Contacts of the helix formed by residues 64 - 71 (chain H) in PDB entry 1Q0K
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 LYS 64 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61H ASP 3.6 7.1 + - - +
62H TYR* 3.1 27.2 + - - +
63H PHE* 1.3 75.1 - - - +
65H PRO* 1.3 80.8 - - + +
66H PRO* 3.2 11.9 - - + -
67H HIS* 2.8 29.9 + - + +
68H PHE* 3.2 16.4 + - - -
9008H SO4 3.2 37.8 + - - -
83I LYS* 4.3 11.2 - - - +
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Residues in contact with PRO 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D SER* 3.3 17.3 - - - +
71D TYR* 3.5 30.3 - - + +
113D GLU* 5.8 2.2 - - - -
64H LYS* 1.3 88.7 - - + +
66H PRO* 1.3 69.7 - - + +
67H HIS 3.1 0.2 + - - -
68H PHE* 3.2 12.9 + - + +
69H GLU* 3.0 27.8 + - + +
79I ASN* 5.7 0.4 - - - +
83I LYS* 4.6 12.8 - - + -
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Residues in contact with PRO 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D GLU 3.6 14.6 - - - +
70D SER* 3.1 25.8 - - - +
72D PRO* 3.7 19.5 - - + +
64H LYS* 3.2 12.8 - - + -
65H PRO* 1.3 95.0 - - + +
67H HIS* 1.3 65.9 + - + +
69H GLU* 3.8 2.1 - - + +
70H SER* 2.7 33.5 + - - -
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Residues in contact with HIS 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H TYR* 3.9 26.1 + + - -
63H PHE* 3.3 24.3 - + + -
64H LYS* 2.8 45.5 + - + +
66H PRO* 1.3 77.4 - - + +
68H PHE* 1.3 59.8 + - - +
70H SER* 3.4 0.8 + - - -
71H TYR* 2.9 41.3 + + + +
74H LEU* 4.3 6.1 - - + -
114H THR* 3.6 34.5 + - + -
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Residues in contact with PHE 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H TRP* 3.6 27.6 - + - -
63H PHE* 3.6 23.8 - + + -
64H LYS 3.4 20.6 - - - -
65H PRO* 3.2 10.3 + - + +
67H HIS* 1.3 77.3 - - - +
69H GLU* 1.3 60.4 + - + +
71H TYR 3.1 20.9 - - - +
72H PRO* 3.6 6.9 - - - +
74H LEU* 3.8 32.3 - - + -
75H HIS* 3.3 52.0 - + + +
79I ASN* 3.6 23.8 - - - -
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Residues in contact with GLU 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D TYR* 2.9 44.1 - - + +
72D PRO* 3.7 1.0 - - + -
73D GLU* 3.0 51.3 + - + +
110D ILE* 3.7 15.4 - - - +
65H PRO 3.0 19.3 + - - +
66H PRO* 3.8 4.7 - - + +
68H PHE* 1.3 76.7 - - + +
70H SER* 1.3 65.0 + - - +
71H TYR 3.1 2.3 + - - -
72H PRO* 3.6 14.9 - - - +
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Residues in contact with SER 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D PRO* 4.2 7.1 - - - +
73D GLU* 3.8 19.1 + - - -
66H PRO 2.7 18.1 + - - -
67H HIS* 4.7 0.4 - - - -
69H GLU* 1.3 77.8 - - - +
71H TYR* 1.3 84.3 + - - +
72H PRO* 3.5 6.6 - - - +
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Residues in contact with TYR 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67H HIS* 2.9 28.9 + + + +
68H PHE* 3.1 11.8 - - - +
70H SER* 1.3 97.8 - - - +
72H PRO* 1.3 62.5 - - - +
73H GLU* 2.9 23.4 + - - +
74H LEU* 3.0 25.1 + - + +
75H HIS* 4.8 0.3 + - - -
110H ILE* 3.9 36.8 - - + -
113H GLU* 3.1 39.3 + - - +
114H THR* 3.7 23.2 + - + +
117H ALA* 5.8 1.6 - - - +
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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