Contacts of the helix formed by residues 88 - 100 (chain X) in PDB entry 1YKX
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 ILE 88 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3X PHE* 3.7 32.5 - - + -
8X LEU* 4.3 9.2 - - + -
11X ALA* 3.7 37.7 - - + +
12X MET* 4.1 12.6 - - + +
15X HIS* 4.3 11.6 - - + +
40X THR* 4.5 9.0 - - + -
55X ILE* 4.9 11.0 - - + -
85X SER 4.9 0.9 - - - -
86X SER 3.5 1.5 + - - +
87X ASP* 1.3 72.5 + - - +
89X THR* 1.3 66.3 + - - +
90X ALA 3.3 2.0 - - - -
91X SER* 3.0 13.3 + - - -
92X VAL* 2.9 41.0 + - + +
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Residues in contact with THR 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15X HIS* 3.0 33.3 + - + +
87X ASP* 2.5 28.9 + - - -
88X ILE* 1.3 77.4 - - - +
90X ALA* 1.3 58.2 + - - +
92X VAL* 3.2 1.1 + - - +
93X ASN* 2.9 46.8 + - - +
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Residues in contact with ALA 90 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78X ILE* 4.9 10.3 - - + +
82X ALA* 3.7 32.5 - - + +
83X LEU* 3.8 10.6 - - + +
87X ASP 4.4 3.4 + - - +
88X ILE 3.3 0.8 - - - -
89X THR* 1.3 80.1 - - - +
91X SER* 1.3 63.5 + - - +
93X ASN* 3.5 6.0 + - - +
94X CYS* 3.1 24.9 + - - +
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Residues in contact with SER 91 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53X TYR 5.2 0.3 + - - -
54X GLY* 5.0 0.5 - - - -
55X ILE* 3.9 29.0 + - - +
56X LEU* 4.5 6.1 + - - +
58X ILE* 3.8 10.3 - - - +
83X LEU* 3.3 40.4 + - - +
87X ASP 5.4 0.2 + - - -
88X ILE* 3.0 13.1 + - - -
90X ALA* 1.3 79.1 - - - +
92X VAL* 1.3 58.9 + - - +
94X CYS 3.5 0.3 + - - -
95X ALA* 2.9 30.0 + - - +
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Residues in contact with VAL 92 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12X MET* 5.2 2.9 - - + -
15X HIS* 3.7 27.8 - - + +
17X LEU* 3.8 33.9 - - + -
55X ILE* 6.4 0.4 - - + -
56X LEU* 5.4 2.0 - - + -
88X ILE* 2.9 41.9 + - + +
89X THR* 3.6 7.9 - - - +
91X SER* 1.3 76.3 - - - +
93X ASN* 1.3 71.4 + - - +
95X ALA* 3.2 7.6 + - - +
96X LYS* 3.0 36.8 + - - +
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Residues in contact with ASN 93 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15X HIS* 5.3 3.4 + - - -
89X THR* 2.9 36.5 + - - +
90X ALA* 4.0 5.9 - - - +
92X VAL* 1.3 84.1 - - - +
94X CYS* 1.3 62.0 + - - +
96X LYS* 3.5 26.6 + - - +
97X LYS* 3.5 11.3 + - - +
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Residues in contact with CYS 94 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58X ILE* 3.7 25.8 - - + -
63X TRP* 3.9 15.7 - - - -
76X CYS* 2.0 53.2 - - + -
78X ILE* 5.4 1.3 - - + -
83X LEU* 4.6 6.5 - - + -
90X ALA 3.1 18.2 + - - +
93X ASN* 1.3 74.5 - - - +
95X ALA* 1.3 65.9 + - - +
97X LYS* 3.1 5.5 + - - +
98X ILE* 3.0 27.1 + - - +
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Residues in contact with ALA 95 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X LEU* 5.2 2.9 - - + -
28X TRP* 4.2 9.2 - - + -
56X LEU* 3.8 24.0 - - + -
58X ILE* 4.2 2.2 - - + +
91X SER 2.9 18.8 + - - +
92X VAL* 3.2 6.9 + - - +
94X CYS* 1.3 76.0 - - - +
96X LYS* 1.3 57.7 + - - +
98X ILE* 3.2 8.2 + - - +
99X VAL* 2.9 32.8 + - - +
108X TRP* 3.8 19.3 - - + -
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Residues in contact with LYS 96 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15X HIS 2.7 29.2 + - - -
16X GLY* 4.1 17.1 + - - -
17X LEU* 4.0 12.8 - - + -
20X TYR* 3.6 40.7 + - + +
92X VAL* 3.0 28.7 + - + +
93X ASN* 3.6 19.7 - - - +
94X CYS 3.2 0.2 - - - -
95X ALA* 1.3 78.3 - - - +
97X LYS* 1.3 59.3 + - - +
99X VAL* 3.4 7.6 - - - +
100X SER* 2.7 24.8 + - - -
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Residues in contact with LYS 97 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63X TRP* 4.1 14.6 - - + -
75X LEU* 2.6 34.1 + - + +
76X CYS* 3.7 23.3 + - - +
77X ASN* 5.7 0.8 - - - +
93X ASN 3.5 8.1 + - - +
94X CYS* 3.1 9.9 + - - +
96X LYS* 1.3 76.5 - - - +
98X ILE* 1.3 65.3 + - - +
100X SER* 3.4 13.8 + - - -
101X ASP* 3.4 11.8 + - - +
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Residues in contact with ILE 98 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58X ILE* 3.8 33.7 - - + -
63X TRP* 3.5 52.7 - - + -
94X CYS* 3.0 15.4 + - - +
95X ALA* 3.6 9.9 - - - +
97X LYS* 1.3 77.0 - - - +
99X VAL* 1.3 58.2 + - - +
101X ASP* 3.0 25.8 + - - +
102X GLY 4.7 0.2 + - - -
104X GLY 4.5 4.0 + - - +
107X ALA* 3.9 24.7 - - + +
108X TRP* 3.7 21.1 - - + -
1903X EOH 4.2 7.4 - - + -
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Residues in contact with VAL 99 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X TYR* 3.6 28.3 - - + -
21X ARG* 4.0 8.9 - - + +
23X TYR* 3.7 25.9 - - + -
28X TRP* 3.8 12.3 - - + -
95X ALA 2.9 15.1 + - - +
96X LYS* 3.4 13.9 - - - +
98X ILE* 1.3 76.6 - - - +
100X SER* 1.3 60.7 + - - +
101X ASP 3.3 1.3 + - - -
102X GLY 4.4 0.5 + - - -
104X GLY* 3.6 41.3 + - - -
105X MET* 3.8 11.7 - - + +
108X TRP* 4.3 4.0 - - + -
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Residues in contact with SER 100 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X TYR* 3.7 1.9 + - - -
21X ARG* 3.0 46.6 + - - +
96X LYS 2.7 21.5 + - - -
97X LYS* 3.4 7.5 + - - -
98X ILE 3.1 1.0 - - - -
99X VAL* 1.3 76.7 - - - +
101X ASP* 1.3 62.3 + - - +
102X GLY* 3.2 5.1 + - - -
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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