Contacts of the helix formed by residues 61 - 69 (chain N) in PDB entry 1K2V
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 61 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1N DEF 4.0 7.8 - - - +
43N TRP* 3.4 13.9 + - + -
59N VAL 3.4 2.0 + - - -
60N ALA* 1.3 77.3 - - - +
62N THR* 1.3 63.0 + - - +
63N ILE* 3.7 7.1 + - - +
64N ASN* 2.5 52.1 + - - +
65N TYR* 3.1 13.2 + - - +
80N ASP* 3.5 8.6 + - - +
82N GLY 2.7 17.6 + - - +
83N LEU* 3.8 21.2 - - - +
84N ARG* 4.1 9.8 - - - -
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Residues in contact with THR 62 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59N VAL* 3.6 34.1 - - + +
60N ALA 4.6 0.2 - - - -
61N ASP* 1.3 73.4 - - - +
63N ILE* 1.3 67.7 + - - +
65N TYR* 3.3 9.8 + - - +
66N ARG* 3.2 39.3 + - - +
74N LEU* 4.2 10.7 - - + +
78N VAL* 4.2 16.4 - - + +
80N ASP* 2.5 40.0 + - + +
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Residues in contact with ILE 63 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61N ASP* 3.2 6.9 - - - +
62N THR* 1.3 82.1 + - - +
64N ASN* 1.3 71.5 + - - +
66N ARG* 3.1 41.9 + - - +
67N LEU* 3.4 17.7 + - + +
80N ASP* 4.6 6.1 - - - +
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Residues in contact with ASN 64 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1N DEF 3.8 16.9 - - + -
43N TRP* 3.5 15.7 - - + -
61N ASP* 2.5 40.2 + - - +
63N ILE* 1.3 79.6 - - - +
65N TYR* 1.3 65.3 + - - +
67N LEU* 2.9 22.5 + - - +
68N TRP* 2.9 37.1 + - + +
83N LEU* 4.6 6.5 - - - +
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Residues in contact with TYR 65 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43N TRP* 3.3 32.2 - + + +
46N VAL* 3.7 21.6 - - + +
47N GLU* 5.4 3.0 + - + +
50N LEU* 3.6 8.0 - - - +
59N VAL* 5.1 0.4 - - + -
61N ASP 3.1 15.0 + - - +
62N THR* 3.3 14.4 - - - +
63N ILE 3.1 0.2 - - - -
64N ASN* 1.3 75.9 - - - +
66N ARG* 1.3 65.3 + - + +
69N VAL* 2.9 48.4 + - + +
70N SER 2.9 28.3 + - - -
72N PRO* 2.6 46.3 + - - +
73N PRO* 4.7 0.4 - - + -
74N LEU* 3.5 33.0 - - + -
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Residues in contact with ARG 66 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62N THR* 3.2 29.7 + - - +
63N ILE* 3.1 33.4 + - - +
64N ASN 3.0 0.6 - - - -
65N TYR* 1.3 88.9 - - + +
67N LEU* 1.3 65.7 + - + +
70N SER* 3.3 26.4 - - - +
73N PRO* 6.5 0.4 - - + -
74N LEU* 5.7 13.4 + - + +
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Residues in contact with LEU 67 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63N ILE* 3.6 22.0 - - + +
64N ASN* 2.9 25.9 + - - +
66N ARG* 1.3 86.3 - - + +
68N TRP* 1.3 69.1 + - + +
70N SER* 5.1 0.2 - - - -
240N HIS* 3.8 22.1 - - - +
241N ASP* 4.4 29.4 - - + +
271N ALA* 3.4 18.6 - - - +
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Residues in contact with TRP 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1N DEF 3.5 52.5 - - + +
43N TRP* 3.9 4.5 - - + -
64N ASN* 2.9 31.9 + - + +
67N LEU* 1.3 91.5 - - + +
69N VAL* 1.3 60.1 + - - +
181N THR* 4.6 2.7 - - + -
182N LEU 5.1 0.7 - - - -
183N ILE* 6.0 2.9 - - - -
240N HIS* 3.2 57.3 + + + -
271N ALA* 3.7 10.8 - - + +
272N VAL 3.6 6.6 - - - +
273N TRP* 3.4 34.8 + + + -
274N PHE* 3.9 32.9 - + - -
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Residues in contact with VAL 69 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N TRP* 3.7 28.9 - - + +
47N GLU* 5.4 4.9 - - + +
65N TYR* 2.9 55.4 + - + +
68N TRP* 1.3 77.9 - - - +
70N SER* 1.3 58.5 + - - +
71N GLU* 2.7 18.4 + - - +
72N PRO* 3.9 12.6 - - + -
271N ALA 4.4 1.4 - - - +
273N TRP* 3.9 28.5 + - + -
280N SER* 5.0 5.2 - - - +
283N HIS* 3.9 14.7 + - - -
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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