Contacts of the helix formed by residues 75 - 95 (chain K) 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 SER 75 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63J ASP* 5.3 0.5 - - - +
19K PHE* 3.8 1.8 - - - -
30K ASP 4.6 0.9 - - - -
31K THR* 4.3 14.9 - - - +
73K GLN* 3.9 1.4 + - - +
74K LEU* 1.3 74.7 - - - +
76K PHE* 1.3 68.0 + - - +
77K GLU* 3.5 17.2 + - - +
78K GLU* 3.0 37.0 + - - +
79K PHE* 2.9 21.0 + - - +
3521K CA 4.4 0.6 - - - -
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Residues in contact with PHE 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I GLY* 3.3 28.5 - - - -
80I VAL* 3.9 10.3 - - + -
83I HIS* 3.4 46.1 - + + +
12K ILE* 5.8 0.2 - - + -
15K ILE* 4.0 17.0 - - + -
16K ILE* 3.7 32.1 - - + -
19K PHE* 3.4 37.6 - + + -
30K ASP 4.5 2.0 + - - -
75K SER* 1.3 74.3 - - - +
77K GLU* 1.3 59.1 + - - +
79K PHE* 3.1 6.0 + + - +
80K ILE* 2.8 60.4 + - + +
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Residues in contact with GLU 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I VAL* 3.8 24.5 - - + +
83I HIS* 5.0 9.1 + - - -
84I LYS* 5.2 7.6 - - - +
61J ASN* 2.7 49.2 + - - +
62J THR* 3.8 19.8 + - - +
63J ASP* 4.2 7.0 - - + -
75K SER* 3.2 17.8 - - - +
76K PHE* 1.3 83.6 + - - +
78K GLU* 1.3 56.9 + - - +
80K ILE* 3.2 18.9 - - - +
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Residues in contact with GLU 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61J ASN* 4.0 5.6 - - - +
63J ASP* 4.1 9.9 - - + +
66K LEU* 3.3 36.3 - - - +
67K ASP* 3.9 0.9 - - - -
68K THR* 3.1 25.3 + - - +
69K ASN* 3.1 15.6 + - - +
73K GLN 3.0 5.5 - - - +
74K LEU* 3.2 8.2 - - + +
75K SER* 3.0 31.3 + - - +
77K GLU* 1.3 77.6 - - - +
79K PHE* 1.3 63.3 + - - +
81K MET* 3.3 20.3 + - - +
3521K CA 2.4 30.4 - - - -
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Residues in contact with PHE 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I LEU* 5.0 3.1 - - + -
15K ILE* 4.1 12.1 - - + -
18K THR* 6.0 0.7 - - + -
19K PHE* 3.6 30.7 - + + -
32K LEU* 3.7 22.9 - - + -
37K PHE* 4.4 18.6 - + - -
40K LEU* 3.9 30.3 - - + -
66K LEU* 5.3 0.4 - - - -
74K LEU* 4.4 11.4 - - + +
75K SER 2.9 16.9 + - - +
76K PHE* 3.5 13.0 - + - +
78K GLU* 1.3 76.2 - - - +
80K ILE* 1.3 66.8 + - - +
82K LEU* 3.0 21.4 + - + +
83K MET* 3.4 49.3 + - + +
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Residues in contact with ILE 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I VAL* 4.9 8.3 - - + +
76I ILE* 4.1 32.5 - - + +
79I GLY* 4.5 10.5 - - - -
80I VAL* 3.9 20.9 - - + -
61J ASN* 4.2 2.0 - - + -
12K ILE* 6.4 1.3 - - + -
15K ILE* 4.3 20.6 - - + -
76K PHE* 2.8 45.0 + - + +
77K GLU 3.2 18.4 - - - +
79K PHE* 1.3 74.2 - - - +
81K MET* 1.3 62.8 + - - +
83K MET* 3.2 12.2 + - + +
84K ALA* 3.0 23.3 + - - +
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Residues in contact with MET 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76I ILE* 4.4 19.7 - - + -
60J ILE* 4.6 2.5 - - + -
61J ASN* 3.4 32.8 - - + +
67J ASN* 3.4 28.7 - - - +
69J GLN* 4.0 22.2 - - + +
70J GLU* 3.2 35.4 - - + +
66K LEU* 4.1 10.1 - - + -
78K GLU 3.3 12.3 + - - +
79K PHE 3.1 0.2 - - - -
80K ILE* 1.3 83.8 - - + +
82K LEU* 1.3 56.2 + - - +
84K ALA* 3.4 5.1 + - - +
85K ARG* 2.9 37.4 + - - +
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Residues in contact with LEU 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K PHE* 3.9 32.8 - - + -
45K LEU* 4.3 14.4 - - + -
49K LEU* 4.8 8.7 - - + -
62K ILE* 4.4 16.6 - - + -
66K LEU* 3.8 21.8 - - + +
79K PHE* 3.0 14.3 + - + +
81K MET* 1.3 78.9 - - - +
83K MET* 1.3 76.0 + - + +
85K ARG* 3.3 11.7 + - + +
86K LEU* 2.9 47.8 + - + +
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Residues in contact with MET 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I LEU* 4.0 26.5 - - + -
9I LEU* 4.1 22.2 - - + +
15K ILE* 3.8 16.2 - - + -
45K LEU* 4.2 14.8 - - + -
79K PHE* 3.5 47.6 - - + +
80K ILE* 3.2 17.8 + - + +
82K LEU* 1.3 99.7 - - + +
84K ALA* 1.3 61.3 + - - +
86K LEU* 3.3 7.4 + - + +
87K THR* 2.8 30.1 + - - -
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Residues in contact with ALA 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I LEU* 3.9 23.2 - - + +
75I VAL* 6.3 2.5 - - + -
76I ILE* 3.9 29.4 - - + -
69J GLN* 5.5 5.2 - - - +
80K ILE* 3.0 15.4 + - - +
81K MET* 3.8 7.0 - - - +
83K MET* 1.3 77.0 - - - +
85K ARG* 1.3 62.1 + - + +
87K THR* 3.3 7.4 + - - -
88K TRP* 3.0 23.7 + - - +
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Residues in contact with ARG 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J ASN* 3.3 25.3 - - - +
69J GLN* 2.7 36.3 + - - +
62K ILE* 6.4 0.4 - - - +
65K ASP* 5.4 11.3 + - - +
66K LEU* 3.7 28.7 - - - +
81K MET* 2.9 24.4 + - - +
82K LEU* 3.3 15.1 + - + +
84K ALA* 1.3 75.9 - - - +
86K LEU* 1.3 62.1 + - + +
88K TRP* 3.5 8.8 + - - +
89K ALA* 3.0 26.9 + - - +
88L TRP* 4.4 21.3 - - + -
92L GLU* 5.8 1.1 - - - -
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Residues in contact with LEU 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I LEU* 4.0 11.4 - - + -
45K LEU* 3.7 40.2 - - + -
48K PHE* 4.2 19.4 - - + +
49K LEU* 4.3 24.7 - - + -
82K LEU* 2.9 39.4 + - + +
83K MET* 3.9 8.1 - - + +
85K ARG* 1.3 78.9 - - + +
87K THR* 1.3 60.8 + - - +
89K ALA* 3.3 9.3 + - + +
90K SER* 2.9 28.9 + - - -
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Residues in contact with THR 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I LEU* 3.4 43.2 - - - +
12I ILE* 4.3 10.6 - - + +
13I ILE* 3.6 7.9 - - + +
68I PHE* 3.7 24.0 - - + -
72I LEU* 4.1 9.6 - - + -
83K MET 2.8 21.2 + - - -
84K ALA* 3.6 7.1 - - - -
85K ARG 3.3 0.2 - - - -
86K LEU* 1.3 75.6 - - - +
88K TRP* 1.3 61.3 + - - +
90K SER* 3.3 5.1 + - - -
91K HIS* 2.9 28.3 + - - +
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Residues in contact with TRP 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I PHE* 3.8 28.4 - + + -
69I GLN* 3.8 46.4 - - + -
72I LEU* 4.2 8.0 - - + +
84K ALA 3.0 17.0 + - - +
85K ARG* 3.6 7.9 - - - +
87K THR* 1.3 76.9 - - - +
89K ALA* 1.3 60.8 + - + +
91K HIS* 3.2 14.3 + + - +
92K GLU* 2.8 71.7 + - + +
85L ARG* 4.4 19.7 - - + -
88L TRP* 4.4 27.1 - + - +
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Residues in contact with ALA 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85K ARG 3.0 17.9 + - - +
86K LEU* 3.8 12.8 - - + +
87K THR 3.3 0.2 - - - -
88K TRP* 1.3 81.6 - - + +
90K SER* 1.3 58.4 + - - +
92K GLU* 3.4 6.3 + - - +
93K LYS* 3.0 27.9 + - - +
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Residues in contact with SER 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I ASN* 2.6 29.9 + - - -
13I ILE* 4.0 5.4 - - - -
48K PHE* 3.8 18.8 - - - -
86K LEU 2.9 17.1 + - - -
87K THR* 3.6 5.8 - - - -
88K TRP 3.3 0.2 - - - -
89K ALA* 1.3 75.0 - - - +
91K HIS* 1.3 63.6 + - - +
93K LYS* 3.2 7.4 + - - +
94K MET* 3.0 31.4 + - - +
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Residues in contact with HIS 91 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I ILE* 3.5 32.8 - - + +
16I TYR* 5.7 1.0 - - - -
17I HIS* 4.3 6.3 + + - -
27I HIS* 5.3 3.6 + - - -
68I PHE* 3.8 42.1 - + + +
87K THR 2.9 13.8 + - - +
88K TRP* 3.4 14.7 - + - +
90K SER* 1.3 76.7 - - - +
92K GLU* 1.3 88.6 + - - +
94K MET* 3.2 15.6 + - - +
95K HIS* 3.2 50.6 + + - +
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Residues in contact with GLU 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88K TRP* 2.8 63.2 + - + +
89K ALA* 3.8 6.5 - - - +
91K HIS* 1.3 104.5 + - - +
93K LYS* 1.3 62.1 - - - +
94K MET 3.4 0.2 + - - -
95K HIS* 3.5 20.7 + - - +
85L ARG* 5.9 0.9 - - - -
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Residues in contact with LYS 93 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89K ALA 3.0 17.4 + - - +
90K SER* 3.2 7.2 + - - +
92K GLU* 1.3 77.6 - - - +
94K MET* 1.3 62.0 + - + +
95K HIS 4.0 4.3 - - - +
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Residues in contact with MET 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I ASN* 3.7 38.1 - - + +
13I ILE* 4.1 27.6 - - + -
17I HIS* 5.7 3.1 - - + -
90K SER* 3.0 20.4 + - - +
91K HIS* 3.2 8.7 + - + +
93K LYS* 1.3 79.9 - - + +
95K HIS* 1.3 69.9 + - + +
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Residues in contact with HIS 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I HIS* 3.9 23.1 + + - -
27I HIS* 3.8 30.7 - + - -
91K HIS* 3.2 48.3 + + + +
92K GLU* 3.5 15.2 + - - +
93K LYS 3.4 4.9 - - - +
94K MET* 1.3 91.5 - - + +
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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
------------------------------------------------------------
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