Contacts of the strand formed by residues 81 - 90 (chain C) in PDB entry 5YXK
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 GLY 81 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C GLN* 3.4 15.3 - - - -
79C ASP 3.5 1.8 + - - -
80C LYS* 1.3 73.9 - - - +
82C LEU* 1.3 59.8 + - - -
83C TYR* 3.4 13.7 - - - -
104C GLU* 4.5 4.7 - - - -
105C LEU 2.7 40.2 + - - -
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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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0C MET* 3.7 24.5 - - - -
34C ASP* 3.6 0.9 - - - -
35C GLN* 3.0 45.6 + - + +
81C GLY* 1.3 73.6 - - - -
83C TYR* 1.3 61.9 + - - +
102C ASN* 4.3 16.2 - - + +
103C SER 3.7 20.6 - - - +
104C GLU* 3.7 17.5 - - + +
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Residues in contact with TYR 83 (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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13C LEU* 4.1 22.7 - - + -
32C TRP* 6.0 1.8 - - + -
33C GLN 3.3 15.9 - - - +
34C ASP* 3.7 21.3 - - + -
40C LEU* 3.8 29.6 - - + -
57C TYR* 4.0 9.6 + - - -
72C LEU* 3.9 10.4 - - + +
79C ASP* 2.5 46.2 + - - +
80C LYS 4.7 0.8 + - - -
81C GLY* 3.4 21.3 - - - -
82C LEU* 1.3 76.9 - - - +
84C GLN* 1.3 62.1 + - - +
101C MET 4.6 0.2 - - - -
102C ASN* 3.3 6.8 - - - +
103C SER* 2.7 43.3 + - - +
105C LEU* 3.8 16.8 - - + -
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Residues in contact with GLN 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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31C PHE 3.7 0.9 - - - +
32C TRP* 3.2 8.1 - - - -
33C GLN* 2.8 45.3 + - + +
34C ASP 5.5 0.4 - - - +
83C TYR* 1.3 75.4 - - - +
85C CYS* 1.3 68.0 - - - +
86C ILE* 3.3 29.4 + - + +
97C ARG* 6.0 0.3 - - - -
100C GLN* 3.6 22.9 - - - +
101C MET 3.5 7.2 - - - +
102C ASN* 2.8 34.0 + - - +
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Residues in contact with CYS 85 (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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14C PRO 4.3 2.5 - - - +
15C CYS* 2.1 59.9 - - + -
30C VAL* 4.3 4.3 - - - -
31C PHE 3.5 4.5 - - - -
32C TRP* 3.6 19.1 - - + +
84C GLN* 1.3 71.4 - - - +
86C ILE* 1.3 64.4 + - - +
87C ILE* 4.0 15.3 - - - -
99C HIS* 5.3 1.8 - - - -
100C GLN* 3.0 8.0 - - - +
101C MET 2.9 37.0 + - - +
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Residues in contact with ILE 86 (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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29C VAL 3.6 2.1 - - - +
30C VAL* 3.4 3.6 - - - +
31C PHE* 2.8 51.3 + - + +
33C GLN* 3.6 23.1 - - - +
84C GLN* 3.3 33.2 - - + +
85C CYS* 1.3 81.6 - - - +
87C ILE* 1.3 65.0 + - - +
88C HIS* 3.2 33.2 - - + +
97C ARG* 3.8 24.2 - - + -
99C HIS 3.5 3.8 - - - +
100C GLN* 4.4 1.6 - - + -
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Residues in contact with ILE 87 (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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15C CYS* 4.4 6.3 - - + -
17C PHE* 3.3 48.0 - - + -
28C LEU* 4.1 24.7 - - + -
29C VAL 3.7 2.7 - - - +
30C VAL* 4.2 11.2 - - + -
68C TRP* 4.3 10.8 - - + -
85C CYS* 4.0 11.2 - - - -
86C ILE* 1.3 77.2 - - - +
88C HIS* 1.3 59.5 + - - +
97C ARG* 3.5 4.2 - - - +
98C ILE* 2.7 51.8 + - + -
99C HIS* 2.8 27.9 + - + +
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Residues in contact with HIS 88 (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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28C LEU* 3.1 13.1 - - - +
29C VAL* 2.8 47.2 + - + +
31C PHE* 3.5 25.7 - + - -
86C ILE* 3.2 31.1 - - + +
87C ILE* 1.3 77.6 - - - +
89C HIS* 1.3 58.8 + - - +
90C LYS 3.9 0.2 - - - -
95C MET* 3.8 48.1 + - + +
96C ILE 3.1 9.4 - - - +
97C ARG* 3.7 21.8 + - + +
98C ILE* 4.5 0.4 - - - -
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Residues in contact with HIS 89 (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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23C GLN* 3.0 27.5 + - - +
27C GLU* 3.4 30.6 + - + +
28C LEU* 4.1 5.2 - - + -
88C HIS* 1.3 71.6 - - - +
90C LYS* 1.3 66.1 + - - +
91C LYS* 3.3 44.0 + - + +
95C MET* 3.3 4.2 - - - -
96C ILE* 2.7 41.7 + - + +
98C ILE* 4.1 17.7 - - + +
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Residues in contact with LYS 90 (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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27C GLU* 3.0 20.1 + - - +
28C LEU* 4.5 0.2 - - - +
29C VAL* 4.6 13.4 - - + +
44C TYR* 3.6 26.0 - - - +
45C LEU* 3.8 26.9 - - + -
88C HIS 3.8 2.2 + - - -
89C HIS* 1.3 81.5 + - - +
91C LYS* 1.3 90.5 + - - +
92C PRO* 3.6 12.5 + - - +
93C THR* 4.6 0.2 - - - +
94C GLY 3.5 17.7 + - - +
95C MET* 4.4 5.4 - - + -
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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