Contacts of the helix formed by residues 72 - 87 (chain E) in PDB entry 1KYZ
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 ASP 72 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E ASN* 2.9 16.8 + - - +
71E PRO* 1.3 83.9 - - - +
73E ALA* 1.3 67.8 + - - +
74E PRO* 3.3 2.6 - - - -
75E VAL* 3.5 9.7 + - + +
76E MET* 3.2 31.1 + - + +
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Residues in contact with ALA 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A VAL* 4.0 27.4 - - + +
63E ALA* 4.2 13.5 - - + -
66E LEU* 4.8 1.8 - - + -
68E THR* 4.4 11.7 - - + -
70E ASN* 3.0 19.1 + - - +
72E ASP* 1.3 75.2 - - - +
74E PRO* 1.3 65.8 - - + +
76E MET* 3.0 9.6 + - - +
77E LEU* 2.8 33.4 + - - +
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Residues in contact with PRO 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E PRO* 3.4 22.1 - - + +
60E ILE* 3.9 35.4 - - + +
63E ALA* 3.7 15.9 - - + -
70E ASN 4.0 1.8 - - - +
71E PRO* 3.3 15.7 - - + +
72E ASP 3.3 4.7 - - - -
73E ALA* 1.3 93.0 - - + +
75E VAL* 1.3 59.0 + - + +
77E LEU* 3.1 2.3 + - + +
78E ASP* 2.8 26.7 + - - +
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Residues in contact with VAL 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E PRO 6.0 0.9 - - - +
72E ASP* 3.5 12.0 + - + +
73E ALA 3.4 0.2 - - - -
74E PRO* 1.3 80.5 - - + +
76E MET* 1.3 65.0 + - + +
78E ASP* 3.3 8.3 + - + +
79E ARG* 3.1 42.5 + - + +
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Residues in contact with MET 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 4.4 0.9 - - + -
146A ALA* 3.7 32.8 - - + +
147A VAL* 3.7 34.5 - - + +
150A GLY* 5.8 0.4 - - - -
151A GLY 4.6 7.2 - - - +
153A PRO* 5.4 0.7 - - + -
321A LEU* 4.0 31.3 - - + +
70E ASN* 4.1 9.9 - - - -
72E ASP* 3.2 23.4 + - + +
73E ALA* 3.0 8.6 + - - +
75E VAL* 1.3 80.4 - - + +
77E LEU* 1.3 63.5 + - - +
79E ARG* 3.3 12.1 + - - +
80E MET* 3.2 26.5 + - - +
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Residues in contact with LEU 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A VAL* 4.2 11.0 - - + -
42E LEU* 4.1 17.0 - - + -
44E LEU* 3.7 27.8 - - + -
59E PRO* 3.8 6.3 - - + +
62E ILE* 3.8 17.5 - - + -
63E ALA* 3.7 39.7 - - + +
66E LEU* 3.9 8.5 - - + -
73E ALA 2.8 19.3 + - - +
74E PRO* 3.5 6.1 - - + +
76E MET* 1.3 72.8 - - - +
78E ASP* 1.3 53.4 + - - +
80E MET* 2.9 10.6 + - - +
81E LEU* 2.7 49.1 + - + +
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Residues in contact with ASP 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E PRO* 3.7 21.6 - - + +
74E PRO 2.8 16.7 + - - +
75E VAL* 3.3 13.9 + - + +
77E LEU* 1.3 71.4 - - - +
79E ARG* 1.3 60.2 + - + +
81E LEU* 3.9 3.1 - - - +
82E ARG* 2.9 29.7 + - - +
104E ARG* 2.6 40.8 + - - +
106E TYR* 2.6 36.1 + - - -
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Residues in contact with ARG 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A VAL* 4.7 1.4 - - - +
317A ASP* 2.8 56.2 + - - +
318A VAL* 3.7 15.8 - - + +
320A MET* 3.7 1.8 - - - +
321A LEU* 3.5 33.9 - - + +
324A ASN 5.9 0.4 + - - -
326A GLY* 5.6 2.4 - - - +
327A GLY 3.1 27.4 + - - -
328A LYS* 3.7 13.1 - - - +
75E VAL* 3.1 33.5 + - + +
76E MET* 3.7 11.1 - - - +
77E LEU 3.2 0.2 - - - -
78E ASP* 1.3 78.6 - - + +
80E MET* 1.3 61.4 + - - +
82E ARG* 3.7 19.2 + - - +
83E LEU 3.6 11.1 + - - -
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Residues in contact with MET 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 3.9 20.2 - - + -
147A VAL* 4.3 13.7 - - - -
318A VAL* 4.8 3.4 - - - -
321A LEU* 3.8 15.9 - - + -
35E ILE* 3.8 27.1 - - + +
38E SER* 3.7 29.8 - - - -
39E ALA* 3.9 17.5 - - + +
42E LEU* 4.0 11.9 - - + -
44E LEU* 4.5 7.0 - - + -
76E MET 3.2 15.8 + - - +
77E LEU* 2.9 16.0 + - - +
79E ARG* 1.3 74.6 - - - +
81E LEU* 1.3 66.5 + - + +
83E LEU* 3.1 14.9 + - - +
84E LEU* 3.3 15.8 + - - +
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Residues in contact with LEU 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E LEU* 3.9 26.0 - - + -
45E LEU* 5.6 0.9 - - + -
48E ILE* 4.6 9.9 - - + -
59E PRO* 5.0 2.9 - - + -
62E ILE* 4.4 16.2 - - + -
77E LEU* 2.7 53.5 + - + +
78E ASP* 3.9 2.7 - - - +
80E MET* 1.3 73.3 - - + +
82E ARG* 1.3 58.1 + - - +
84E LEU* 3.1 13.0 + - + +
85E ALA* 2.9 28.9 + - - +
90E LEU* 3.6 20.2 - - + +
106E TYR* 3.5 38.2 - - + -
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Residues in contact with ARG 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A LEU* 3.5 35.3 - - - +
301A PRO 5.1 6.3 + - - -
302A VAL 5.4 1.8 - - - -
304A PRO* 4.0 20.6 - - + -
314A VAL* 4.1 26.9 - - + +
317A ASP* 3.2 28.1 + - - -
329A GLU 5.1 0.8 + - - -
78E ASP* 2.9 17.4 + - - +
79E ARG* 3.8 19.4 + - - +
80E MET 3.2 0.2 - - - -
81E LEU* 1.3 77.4 - - - +
83E LEU* 1.3 61.8 + - - +
85E ALA* 3.3 3.6 + - - +
86E CYS* 3.0 23.0 + - - -
104E ARG* 3.9 35.7 - - - +
106E TYR* 3.3 15.8 + - - +
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Residues in contact with LEU 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A LYS* 5.9 0.4 - - - -
314A VAL* 3.7 27.8 - - + +
315A HIS* 3.9 17.7 - - + +
318A VAL* 4.1 9.2 - - + -
31E VAL* 3.4 31.9 - - + +
32E LEU* 3.9 13.2 - - + -
35E ILE* 3.6 26.5 - - + -
79E ARG 3.6 2.0 + - - -
80E MET 3.1 10.3 + - - +
82E ARG* 1.3 80.3 - - - +
84E LEU* 1.3 62.7 + - + +
86E CYS* 3.1 13.0 + - + +
87E TYR* 3.2 41.1 + - + -
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Residues in contact with LEU 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LEU* 4.0 15.0 - - + -
35E ILE* 4.2 12.1 - - + -
36E LEU* 4.1 26.2 - - + +
39E ALA* 3.9 27.1 - - + -
45E LEU* 4.6 9.0 - - + -
80E MET* 3.3 12.3 + - + +
81E LEU* 3.1 13.8 + - + +
83E LEU* 1.3 78.4 - - + +
85E ALA* 1.3 59.4 + - - +
87E TYR* 3.3 6.8 + - - -
89E ILE* 2.9 53.5 + - + +
90E LEU* 3.8 24.2 - - + -
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Residues in contact with ALA 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A PRO* 3.8 24.0 - - + -
305A ASP* 5.3 1.2 + - - -
81E LEU 2.9 15.3 + - - +
82E ARG 3.6 5.6 - - - +
83E LEU 3.1 0.2 - - - -
84E LEU* 1.3 76.4 - - - +
86E CYS* 1.3 64.2 + - - +
88E ILE* 3.0 20.6 + - - +
90E LEU* 3.5 21.5 - - + +
92E CYS* 4.2 7.4 - - + -
106E TYR* 4.0 15.3 - - + -
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Residues in contact with CYS 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A PRO* 3.7 15.7 - - - -
305A ASP 3.3 26.9 - - - +
306A SER* 3.2 18.7 - - - -
310A THR* 4.0 6.1 - - - -
311A LYS* 3.2 33.3 - - + -
314A VAL* 3.9 26.9 - - - -
82E ARG 3.0 23.2 + - - -
83E LEU* 3.1 10.5 + - + +
85E ALA* 1.3 76.3 - - - +
87E TYR* 1.3 59.1 + - + +
88E ILE 3.2 1.7 + - - -
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Residues in contact with TYR 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE* 3.6 20.3 - - + -
311A LYS* 3.5 27.0 - - + +
315A HIS* 2.6 35.0 + - - -
7E THR* 5.1 0.3 - - - +
8E GLN 5.2 2.1 - - - +
9E ILE* 3.1 35.0 - - + -
25E GLN* 3.0 20.4 + - - +
32E LEU* 3.6 47.1 - - + +
83E LEU* 3.2 38.1 + - + +
84E LEU 3.3 3.6 + - - +
85E ALA 3.1 1.0 - - - -
86E CYS* 1.3 77.9 - - + +
88E ILE* 1.3 71.5 + - - +
89E ILE* 3.2 7.8 + - + +
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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