Contacts of the helix formed by residues 67 - 74 (chain B) in PDB entry 1KKC
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 ASP 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B ALA* 3.0 16.7 + - - +
65B ALA* 4.3 12.6 - - + +
66B THR* 1.3 74.2 - - - +
68B VAL* 1.3 61.1 + - - +
69B PRO* 3.1 15.7 - - - +
70B LYS* 2.9 35.6 + - + +
71B LEU* 2.9 21.6 + - - +
16Y TYR* 4.0 0.4 + - - -
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B THR 3.5 3.2 + - - +
67B ASP* 1.3 72.3 - - - +
69B PRO* 1.3 72.7 - - + +
71B LEU* 3.0 10.7 + - + +
72B VAL* 2.9 26.1 + - + +
16Y TYR* 3.4 40.2 - - + +
52Y LEU* 4.2 13.0 - - + -
82Y GLY* 3.6 21.5 - - - +
85Y HIS* 4.4 7.9 - - + +
86Y ILE* 3.5 27.4 - - + -
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Residues in contact with PRO 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B THR 5.4 0.2 - - - +
67B ASP* 3.1 12.3 - - - +
68B VAL* 1.3 95.3 - - + +
70B LYS* 1.3 56.7 + - - +
72B VAL* 3.6 2.4 + - - +
73B SER* 3.1 27.4 + - - -
86Y ILE* 3.7 26.5 - - + -
163Y PRO* 6.1 0.2 - - + -
165Y THR* 5.5 3.5 - - - +
213Y LYS 5.3 9.0 - - - +
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Residues in contact with LYS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ALA* 5.3 13.7 - - + +
62B ALA* 3.8 18.6 - - + +
67B ASP* 2.9 31.4 + - - +
69B PRO* 1.3 73.8 - - - +
71B LEU* 1.3 66.4 + - - +
73B SER* 2.5 28.9 + - - +
74B VAL* 3.2 14.4 + - + +
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLN* 3.3 52.6 - - + +
62B ALA* 4.0 4.0 - - - +
63B ALA* 3.7 28.7 - - + +
67B ASP 2.9 15.8 + - - +
68B VAL* 3.0 13.2 + - + +
70B LYS* 1.3 78.1 - - - +
72B VAL* 1.3 60.9 + - + +
74B VAL* 3.1 23.1 - - - +
75B GLN* 3.7 1.9 + - - +
16Y TYR* 3.9 19.5 - - + +
52Y LEU* 5.7 1.6 - - + -
56Y LEU* 3.6 36.1 - - + -
78Y ILE* 4.3 9.0 - - + +
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Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B VAL* 2.9 21.9 + - + +
69B PRO 4.0 2.9 - - - +
71B LEU* 1.3 75.9 - - + +
73B SER* 1.3 63.1 + - - +
75B GLN* 3.0 29.0 - - - +
76B GLN 4.4 0.2 + - - -
78Y ILE* 3.8 26.5 - - + +
79Y LYS* 4.2 18.8 - - + +
82Y GLY* 3.9 22.2 - - - -
83Y GLY 4.0 0.2 - - - +
86Y ILE* 4.2 3.4 - - + -
163Y PRO* 3.7 32.8 - - + -
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Residues in contact with SER 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PRO 3.1 13.5 + - - -
70B LYS* 2.5 42.8 + - - +
72B VAL* 1.3 79.3 - - - +
74B VAL* 1.3 59.6 + - - +
75B GLN 3.5 0.2 + - - -
76B GLN* 4.0 11.8 + - - +
77B ALA* 4.7 1.6 + - - +
165Y THR* 5.0 17.2 - - - +
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Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ALA* 3.1 38.1 - - + +
58B ALA* 3.8 16.6 - - + -
59B GLN* 3.2 35.0 - - + +
70B LYS* 3.2 9.4 + - + +
71B LEU 3.1 18.4 - - - +
73B SER* 1.3 80.0 + - - +
75B GLN* 1.3 64.0 + - - +
76B GLN 3.2 1.1 - - - -
77B ALA* 3.0 18.5 + - + +
78B ILE* 3.0 10.9 + - + +
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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