Contacts of the helix formed by residues 74 - 84 (chain C) in PDB entry 1H88
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 74 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67C ALA* 4.6 0.4 - - - -
72C ASN 5.9 0.7 - - - -
73C ARG* 1.3 78.0 - - - +
75C ASP* 1.3 68.2 + - - +
76C VAL* 2.9 30.0 + - - +
77C GLN* 2.6 35.8 + - - +
78C CYS* 3.2 10.7 + - - -
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Residues in contact with ASP 75 (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* 3.2 48.5 - - - +
64C LYS* 4.1 10.1 + - + +
67C ALA* 3.6 9.4 - - + +
74C THR* 1.3 73.7 - - - +
76C VAL* 1.3 87.7 + - - +
78C CYS* 3.5 2.1 + - - +
79C GLN* 3.4 19.6 + - - +
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Residues in contact with VAL 76 (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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74C THR* 2.9 17.9 - - - +
75C ASP* 1.3 94.5 - - - +
77C GLN* 1.3 84.6 + - + +
79C GLN* 3.0 32.3 - - - +
80C HIS* 3.2 17.7 + - + +
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Residues in contact with GLN 77 (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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39C GLY* 3.8 11.8 - - - -
40C LYS* 3.3 32.5 - - - +
43C TRP* 3.9 16.2 + - + +
72C ASN 3.9 3.1 - - - +
73C ARG* 3.3 11.8 - - - -
74C THR* 2.6 47.9 + - - +
76C VAL* 1.3 88.3 - - + +
78C CYS* 1.3 58.3 + - - +
80C HIS* 3.2 7.5 + - - +
81C ARG* 2.8 31.2 + - - +
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Residues in contact with CYS 78 (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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43C TRP* 4.0 8.1 - - - -
51C LEU* 3.6 22.7 - - + +
63C TRP* 4.0 10.7 - - + +
66C ILE* 4.2 2.9 - - + -
67C ALA* 4.0 20.9 - - + -
70C LEU* 3.9 21.3 - - - -
73C ARG* 3.9 21.1 - - - -
74C THR 3.2 17.0 + - - -
75C ASP* 3.6 10.1 - - - +
76C VAL 3.2 0.2 - - - -
77C GLN* 1.3 77.5 - - - +
79C GLN* 1.3 62.7 + - - +
81C ARG* 3.3 1.2 + - - +
82C TRP* 3.2 18.2 + - - +
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Residues in contact with GLN 79 (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* 3.2 50.1 - - + +
75C ASP* 3.4 8.4 + - - +
76C VAL* 3.0 32.1 - - - +
78C CYS* 1.3 78.3 - - - +
80C HIS* 1.3 63.0 + - + +
83C GLN* 2.7 66.8 + - - +
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Residues in contact with HIS 80 (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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76C VAL* 3.2 22.4 + - + +
77C GLN* 3.7 7.4 - - - +
79C GLN* 1.3 85.4 + - + +
81C ARG* 1.3 65.2 + - - +
83C GLN* 3.8 15.7 - - - -
84C LYS* 3.1 61.3 + - + +
85C VAL* 4.8 0.9 - - - +
1E C 4.0 37.5 + - - -
2E C 3.7 17.4 + - - -
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Residues in contact with ARG 81 (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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43C TRP* 3.4 63.6 + - + +
45C ARG* 3.9 8.7 - - - +
48C ASP* 3.0 36.5 + - - -
51C LEU* 4.3 0.4 - - + -
77C GLN 2.8 16.3 + - - +
78C CYS 3.3 5.4 + - - +
80C HIS* 1.3 77.5 - - - +
82C TRP* 1.3 57.8 + - - +
85C VAL* 3.0 60.6 + - - +
86C LEU* 3.1 14.9 + - + +
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Residues in contact with TRP 82 (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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51C LEU* 3.7 11.2 - - + -
52C LYS* 4.9 6.9 - - - +
55C VAL* 3.6 39.7 - - + +
56C GLU* 4.6 7.4 + - - -
60C THR* 3.9 30.1 - - + -
63C TRP* 4.1 12.8 - + + -
78C CYS 3.2 15.6 + - - +
79C GLN 3.9 1.8 - - - +
81C ARG* 1.3 74.7 - - - +
83C GLN* 1.3 94.1 + - + +
84C LYS 3.1 1.6 + - - -
85C VAL 3.1 4.9 + - - -
86C LEU* 3.8 22.2 - - + -
87C ASN* 2.8 66.4 + - + +
88C PRO* 4.3 10.7 - - + +
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Residues in contact with GLN 83 (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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60C THR* 4.3 15.6 - - - +
63C TRP* 4.5 2.3 - - + +
79C GLN* 2.7 65.6 + - + +
80C HIS* 3.8 11.4 - - - +
82C TRP* 1.3 97.7 - - + +
84C LYS* 1.3 63.2 + - + +
85C VAL 3.9 0.2 + - - -
87C ASN* 4.2 5.7 + - - +
90C LEU* 3.9 19.9 - - - +
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Residues in contact with LYS 84 (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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80C HIS* 3.1 61.3 + - + +
83C GLN* 1.3 83.1 - - + +
85C VAL* 1.3 67.3 + - + +
90C LEU* 3.9 9.2 - - - +
2E C 4.7 14.1 - - - +
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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