Contacts of the helix formed by residues 64 - 84 (chain R) in PDB entry 1KYO
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 PRO 64 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62R ARG 3.3 8.2 - - - +
63R LEU* 1.3 87.8 - - + +
65R GLU* 1.3 65.2 + - - +
66R ASP* 3.4 11.9 - - - +
67R GLU* 3.0 32.7 + - + +
68R SER 3.1 8.3 + - - -
106R TYR* 3.1 27.4 - - + +
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Residues in contact with GLU 65 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63R LEU 3.6 1.4 + - - -
64R PRO* 1.3 71.0 - - - +
66R ASP* 1.3 70.9 + - - +
68R SER* 2.9 8.1 + - - -
69R TYR* 2.9 61.5 + - + +
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Residues in contact with ASP 66 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302O PHE* 5.4 0.9 - - - -
305O PRO 5.6 2.2 - - - +
64R PRO* 4.2 15.2 - - - +
65R GLU* 1.3 78.6 - - - +
67R GLU* 1.3 67.5 + - + +
69R TYR* 3.6 7.1 + - - +
70R ALA* 3.2 23.4 + - - +
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Residues in contact with GLU 67 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44R LYS* 5.2 6.6 + - - -
63R LEU* 3.8 21.2 - - + +
64R PRO* 3.0 24.9 + - + +
66R ASP* 1.3 86.0 - - + +
68R SER* 1.3 58.2 + - - +
70R ALA* 3.6 5.2 + - - +
71R ARG* 2.9 29.5 + - - +
74R ARG* 4.7 6.8 + - - -
102R TYR* 3.9 32.4 - - + +
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Residues in contact with SER 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60R LEU* 4.7 8.3 + - - +
63R LEU* 4.1 22.9 + - - +
64R PRO 3.1 10.0 + - - -
65R GLU* 2.9 12.8 + - - -
67R GLU* 1.3 75.0 - - - +
69R TYR* 1.3 61.7 + - - -
71R ARG* 3.1 9.7 + - - +
72R ALA* 2.8 29.8 + - - +
19S PRO* 4.1 19.2 - - - +
20S LYS 5.4 3.1 + - - -
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Residues in contact with TYR 69 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254L THR* 3.5 23.0 - - + +
302O PHE* 3.7 16.5 - - + -
305O PRO* 4.1 19.7 - - + -
65R GLU* 2.9 68.1 + - + +
66R ASP* 4.1 6.1 - - - +
68R SER* 1.3 73.4 - - - +
70R ALA* 1.3 58.2 + - - +
72R ALA* 3.2 9.5 - - - +
73R TYR* 3.0 22.5 + - - +
20S LYS* 3.5 27.9 - - + +
21S GLN 4.2 0.7 - - - -
22S LYS* 3.2 50.7 - - + +
24S ILE* 4.3 2.1 - - - +
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Residues in contact with ALA 70 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302O PHE* 3.7 23.3 - - + -
66R ASP 3.2 16.9 + - - +
67R GLU* 3.7 7.0 - - - +
68R SER 3.2 0.4 - - - -
69R TYR* 1.3 75.4 - - - +
71R ARG* 1.3 54.6 + - - +
73R TYR* 2.8 5.9 + - - +
74R ARG* 2.7 52.7 + - - +
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Residues in contact with ARG 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213N THR* 4.7 3.4 - - - +
216N LEU* 5.2 0.6 - - - +
46R ASP 5.3 0.4 + - - -
47R ASP* 3.6 20.7 + - - +
49R ILE 5.3 1.0 + - - -
51R GLU* 3.0 29.1 + - - +
56R MET* 4.7 7.5 - - - +
60R LEU* 3.2 39.8 - - - +
63R LEU* 4.5 5.4 - - + +
67R GLU 2.9 19.1 + - - +
68R SER* 3.4 9.7 + - - +
70R ALA* 1.3 75.2 - - - +
72R ALA* 1.3 64.4 + - - +
74R ARG* 3.2 17.2 + - - +
75R ILE* 2.9 52.7 + - + +
102R TYR* 3.3 27.9 + - + +
103R LEU* 5.0 1.6 - - - +
19S PRO* 4.9 20.2 - - - +
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Residues in contact with ALA 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216N LEU* 3.4 23.9 - - + +
68R SER 2.8 13.0 + - - +
69R TYR* 3.2 15.3 - - - +
70R ALA 3.1 0.2 - - - -
71R ARG* 1.3 79.0 - - - +
73R TYR* 1.3 62.3 + - - +
76R ILE* 3.0 31.0 + - - +
19S PRO* 4.4 13.0 - - + -
20S LYS 5.1 2.9 - - - +
21S GLN* 4.5 10.3 - - + -
22S LYS 6.0 0.2 - - - +
24S ILE* 4.3 9.6 - - + -
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Residues in contact with TYR 73 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300O PHE* 3.9 26.5 + - + -
301O VAL* 4.1 4.5 - - - -
302O PHE* 3.4 58.4 + + + -
69R TYR 3.0 11.5 + - - +
70R ALA 2.8 9.4 + - - +
72R ALA* 1.3 72.6 - - - +
74R ARG* 1.3 73.9 + - + +
75R ILE 3.1 0.3 + - - -
76R ILE* 3.1 2.5 + - + -
77R ARG* 2.8 73.9 + - + +
92R GLU* 5.3 2.1 + - - -
24S ILE* 3.5 27.1 - - + +
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Residues in contact with ARG 74 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R GLY 3.4 24.2 - - - +
43R LEU* 3.2 12.6 - - + +
44R LYS* 3.6 32.7 - - - +
47R ASP* 2.7 43.2 + - - +
67R GLU* 4.7 6.1 + - - -
70R ALA* 2.7 34.4 + - - +
71R ARG* 3.2 22.9 + - - +
73R TYR* 1.3 77.5 - - + +
75R ILE* 1.3 55.2 + - - +
77R ARG* 3.4 16.2 - - - +
78R ALA* 2.9 23.4 + - - -
94R ILE* 4.3 9.2 - - + -
102R TYR* 3.7 20.6 + - - -
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Residues in contact with ILE 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212N ILE* 3.9 19.3 - - + -
213N THR* 4.1 14.4 - - + +
216N LEU* 4.1 18.6 - - + -
43R LEU* 4.1 5.4 - - + -
47R ASP* 4.6 17.9 - - + +
71R ARG* 2.9 60.8 + - + +
72R ALA 3.8 2.9 - - - +
74R ARG* 1.3 74.4 - - + +
76R ILE* 1.3 69.2 + - - +
78R ALA* 3.1 3.6 + - - +
79R HIS* 3.1 46.2 + - + +
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Residues in contact with ILE 76 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216N LEU* 3.5 39.3 - - + +
217N ASP* 4.4 10.4 - - + +
300O PHE* 3.6 44.4 - - + -
72R ALA 3.0 24.1 + - - +
73R TYR* 3.7 3.8 - - + +
75R ILE* 1.3 76.2 - - - +
77R ARG* 1.3 64.1 + - - +
79R HIS* 3.2 7.6 + - - +
80R GLN* 3.1 20.8 + - - +
21S GLN* 3.7 23.3 - - - +
24S ILE* 3.7 20.9 - - + -
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Residues in contact with ARG 77 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300O PHE* 5.4 6.7 - - + +
41R LEU 4.7 1.6 - - - -
42R GLY* 2.9 35.8 + - - -
73R TYR* 2.8 64.4 + - + +
74R ARG* 3.4 17.3 - - - +
76R ILE* 1.3 77.9 - - - +
78R ALA* 1.3 52.7 + - - +
80R GLN* 3.3 8.6 + - - +
81R THR* 2.5 39.1 + - - +
88R LEU* 3.4 34.5 - - + +
92R GLU* 4.3 22.0 + - - +
94R ILE* 5.2 5.3 - - - +
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Residues in contact with ALA 78 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210N LEU* 3.7 18.6 - - + +
212N ILE* 5.2 0.4 - - + -
41R LEU* 3.9 17.5 + - + +
43R LEU* 3.5 36.6 - - + -
74R ARG 2.9 5.6 + - - +
75R ILE* 3.1 7.1 + - - +
77R ARG* 1.3 73.2 - - - +
79R HIS* 1.3 55.2 + - - +
81R THR* 3.2 6.7 + - - -
82R GLU* 2.7 36.7 + - - +
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Residues in contact with HIS 79 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23N PRO* 5.5 3.1 - - + -
24N SER* 3.9 16.8 - - - +
25N SER* 2.7 32.8 - - - -
208N ASN* 3.6 24.0 + - + -
210N LEU* 3.8 12.9 - - + +
212N ILE* 4.0 10.3 - - + +
213N THR 3.3 25.4 - - - -
214N GLY* 4.3 6.3 - - - -
216N LEU* 6.1 1.0 - - + +
217N ASP* 4.6 11.0 + - + +
75R ILE* 3.1 34.2 + - + +
76R ILE* 3.7 8.7 - - - +
78R ALA* 1.3 75.7 - - - +
80R GLN* 1.3 54.6 + - - +
82R GLU* 3.1 2.0 + - - +
83R LEU* 2.8 39.0 + - - +
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Residues in contact with GLN 80 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N SER* 5.0 0.2 + - - -
295O ILE 3.2 21.1 + - - +
296O LYS 3.8 4.4 + - - -
298O ARG* 2.6 60.4 + - - +
299O LYS* 5.8 0.2 - - - -
300O PHE* 3.7 21.5 - - + -
76R ILE 3.1 12.2 + - - +
77R ARG* 3.3 9.8 + - - +
79R HIS* 1.3 76.7 - - - +
81R THR* 1.3 60.0 + - - +
83R LEU* 3.5 10.4 - - - +
84R THR* 2.9 47.2 + - + +
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Residues in contact with THR 81 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41R LEU* 4.3 9.8 + - + -
77R ARG* 2.5 27.7 + - - +
78R ALA* 3.6 5.3 - - - -
80R GLN* 1.3 76.5 - - - +
82R GLU* 1.3 64.9 + - - +
84R THR* 2.7 25.5 + - - +
85R HIS 3.2 6.1 + - - -
86R HIS* 3.5 26.5 - - + +
87R LEU* 3.8 22.4 - - - +
88R LEU* 3.8 27.7 - - + +
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Residues in contact with GLU 82 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N SER* 4.2 6.6 - - - +
27N ASN* 5.8 1.9 + - - +
209N PRO* 4.1 26.7 - - + +
210N LEU* 3.7 30.6 - - + +
317N THR* 5.3 6.2 - - - +
41R LEU* 3.9 16.9 - - + +
78R ALA 2.7 21.1 + - - +
79R HIS* 3.5 6.3 - - - +
81R THR* 1.3 73.1 - - - +
83R LEU* 1.3 61.0 + - - +
85R HIS* 3.1 32.2 + - - +
86R HIS 4.9 3.4 - - - -
51S ARG* 4.2 13.7 + - - +
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Residues in contact with LEU 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N SER* 3.5 48.9 - - - +
25N SER* 3.9 10.1 - - - +
292O TRP* 4.7 4.9 - - + -
295O ILE* 3.9 18.8 - - + -
296O LYS* 3.1 54.5 + - + -
79R HIS 2.8 15.8 + - - +
80R GLN* 3.5 23.1 - - - +
82R GLU* 1.3 74.5 - - - +
84R THR* 1.3 69.4 + - + +
85R HIS* 3.3 8.7 + - - -
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Residues in contact with THR 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296O LYS* 3.5 32.5 + - - +
80R GLN* 2.9 32.5 - - + +
81R THR* 2.7 22.3 + - - +
83R LEU* 1.3 82.3 - - + +
85R HIS* 1.3 66.2 + - - +
86R HIS* 3.0 38.7 + - - +
47S ASN* 5.1 0.5 + - - -
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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