Contacts of the helix formed by residues 50 - 60 (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 TYR 50 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C LEU* 4.0 18.5 - - + +
41C SER* 3.6 27.0 + - - -
43C GLY 5.7 0.2 + - - -
45C ALA* 4.4 23.9 - - + +
46C LYS 4.7 1.3 - - - -
47C GLY* 3.7 14.1 + - - +
48C ILE 3.2 0.6 - - - -
49C SER* 1.3 83.5 - - - +
51C LEU* 1.3 63.5 + - - +
52C GLY 3.5 1.6 - - - -
53C MET* 3.5 26.5 + - + +
54C ILE* 3.3 27.3 + - - +
74C ALA* 4.3 4.7 - - + +
75C GLY* 3.7 22.4 + - - -
78C THR* 3.7 36.1 - - + +
95C ILE* 6.1 0.9 - - - -
309C VAL* 3.9 24.0 + - + -
311C ALA* 4.6 8.1 - - + +
374C ILE* 4.6 3.4 - - + -
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Residues in contact with LEU 51 (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 4.4 1.4 + - - -
48C ILE* 3.4 14.9 + - + +
49C SER 3.4 1.4 - - - -
50C TYR* 1.3 77.9 - - - +
52C GLY* 1.3 62.7 + - - +
53C MET 3.3 0.3 + - - -
54C ILE* 3.3 5.4 + - + +
55C GLN* 3.2 45.7 + - + +
91C ILE* 4.3 9.9 - - + -
92C LYS* 3.8 36.1 - - + -
95C ILE* 3.8 33.4 - - + -
96C GLU* 4.8 11.2 - - + +
395C VAL* 3.7 24.7 - - + -
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Residues in contact with GLY 52 (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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49C SER 4.7 2.0 + - - -
51C LEU* 1.3 79.2 - - - +
53C MET* 1.3 59.3 + - - +
55C GLN* 4.0 7.4 - - - -
56C ALA* 3.3 16.3 + - - +
395C VAL* 3.5 36.5 + - - +
398C GLY* 3.5 7.6 - - - -
399C TYR* 3.3 19.4 - - - -
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Residues in contact with MET 53 (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* 4.4 7.6 - - + -
40C LEU* 3.6 31.0 - - + -
50C TYR* 3.5 32.4 + - + +
51C LEU 3.2 0.4 - - - -
52C GLY* 1.3 79.1 - - - +
54C ILE* 1.3 70.1 + - + +
56C ALA* 3.4 3.3 + - - +
57C LEU* 3.2 49.0 + - - +
78C THR* 5.2 0.2 - - + -
309C VAL* 4.2 20.4 - - + -
372C ILE* 4.6 3.1 - - + -
374C ILE* 4.0 15.7 - - + -
398C GLY* 3.3 12.5 + - - +
402C THR* 3.4 23.7 - - + +
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Residues in contact with ILE 54 (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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50C TYR 3.4 13.0 - - - +
51C LEU* 3.3 9.1 + - + +
53C MET* 1.3 88.2 - - + +
55C GLN* 1.3 64.9 + - + +
57C LEU* 3.3 7.5 + - + +
58C GLN* 3.0 23.3 + - + +
63C ILE* 4.0 17.0 - - + +
78C THR* 3.7 26.7 - - + +
81C ILE* 5.4 1.1 - - + -
82C LEU* 3.9 30.3 - - + -
88C ILE* 5.2 10.8 - - + -
91C ILE* 4.2 32.5 - - + -
95C ILE* 5.7 1.3 - - + -
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Residues in contact with GLN 55 (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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51C LEU* 3.2 39.7 + - + +
52C GLY* 3.9 11.0 - - - +
54C ILE* 1.3 78.3 - - + +
56C ALA* 1.3 62.6 + - - +
58C GLN* 3.6 2.8 + - - +
59C GLU* 3.2 22.5 + - - +
88C ILE* 4.7 21.4 - - + +
92C LYS* 3.7 29.4 - - + +
395C VAL* 4.5 5.7 - - - +
399C TYR* 4.2 15.1 - - + -
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Residues in contact with ALA 56 (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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52C GLY 3.3 12.5 + - - +
53C MET 3.5 9.0 - - - +
54C ILE 3.2 0.4 - - - -
55C GLN* 1.3 80.8 - - - +
57C LEU* 1.3 57.3 + - - +
59C GLU* 3.2 5.4 + - - +
60C ARG* 3.0 32.9 + - - +
399C TYR* 3.8 15.2 - - + +
402C THR* 3.8 18.6 - - + -
403C MET* 3.5 26.0 - - - -
406C LEU* 5.1 0.4 - - + -
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Residues in contact with LEU 57 (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* 4.0 19.5 - - + -
53C MET* 3.2 38.2 + - - +
54C ILE* 3.3 6.0 + - + +
56C ALA* 1.3 78.2 - - - +
58C GLN* 1.3 52.0 + - - +
60C ARG* 3.3 0.7 + - - -
61C GLY 2.7 12.6 + - - -
62C LYS* 2.7 55.4 + - + -
63C ILE* 3.6 22.4 - - + -
66C LEU* 5.3 3.4 - - + -
307C LEU* 4.1 20.2 - - + -
372C ILE* 5.2 1.8 - - + -
402C THR* 4.0 11.2 - - + -
406C LEU* 4.0 14.6 - - + -
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Residues in contact with GLN 58 (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 3.0 15.7 + - - +
55C GLN 3.9 2.0 - - - +
56C ALA 3.3 0.2 - - - -
57C LEU* 1.3 72.9 - - - +
59C GLU* 1.3 67.4 + - - +
61C GLY* 3.1 14.0 + - - +
63C ILE* 3.9 20.6 - - + +
88C ILE* 3.5 42.9 - - + +
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Residues in contact with GLU 59 (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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55C GLN 3.2 10.4 + - - +
56C ALA 3.2 9.5 + - - +
58C GLN* 1.3 81.1 - - - +
60C ARG* 1.3 66.8 + - - +
61C GLY 3.5 0.2 + - - -
399C TYR* 2.3 34.8 + - - -
403C MET* 3.5 15.6 - - + +
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Residues in contact with ARG 60 (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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56C ALA 3.0 18.1 + - - +
59C GLU* 1.3 85.3 + - - +
61C GLY* 1.3 63.4 + - - +
62C LYS* 3.4 26.4 + - + +
403C MET* 3.3 40.9 - - + +
406C LEU* 3.6 31.4 + - + +
407C ASP* 2.6 34.9 + - - +
410C LYS* 5.8 3.6 - - - +
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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