3.5 28.2 - - + +
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Residues in contact with GLY 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I VAL 2.9 17.4 + - - -
76I ILE 3.7 0.7 - - - -
78I MET* 1.3 74.5 - - - +
80I VAL* 1.3 65.0 + - - +
82I ALA* 3.4 1.4 + - - +
83I HIS 2.9 19.8 + - - -
12K ILE* 3.8 22.5 - - - +
16K ILE* 4.1 0.7 - - - +
76K PHE* 3.3 20.8 - - - -
80K ILE* 4.5 7.9 - - - -
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Residues in contact with VAL 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76I ILE* 2.9 26.3 + - + +
77I LYS* 3.9 5.6 - - - +
79I GLY* 1.3 76.2 - - - +
81I ALA* 1.3 63.1 + - - +
83I HIS* 3.3 3.1 + - - +
84I LYS* 3.1 28.8 + - + +
60J ILE 5.5 0.2 - - - +
61J ASN* 4.1 14.4 - - - +
62J THR* 3.9 15.9 - - - +
76K PHE* 3.9 8.3 - - + -
77K GLU* 3.8 27.3 - - + +
80K ILE* 3.9 24.2 - - + -
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Residues in contact with ALA 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I TYR* 3.7 25.8 - - + -
46I ILE* 4.3 8.3 - - + -
77I LYS 3.0 19.3 + - - +
78I MET 3.7 2.2 - - - +
80I VAL* 1.3 79.4 - - - +
82I ALA* 1.3 56.2 - - - +
84I LYS* 3.2 12.8 + - - +
85I LYS* 3.0 32.2 + - + +
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Residues in contact with ALA 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45I TYR* 3.4 18.1 + - - +
78I MET 2.9 21.1 + - - +
79I GLY 3.8 1.3 - - - +
81I ALA* 1.3 69.8 - - - +
83I HIS* 1.3 59.7 + - - +
85I LYS* 3.3 4.9 + - - +
86I SER* 2.9 29.6 + - - -
12K ILE* 3.9 10.8 - - + -
16K ILE* 3.6 20.6 - - + +
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Residues in contact with HIS 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I GLY 2.9 9.8 + - - +
80I VAL 3.7 3.2 + - - +
82I ALA* 1.3 75.8 - - - +
84I LYS* 1.3 69.2 + - - +
86I SER* 3.2 24.7 + - - -
87I HIS* 3.4 24.3 + + - -
16K ILE* 3.6 16.8 - - + +
19K PHE* 4.4 5.5 - + - -
30K ASP* 2.8 42.5 + - - -
76K PHE* 3.4 60.9 - + + +
77K GLU* 5.0 9.3 + - - -
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Residues in contact with LYS 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80I VAL* 3.1 20.3 + - + +
81I ALA* 3.3 13.7 - - - +
83I HIS* 1.3 82.2 + - - +
85I LYS* 1.3 63.0 + - + +
87I HIS* 3.4 29.1 + - + +
77K GLU* 5.2 8.3 - - - +
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Residues in contact with LYS 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45I TYR* 3.8 54.3 - - + +
48I LYS* 5.9 1.2 - - - +
81I ALA* 3.0 20.3 + - - +
82I ALA* 3.6 6.5 - - - +
83I HIS 3.3 0.2 - - - -
84I LYS* 1.3 72.4 - - + +
86I SER* 1.3 59.1 + - - +
87I HIS* 2.9 16.4 + - - -
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Residues in contact with SER 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I ALA 2.9 15.8 + - - -
83I HIS* 3.2 14.1 + - - -
85I LYS* 1.3 75.2 - - - +
87I HIS* 1.3 61.6 + - - +
16K ILE* 3.8 25.8 - - - +
17K ASN* 6.0 0.7 - - - -
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Residues in contact with HIS 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83I HIS* 3.4 28.4 + + - -
84I LYS* 3.4 21.9 + - + +
85I LYS 3.0 6.0 - - - -
86I SER* 1.3 81.9 + - - +
30K ASP* 3.3 34.8 + - + +
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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
------------------------------------------------------------
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