Contacts of the helix formed by residues 64 - 77 (chain C) in PDB entry 1YLK
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 THR 64 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62C VAL* 3.0 31.0 + - + +
63C VAL* 1.3 76.3 - - - +
65C ASP* 1.3 64.3 + - - +
66C ASP 3.3 4.6 + - - -
67C VAL* 3.0 15.2 + - - +
68C ILE* 3.0 23.6 + - - +
118C GLU* 4.1 9.6 - - + +
133C ARG* 4.5 2.9 - - - +
66D ASP* 2.6 43.6 + - + +
69D ARG* 4.2 7.9 - - - +
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Residues in contact with ASP 65 (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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64C THR* 1.3 73.4 - - - +
66C ASP* 1.3 56.7 + - - +
68C ILE* 3.7 9.5 - - - +
69C ARG* 2.8 30.5 + - - +
114D THR* 3.9 10.1 + - - -
115D TRP* 3.5 35.5 - - + -
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Residues in contact with ASP 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ILE* 5.7 0.4 - - - -
64C THR* 3.1 10.7 + - - +
65C ASP* 1.3 75.5 - - - +
67C VAL* 1.3 60.3 + - + +
69C ARG* 2.8 35.9 + - - +
70C SER* 2.9 33.7 + - - -
58D ASN* 2.7 24.8 + - - +
64D THR* 2.6 30.2 + - - +
66D ASP* 3.5 21.9 - - + +
67D VAL* 4.1 2.4 - - - +
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Residues in contact with VAL 67 (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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33C VAL* 3.9 26.2 - - + -
56C ILE* 3.9 19.5 - - + -
58C ASN* 3.3 16.6 - - - +
62C VAL 3.2 22.9 - - - +
63C VAL* 4.0 14.8 - - + -
64C THR* 3.0 15.4 + - - +
66C ASP* 1.3 72.9 - - + +
68C ILE* 1.3 61.8 + - - +
70C SER* 3.3 4.7 + - - -
71C LEU* 2.8 49.4 + - + +
66D ASP* 4.3 1.1 - - - +
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Residues in contact with ILE 68 (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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63C VAL* 3.5 27.8 - - + +
64C THR 3.0 19.0 + - - +
65C ASP* 3.7 11.9 - - - +
67C VAL* 1.3 77.8 - - - +
69C ARG* 1.3 56.1 + - - +
71C LEU* 3.7 1.9 - - + -
72C ALA* 2.8 29.5 + - - +
133C ARG 4.7 2.9 - - - +
134C ILE* 4.5 9.4 - - + -
137C ASN* 3.5 47.3 - - + +
139C PHE* 4.5 0.7 - - + -
140C VAL* 3.7 17.8 - - + +
115D TRP* 3.6 26.5 - - + +
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Residues in contact with ARG 69 (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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65C ASP 2.8 21.7 + - - +
66C ASP* 2.8 32.1 + - - +
68C ILE* 1.3 74.9 - - - +
70C SER* 1.3 62.4 + - - +
72C ALA* 3.3 1.7 + - - +
73C ILE* 3.1 28.8 + - + +
58D ASN* 3.4 17.4 - - - +
59D ALA* 2.8 42.2 + - - +
62D VAL* 4.0 5.5 - - - +
64D THR* 4.3 5.9 - - - +
93D MET* 3.6 9.1 - - - +
115D TRP* 3.7 34.9 - - + -
116D SER 3.1 24.2 - - - -
117D PRO 3.0 22.1 + - - +
118D GLU* 3.8 11.4 - - - +
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Residues in contact with SER 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ILE* 3.5 26.4 - - - +
66C ASP* 2.9 24.2 + - - -
67C VAL* 3.3 3.3 + - - -
69C ARG* 1.3 75.4 + - - +
71C LEU* 1.3 58.6 + - - +
73C ILE* 3.4 0.5 + - - +
74C SER* 2.8 29.1 + - - -
36D MET* 3.3 7.5 - - - +
58D ASN* 3.5 8.8 - - - +
59D ALA* 2.9 38.5 + - - +
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Residues in contact with LEU 71 (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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31C ALA* 3.8 22.0 - - + -
33C VAL* 4.1 11.4 - - + -
56C ILE* 3.6 21.8 - - + -
67C VAL* 2.8 41.6 + - + +
68C ILE* 3.8 4.0 - - + +
70C SER* 1.3 71.8 - - - +
72C ALA* 1.3 60.4 + - - +
74C SER* 3.3 3.6 + - - -
75C GLN* 2.9 36.5 + - + +
83C ILE* 4.2 16.8 - - + -
134C ILE* 4.2 25.1 - - + -
140C VAL* 4.0 25.1 - - + -
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Residues in contact with ALA 72 (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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68C ILE 2.8 21.1 + - - +
69C ARG 3.3 3.8 + - - +
71C LEU* 1.3 70.1 - - - +
73C ILE* 1.3 60.6 + - - +
75C GLN* 4.7 2.0 - - - -
76C ARG* 2.8 41.6 + - - +
139C PHE* 3.6 26.5 - - + +
140C VAL* 4.1 2.4 - - + +
101D PHE* 3.9 8.2 - - + -
105D ILE* 4.7 0.2 - - + -
115D TRP* 4.0 22.7 - - + -
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Residues in contact with ILE 73 (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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69C ARG* 3.1 29.3 + - + +
70C SER 3.7 3.6 - - - +
72C ALA* 1.3 74.3 - - - +
74C SER* 1.3 66.6 + - - +
77C LEU* 2.9 34.8 + - + +
78C LEU* 3.3 10.1 + - + +
504C SCN 4.2 15.0 - - - -
36D MET* 4.2 12.3 - - + -
59D ALA* 3.8 18.2 - - + -
92D GLY* 6.0 0.7 - - - -
93D MET* 4.0 2.7 - - + -
96D PHE* 4.0 20.6 - - + -
101D PHE* 3.8 23.3 - - + -
117D PRO* 3.8 23.8 - - + +
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Residues in contact with SER 74 (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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31C ALA* 3.7 11.9 - - - +
54C HIS* 2.7 36.7 + - - -
70C SER 2.8 18.3 + - - -
71C LEU* 3.4 10.5 - - - -
73C ILE* 1.3 77.4 - - - +
75C GLN* 1.3 57.1 + - - +
78C LEU* 3.2 7.9 - - - +
79C GLY 3.0 22.2 + - - -
80C THR* 2.7 29.3 + - - +
36D MET* 3.8 4.9 - - - -
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Residues in contact with GLN 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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71C LEU* 2.9 17.5 + - + +
72C ALA* 4.2 2.2 - - - +
74C SER* 1.3 77.6 - - - +
76C ARG* 1.3 67.9 + - + +
79C GLY* 3.4 8.5 + - - -
80C THR* 3.3 28.5 + - - +
81C ARG* 2.9 26.6 + - - +
83C ILE* 3.4 21.6 - - - +
139C PHE 4.8 1.0 - - - +
140C VAL* 3.7 13.2 - - - +
141C THR 3.5 9.4 + - - -
142C LYS* 3.2 34.1 + - + +
143C HIS* 3.3 33.5 + - - +
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Residues in contact with ARG 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ALA* 2.8 29.9 + - - +
75C GLN* 1.3 80.0 - - + +
77C LEU* 1.3 66.7 + - + +
79C GLY 5.1 0.2 + - - -
81C ARG* 5.9 0.2 + - - -
139C PHE* 4.6 7.9 - - - +
142C LYS* 4.1 28.4 + - + +
101D PHE* 4.1 15.4 - - + -
104D ALA* 3.8 30.5 - - - +
105D ILE* 3.4 34.9 - - - +
108D GLU* 2.6 43.2 + - - +
109D THR* 5.7 3.6 - - - +
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Residues in contact with LEU 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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73C ILE* 2.9 19.3 + - + +
76C ARG* 1.3 86.6 - - + +
78C LEU* 1.3 73.1 + - + +
79C GLY 3.7 1.1 - - - -
95D THR* 5.2 4.5 - - - +
96D PHE* 3.4 45.5 - - + -
101D PHE* 3.5 37.9 - - + -
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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