Contacts of the helix formed by residues 74 - 84 (chain C) 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 ALA 74 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C ALA* 3.3 29.6 - - + +
46C LYS 4.4 0.2 - - - -
47C GLY* 4.0 21.8 - - - +
50C TYR* 4.3 6.2 - - + -
73C SER* 1.3 81.3 - - - +
75C GLY* 1.3 57.2 + - - +
76C ALA 3.1 3.9 + - - -
77C MET* 3.5 16.3 + - - +
78C THR* 3.6 11.8 + - - -
269C GLY* 4.8 1.1 - - - -
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Residues in contact with GLY 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LEU* 3.5 19.0 - - - +
41C SER 4.9 0.2 + - - -
50C TYR* 3.7 23.3 + - - -
71C GLY* 3.6 4.0 - - - -
72C ALA 3.0 14.7 + - - -
74C ALA* 1.3 76.2 - - - +
76C ALA* 1.3 58.6 + - - +
77C MET 3.4 0.2 - - - -
78C THR* 3.9 4.0 - - - -
79C ALA* 3.2 27.0 + - - +
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Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C GLY* 4.0 15.5 - - - +
72C ALA 3.5 1.9 + - - -
73C SER 3.1 15.5 + - - +
74C ALA 3.1 1.0 - - - -
75C GLY* 1.3 77.6 - - - +
77C MET* 1.3 60.9 + - - +
79C ALA* 4.0 1.7 - - - +
80C SER* 3.0 27.5 + - - -
238C VAL* 4.1 12.1 - - + +
265C VAL* 3.7 16.5 - - + +
268C SER* 3.7 26.5 - - - +
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Residues in contact with MET 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C GLY* 6.2 4.0 - - - -
73C SER 4.3 0.6 + - - -
74C ALA* 3.5 10.3 + - - +
75C GLY 3.4 0.2 - - - -
76C ALA* 1.3 76.1 - - - +
78C THR* 1.3 62.2 + - - +
80C SER* 2.6 21.1 + - - +
81C ILE* 2.9 32.8 + - + +
94C LEU* 4.7 18.2 - - + +
95C ILE* 4.8 15.3 - - - -
98C LEU* 4.6 16.8 - - + +
100C ILE* 5.3 11.4 - - + -
118C PHE* 3.5 35.0 - - + -
122C LEU* 4.2 15.3 - - + -
125C ILE* 6.0 0.4 - - + -
265C VAL* 3.5 14.1 - - + +
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Residues in contact with THR 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LEU* 3.8 20.4 - - + -
47C GLY* 4.3 8.8 + - - -
50C TYR* 3.7 30.5 - - + +
53C MET* 5.2 0.2 - - + -
54C ILE* 3.7 27.6 - - + -
74C ALA 3.6 10.5 + - - -
75C GLY* 4.2 3.4 - - - -
76C ALA 3.4 0.2 - - - -
77C MET* 1.3 80.2 - - - +
79C ALA* 1.3 60.1 - - - +
81C ILE* 3.2 18.3 - - + +
82C LEU* 3.2 20.4 - - + +
95C ILE* 4.3 9.4 - - + +
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Residues in contact with ALA 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LEU* 4.1 4.0 - - + +
69C VAL* 3.7 27.5 - - + +
70C SER 3.8 16.4 - - - +
71C GLY* 4.3 1.3 - - - +
75C GLY 3.2 21.2 + - - +
76C ALA* 4.0 3.1 - - - +
77C MET 3.2 0.2 - - - -
78C THR* 1.3 75.9 - - - +
80C SER* 1.3 58.8 + - - +
82C LEU* 3.3 6.2 + - - +
83C ALA* 2.9 28.2 + - - +
236C LEU* 3.8 13.5 - - + -
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Residues in contact with SER 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ALA 3.0 16.8 + - - -
77C MET* 2.6 23.4 + - - +
79C ALA* 1.3 73.3 - - - +
81C ILE* 1.3 56.5 + - - +
82C LEU 3.1 4.7 - - - -
83C ALA* 3.5 1.8 + - - +
84C VAL* 3.2 27.9 + - - +
126C TYR* 2.7 34.7 + - - -
218C LEU* 5.5 1.4 - - - +
236C LEU* 3.7 26.1 - - - +
261C ILE* 4.5 1.0 - - - +
265C VAL* 3.9 4.4 - - - +
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Residues in contact with ILE 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ILE* 5.4 0.2 - - + -
77C MET* 2.9 22.5 + - + +
78C THR* 3.2 25.4 - - + +
80C SER* 1.3 80.4 - - - +
82C LEU* 1.3 59.2 + - + +
84C VAL* 3.4 8.6 - - - +
86C MET* 3.3 42.0 + - + +
91C ILE* 4.4 22.2 - - + +
94C LEU* 4.8 13.0 - - + -
95C ILE* 3.9 32.3 - - + -
122C LEU* 6.0 0.7 - - + -
125C ILE* 4.5 21.8 - - + -
126C TYR* 4.7 5.4 - - + -
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Residues in contact with LEU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU* 4.1 25.6 - - + -
40C LEU* 5.5 2.0 - - + -
53C MET* 5.9 0.2 - - + -
54C ILE* 3.9 29.4 - - + -
63C ILE* 4.7 20.4 - - + -
66C LEU* 6.0 1.8 - - + -
69C VAL* 4.6 9.0 - - + -
78C THR* 3.2 23.6 - - + +
79C ALA* 3.3 11.4 + - - +
80C SER 3.1 0.4 - - - -
81C ILE* 1.3 78.8 - - + +
83C ALA* 1.3 63.2 + - - +
84C VAL 3.1 1.8 - - - -
85C GLY* 3.2 13.2 + - - -
86C MET 5.1 2.2 - - - +
91C ILE* 3.7 25.1 - - + -
232C LEU 4.0 0.2 - - - +
234C LYS* 3.3 17.7 - - + +
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Residues in contact with ALA 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C VAL* 3.7 6.7 - - + +
79C ALA 2.9 16.9 + - - +
80C SER 3.5 5.6 + - - +
82C LEU* 1.3 76.6 - - - +
84C VAL* 1.3 59.0 + - - +
218C LEU* 4.1 8.3 - - + +
233C ILE* 3.3 15.1 - - - +
234C LYS* 3.1 46.4 + - - +
236C LEU* 3.7 23.8 - - + -
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Residues in contact with VAL 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C SER 3.2 14.4 + - - +
81C ILE* 3.4 22.2 - - + +
82C LEU 3.1 0.6 - - - -
83C ALA* 1.3 78.6 - - - +
85C GLY* 1.3 61.7 + - - +
86C MET* 3.8 11.9 - - + +
125C ILE* 5.7 0.9 - - + +
126C TYR* 4.4 18.6 - - + +
129C GLN* 3.9 20.8 - - + +
130C MET* 3.6 34.7 - - + +
133C HIS* 3.5 18.5 + - - -
218C LEU* 4.7 9.6 - - + -
233C ILE* 3.6 12.1 - - + +
261C ILE* 6.0 0.4 - - + -
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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