Contacts of the helix formed by residues 67 - 72 (chain C) in PDB entry 1KI1
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 LEU 67 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61C GLN* 4.6 4.0 - - + -
64C TYR* 2.9 21.5 + - + +
66C ARG* 1.3 78.1 - - - +
68C ARG* 1.3 66.7 + - - +
69C PRO 3.4 0.4 - - - -
70C LEU* 3.0 31.9 + - + +
1333D CYS* 4.7 0.7 - - + -
1379D MET* 3.9 24.3 - - + +
1382D VAL* 5.4 0.9 - - + -
1383D THR* 3.6 27.8 - - + -
1417D CYS* 4.1 18.8 - - + +
1420D VAL* 3.9 20.0 - - + -
1421D ASN* 3.5 14.4 - - - +
1424D VAL* 3.8 27.8 - - + -
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Residues in contact with ARG 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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58C THR* 5.9 3.1 - - + -
61C GLN* 2.8 50.2 + - + +
62C GLU* 3.5 14.0 + - - +
64C TYR 3.2 8.2 + - - +
65C ASP* 3.4 27.6 - - - +
67C LEU* 1.3 76.0 - - - +
69C PRO* 1.3 67.4 - - + +
70C LEU 3.0 1.4 + - - -
71C SER* 3.1 15.1 + - - -
72C TYR* 3.5 23.9 - - + +
96C LYS* 3.5 22.9 - - - +
97C TRP* 3.2 29.6 - - - -
100C GLU* 2.5 44.0 + - - +
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Residues in contact with PRO 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 3.1 24.0 - - - +
66C ARG* 3.9 21.5 - - - +
67C LEU 3.5 1.3 - - - -
68C ARG* 1.3 92.3 - - + +
70C LEU* 1.3 63.6 + - + +
71C SER 3.1 1.3 - - - -
72C TYR* 3.1 27.8 + - + +
73C PRO* 3.3 11.1 - - - +
100C GLU* 5.0 4.3 - - - +
104C HIS* 3.5 39.6 + - + +
1337D LEU* 5.1 3.5 - - + +
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Residues in contact with LEU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ARG 3.7 17.3 - - - +
67C LEU* 3.0 34.4 + - + +
68C ARG 3.0 1.4 + - - -
69C PRO* 1.3 80.2 - - + +
71C SER* 1.3 57.7 + - - +
72C TYR 3.4 0.2 - - - -
73C PRO* 3.8 9.7 - - - +
1333D CYS* 4.3 12.1 - - + +
1336D GLN* 4.1 32.9 + - + +
1337D LEU* 3.9 42.7 - - + +
1376D LEU* 3.0 20.8 - - - +
1379D MET* 4.3 13.2 - - + -
1424D VAL* 4.7 8.5 - - + -
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Residues in contact with SER 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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5C LYS* 2.8 30.5 + - - -
7C VAL* 4.0 8.1 - - - +
56C PHE* 5.7 4.5 - - - -
57C ASP 5.0 1.4 + - - -
58C THR* 4.4 12.3 - - - +
61C GLN* 3.3 23.7 + - - -
68C ARG 3.1 8.6 + - - -
69C PRO 3.1 0.8 - - - -
70C LEU* 1.3 79.0 - - - +
72C TYR* 1.3 64.5 + - - +
73C PRO* 3.7 1.1 - - - -
75C THR* 3.9 1.0 + - - -
1376D LEU* 4.0 16.5 - - - +
1379D MET* 3.6 12.6 - - - +
1380D GLN* 5.0 2.4 + - - -
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Residues in contact with TYR 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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7C VAL* 4.6 4.7 - - + -
9C VAL* 4.1 20.4 - - + +
58C THR* 5.0 3.3 - - + +
68C ARG* 3.5 20.3 - - + +
69C PRO* 3.1 25.5 + - + +
71C SER* 1.3 83.8 - - - +
73C PRO* 1.3 67.7 - - + +
74C GLN 3.3 0.2 + - - -
75C THR* 2.5 27.4 + - - -
78C PHE* 3.7 25.4 - + + -
97C TRP* 4.2 7.3 - - - -
100C GLU* 2.8 42.3 + - + +
101C ILE* 4.4 12.8 - - + +
104C HIS* 3.8 23.1 - + + +
105C CYS* 3.7 19.6 - - - -
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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