Contacts of the helix formed by residues 50 - 61 (chain E) in PDB entry 4KYI
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 TYR 50 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40E LEU* 4.0 14.6 - - + -
41E SER* 3.5 31.2 + - - -
45E ALA* 4.2 15.2 - - + +
46E LYS 4.0 18.8 - - - -
47E GLY* 3.6 6.7 + - - +
48E ILE 3.3 0.6 - - - -
49E SER* 1.3 78.0 - - - +
51E LEU* 1.3 64.5 + - - +
52E GLY 3.2 2.5 - - - -
53E MET* 3.1 24.8 + - + +
54E ILE* 3.0 28.5 + - - +
74E ALA* 4.2 6.4 - - + +
75E GLY* 4.0 23.0 + - - -
78E THR* 3.7 35.0 - - + -
95E ILE* 5.9 0.4 - - - -
309E VAL* 4.0 23.6 - - + -
311E ALA* 4.5 8.8 - - + +
374E ILE* 4.9 1.8 - - + -
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Residues in contact with LEU 51 (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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47E GLY 3.9 2.0 + - - -
48E ILE* 3.6 12.2 + - + +
49E SER 3.4 1.0 - - - -
50E TYR* 1.3 78.3 - - - +
52E GLY* 1.3 57.2 + - - +
54E ILE* 3.8 5.6 + - + +
55E GLN* 3.2 53.5 + - + +
88E ILE* 6.0 2.9 - - + +
91E ILE* 4.6 6.1 - - + -
92E LYS* 3.9 29.8 - - + +
95E ILE* 3.7 36.3 - - + +
96E GLU* 4.0 22.7 - - + +
395E VAL* 3.8 24.0 - - + -
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Residues in contact with GLY 52 (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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550A LYS* 5.5 0.2 - - - -
49E SER 4.2 3.6 + - - -
51E LEU* 1.3 76.9 - - - +
53E MET* 1.3 62.0 - - - +
55E GLN* 3.8 5.1 - - - +
56E ALA* 3.2 16.5 + - - +
395E VAL* 3.4 36.9 + - - +
398E GLY* 4.3 1.3 - - - -
399E TYR* 3.4 24.5 - - - +
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Residues in contact with MET 53 (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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38E LEU* 4.5 7.0 - - + -
40E LEU* 3.7 32.5 - - + -
49E SER 4.3 0.6 + - - -
50E TYR* 3.1 25.3 + - + +
52E GLY* 1.3 74.9 - - - +
54E ILE* 1.3 84.2 + - + +
56E ALA* 3.2 4.7 + - - +
57E LEU* 3.2 44.4 + - - +
82E LEU* 5.4 0.2 - - + -
309E VAL* 4.0 24.9 - - + -
372E ILE* 4.7 0.7 - - + -
374E ILE* 4.1 13.5 - - + -
398E GLY 4.0 3.2 + - - -
402E THR* 3.6 30.6 - - + +
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Residues in contact with ILE 54 (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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50E TYR 3.0 16.6 + - - +
51E LEU* 4.1 7.6 - - + +
53E MET* 1.3 89.6 - - + +
55E GLN* 1.3 58.2 + - - +
56E ALA 3.0 0.4 - - - -
57E LEU* 3.2 7.9 + - + +
58E GLN* 3.0 27.7 + - - +
63E ILE* 3.9 19.6 - - + +
78E THR* 3.6 28.3 - - + +
82E LEU* 4.1 29.2 - - + -
88E ILE* 4.2 18.4 - - + -
91E ILE* 4.1 23.8 - - + -
95E ILE* 5.5 1.3 - - + -
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Residues in contact with GLN 55 (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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27A GLN* 5.8 0.2 - - - +
548A LEU* 4.9 10.1 + - - +
550A LYS* 4.0 31.5 + - + +
51E LEU* 3.2 41.9 + - + +
52E GLY* 3.8 7.4 - - - +
53E MET 3.3 0.4 - - - -
54E ILE* 1.3 77.9 - - - +
56E ALA* 1.3 58.3 + - - +
58E GLN* 4.1 4.6 - - + +
59E GLU* 3.9 14.0 + - - +
88E ILE* 4.2 18.6 - - + -
92E LYS* 4.5 20.7 - - - +
395E VAL* 4.3 1.9 - - - +
399E TYR* 4.0 11.8 - - + -
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Residues in contact with ALA 56 (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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52E GLY 3.2 15.8 + - - +
53E MET 3.5 5.4 - - - +
54E ILE 3.0 0.6 - - - -
55E GLN* 1.3 78.0 - - - +
57E LEU* 1.3 65.1 + - - +
58E GLN 3.2 1.8 - - - -
59E GLU* 3.4 4.4 + - - +
60E ARG* 3.2 26.8 + - - +
399E TYR* 3.6 16.6 - - + +
402E THR* 3.9 17.5 - - + -
403E MET* 3.6 24.4 - - - +
406E LEU* 5.1 0.7 - - - -
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Residues in contact with LEU 57 (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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38E LEU* 4.3 23.1 - - + -
53E MET* 3.2 35.1 + - - +
54E ILE* 3.2 8.0 + - + +
56E ALA* 1.3 76.8 - - - +
58E GLN* 1.3 52.3 + - - +
60E ARG* 3.3 0.8 + - - -
61E GLY 2.6 30.5 + - - -
62E LYS* 2.8 40.6 + - + -
63E ILE* 3.8 19.7 - - + -
66E LEU* 5.1 4.3 - - + -
82E LEU* 6.3 0.2 - - + -
307E LEU* 4.0 17.5 - - + -
372E ILE* 5.2 1.8 - - + -
402E THR* 4.1 10.3 - - + -
406E LEU* 4.1 13.5 - - + -
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Residues in contact with GLN 58 (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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54E ILE 3.0 10.3 + - - +
55E GLN* 4.1 6.5 - - + +
56E ALA 3.2 0.2 - - - -
57E LEU* 1.3 77.1 - - - +
59E GLU* 1.3 65.3 + - + +
61E GLY* 3.2 13.0 + - - -
63E ILE* 4.1 17.3 - - + +
88E ILE* 3.5 48.0 - - + +
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Residues in contact with GLU 59 (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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549A PHE* 3.1 43.8 - - + -
550A LYS 5.3 0.3 + - - -
551A GLY* 4.7 1.2 - - - -
554A GLN* 4.1 12.3 + - - +
55E GLN 3.9 8.3 + - - +
56E ALA 3.4 8.0 + - - +
57E LEU 3.4 0.4 - - - -
58E GLN* 1.3 83.1 - - + +
60E ARG* 1.3 70.4 + - - +
61E GLY 3.7 0.2 + - - -
399E TYR* 2.5 34.9 + - - -
403E MET* 3.6 13.7 - - + +
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Residues in contact with ARG 60 (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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554A GLN* 4.5 13.1 - - - +
56E ALA 3.2 14.7 + - - +
59E GLU* 1.3 89.6 + - - +
61E GLY* 1.3 62.5 + - - +
62E LYS* 3.7 26.8 - - + +
403E MET* 3.4 34.0 - - + +
406E LEU* 3.6 28.5 + - + +
407E ASP* 2.8 31.9 + - - -
410E LYS* 6.4 0.2 - - - +
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Residues in contact with GLY 61 (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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57E LEU 2.6 12.9 + - - -
58E GLN* 3.2 12.7 + - - -
59E GLU 3.3 0.2 - - - -
60E ARG* 1.3 76.5 - - - +
62E LYS* 1.3 60.5 + - - +
63E ILE* 3.3 3.1 - - - -
64E LYS* 4.5 6.6 + - - +
65E ASN* 3.8 17.2 - - - +
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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