Contacts of the strand formed by residues 73 - 80 (chain C) in PDB entry 3IXK
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 GLN 73 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C MET 3.4 1.4 - - - +
67C THR* 3.1 6.3 - - - -
68C VAL* 2.7 54.3 + - + +
71C PRO 3.7 9.4 - - - +
72C PRO* 1.3 73.5 - - - +
74C THR* 1.3 62.7 + - - +
75C LEU* 5.3 4.5 - - + -
99C TYR 4.0 4.3 - - - +
100C TYR* 3.8 16.5 - - + -
101C GLN* 3.1 50.6 + - - +
104C LEU* 4.1 14.2 + - - +
105C SER* 4.0 19.2 - - - -
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Residues in contact with THR 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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65C GLU* 3.7 37.0 + - + +
66C MET 3.4 4.3 - - - +
67C THR* 4.0 11.0 - - + +
72C PRO 4.1 3.8 + - - -
73C GLN* 1.3 74.8 - - - +
75C LEU* 1.3 75.5 + - - +
76C ASN* 5.6 0.4 - - - +
98C ARG* 3.0 37.9 + - - +
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Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLU* 3.7 2.8 - - - +
66C MET* 2.8 34.4 + - + +
68C VAL* 3.9 24.7 - - + -
73C GLN* 4.5 3.4 - - + +
74C THR* 1.3 90.8 - - - +
76C ASN* 1.3 65.6 + - - +
77C ILE* 3.8 14.6 + - + +
88C VAL* 3.9 33.7 - - + -
89C GLY 5.1 0.4 - - - +
98C ARG* 4.0 22.2 - - + +
99C TYR* 4.1 20.2 - - - +
100C TYR* 4.1 11.0 - - + +
164C GLU* 3.4 15.3 - - + +
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Residues in contact with ASN 76 (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 TYR* 3.4 30.8 - - + -
64C VAL 3.7 0.4 - - - -
65C GLU* 3.7 28.1 + - - +
74C THR* 5.6 0.4 - - - +
75C LEU* 1.3 73.3 + - - +
77C ILE* 1.3 65.6 + - - +
98C ARG* 3.3 18.1 + - - +
162C ASN* 3.3 37.1 + - - +
163C TRP* 3.4 4.1 - - - +
164C GLU* 2.8 36.8 + - - +
165C GLY 3.4 0.5 + - - -
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Residues in contact with ILE 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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63C TYR* 2.9 7.0 - - - +
64C VAL* 2.8 40.5 + - + +
66C MET* 3.5 37.9 - - + -
68C VAL* 6.5 0.2 - - + -
75C LEU* 3.8 22.7 - - + +
76C ASN* 1.3 83.6 - - - +
78C LEU* 1.3 65.6 + - - +
79C VAL 3.4 0.7 + - - -
86C PHE* 4.1 6.5 - - + -
88C VAL* 4.3 15.0 - - + -
165C GLY* 3.7 15.9 - - - -
166C ILE 3.5 8.7 - - - +
167C LEU* 3.5 36.8 - - + +
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Residues in contact with LEU 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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61C GLY* 3.5 29.2 - - - -
62C TYR 3.4 17.9 - - - +
63C TYR* 3.8 3.9 - - - +
76C ASN 4.0 0.8 + - - -
77C ILE* 1.3 69.6 - - - +
79C VAL* 1.3 66.3 + - - +
80C ASP* 3.4 3.4 + - + -
163C TRP* 3.9 37.5 - - + +
165C GLY 2.9 19.2 + - - +
166C ILE* 3.6 27.2 - - + +
167C LEU* 2.9 30.5 + - - +
277C SER 5.8 0.2 - - - +
278C GLY* 5.0 3.8 - - - -
500C 929 4.0 27.8 - - + +
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Residues in contact with VAL 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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54C LEU* 3.9 27.6 - - + -
62C TYR* 2.8 23.9 + - + +
64C VAL* 4.0 21.5 - - + +
77C ILE 4.1 1.8 - - - +
78C LEU* 1.3 72.9 - - - +
80C ASP* 1.3 60.4 + - - +
167C LEU* 4.2 6.7 - - + -
169C LEU* 3.8 20.9 - - + -
200C LEU* 3.8 22.4 - - + -
202C LEU* 5.9 1.1 - - + -
222C MET* 4.0 9.4 - - - -
277C SER* 2.9 32.9 + - - +
278C GLY* 4.0 2.3 + - - -
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Residues in contact with ASP 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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78C LEU* 3.4 2.0 + - + +
79C VAL* 1.3 74.5 - - - +
81C THR* 1.3 61.3 + - - +
82C GLY 3.2 2.9 + - - -
83C SER* 2.7 32.5 + - - +
166C ILE* 3.7 21.0 - - + +
167C LEU 3.0 15.8 + - - +
168C GLY* 3.4 2.3 - - - -
169C LEU* 2.8 24.8 + - - -
276C ASP* 3.0 10.9 - - - +
277C SER* 3.5 0.7 - - - -
278C GLY* 3.3 8.1 - - - -
500C 929 2.6 42.8 + - - +
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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