Contacts of the helix formed by residues 89 - 98 (chain C) in PDB entry 1KIP
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 89 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C HIS* 3.3 27.5 + - + +
87C ASP* 2.8 32.8 + - - -
88C ILE* 1.3 77.4 - - - +
90C ALA* 1.3 65.9 + - - +
92C VAL* 3.0 6.3 + - - +
93C ASN* 2.9 45.0 + - - +
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Residues in contact with ALA 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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78C ILE* 4.3 22.9 - - + +
82C ALA* 4.3 17.7 - - + +
83C LEU* 3.5 20.6 - - + +
87C ASP 4.6 3.6 + - - +
88C ILE 3.4 0.8 - - - -
89C THR* 1.3 82.1 - - - +
91C SER* 1.3 61.9 + - - +
93C ASN* 4.0 6.5 - - - +
94C CYS* 3.2 18.9 + - - +
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Residues in contact with SER 91 (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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53C TYR 4.9 0.3 + - - -
55C ILE* 3.9 28.4 + - - +
56C LEU* 4.1 7.2 - - - +
58C ILE* 3.9 16.3 - - - +
83C LEU* 3.5 36.5 + - - +
87C ASP 5.3 0.4 + - - -
88C ILE* 2.8 18.4 + - - -
90C ALA* 1.3 73.8 - - - +
92C VAL* 1.3 55.7 + - - -
94C CYS* 3.5 1.9 + - - +
95C ALA* 3.1 29.1 + - - +
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Residues in contact with VAL 92 (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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12C MET* 5.3 2.7 - - + -
15C HIS* 3.7 33.9 - - + +
17C LEU* 3.8 33.6 - - + +
56C LEU* 5.1 3.8 - - + -
88C ILE* 2.9 47.7 + - + +
89C THR* 3.7 6.3 - - - +
91C SER* 1.3 74.5 - - - +
93C ASN* 1.3 62.3 + - - +
95C ALA* 3.5 5.6 + - - +
96C LYS* 3.0 32.9 + - - +
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Residues in contact with ASN 93 (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 HIS* 5.8 3.6 + - - +
89C THR* 2.9 38.8 + - - +
90C ALA* 4.0 6.8 + - - +
92C VAL* 1.3 80.0 - - - +
94C CYS* 1.3 64.2 + - - +
96C LYS* 3.4 23.0 + - - +
97C LYS* 3.2 19.9 + - - +
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Residues in contact with CYS 94 (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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58C ILE* 4.0 12.8 - - + -
63C TRP* 3.8 15.9 - - - -
76C CYS* 2.0 53.8 - - + -
78C ILE* 5.2 1.6 - - + -
83C LEU* 4.7 10.1 - - + -
90C ALA 3.2 15.9 + - - +
91C SER 4.1 3.4 - - - +
93C ASN* 1.3 75.0 - - - +
95C ALA* 1.3 61.0 + - - +
97C LYS* 2.9 8.1 + - - +
98C ILE* 2.9 39.4 + - - +
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Residues in contact with ALA 95 (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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17C LEU* 5.5 1.6 - - + -
28C TRP* 4.4 10.3 - - + -
56C LEU* 3.7 17.0 - - + -
58C ILE* 5.3 1.3 - - + +
91C SER 3.1 17.3 + - - +
92C VAL* 3.9 5.4 - - - +
93C ASN 3.3 0.2 - - - -
94C CYS* 1.3 77.9 - - - +
96C LYS* 1.3 57.3 + - - +
98C ILE* 3.5 12.5 - - - +
99C VAL* 2.9 34.4 + - - +
108C TRP* 3.7 21.8 - - + -
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Residues in contact with LYS 96 (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 HIS 3.1 28.9 + - - -
16C GLY* 3.8 18.3 + - - -
17C LEU* 4.2 10.3 - - + -
20C TYR* 2.6 50.9 + - + +
21C ARG* 4.9 1.4 + - - -
92C VAL* 3.0 29.2 + - - +
93C ASN* 3.6 23.1 - - - +
94C CYS 3.2 0.4 - - - -
95C ALA* 1.3 78.2 - - - +
97C LYS* 1.3 59.2 + - - +
99C VAL 3.3 8.0 - - - +
100C SER* 5.1 0.3 - - - -
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Residues in contact with LYS 97 (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 TRP* 4.9 8.1 - - + -
75C LEU* 2.8 29.8 + - + +
76C CYS* 3.8 25.2 + - - +
77C ASN* 4.5 6.1 - - - +
93C ASN 3.2 10.1 + - - +
94C CYS* 2.9 14.1 + - - +
96C LYS* 1.3 80.5 - - - +
98C ILE* 1.3 61.5 + - + +
99C VAL 4.6 0.4 - - - -
100C SER* 4.4 9.7 + - - -
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Residues in contact with ILE 98 (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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58C ILE* 4.1 15.7 - - + -
63C TRP* 3.8 52.5 - - + +
94C CYS* 2.9 32.6 + - - +
95C ALA* 3.5 14.6 - - - +
97C LYS* 1.3 79.8 - - - +
99C VAL* 1.3 58.3 + - - +
100C SER* 3.0 10.2 + - - -
104C GLY* 4.6 4.3 - - - +
107C ALA* 3.4 32.0 - - + +
108C TRP* 4.3 12.6 - - + -
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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