Contacts of the helix formed by residues 80 - 88 (chain C) in PDB entry 2H35
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 80 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C ALA* 4.8 14.1 - - + +
68C ASN* 3.7 27.1 - - + +
69C ALA* 4.4 9.0 - - + +
76C MET* 2.8 48.5 + - + +
77C PRO 4.2 1.8 - - - -
79C ALA* 1.3 75.7 - - - +
81C SER* 1.3 64.4 + - - +
82C ALA 3.1 3.2 + - - -
83C LEU* 3.3 42.9 + - + +
84C SER 3.6 3.5 + - - -
132C VAL* 4.9 8.5 - - + -
135C VAL* 3.8 29.9 - - + +
136C LEU* 5.2 0.2 - - - -
142C HEM 6.4 0.2 - - + -
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Residues in contact with SER 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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77C PRO 3.3 18.1 + - - -
78C ASN* 3.1 19.9 + - - -
79C ALA 3.1 1.8 - - - -
80C LEU* 1.3 79.7 - - - +
82C ALA* 1.3 62.7 + - - +
84C SER* 3.4 10.0 + - - -
85C ASP* 3.2 17.3 + - - +
135C VAL 4.8 1.3 - - - -
138C SER* 6.0 0.4 - - - -
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Residues in contact with ALA 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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78C ASN 4.7 0.6 + - - -
79C ALA 4.0 7.9 + - - +
80C LEU 3.1 0.6 - - - -
81C SER* 1.3 76.4 - - - +
83C LEU* 1.3 66.3 + - + +
85C ASP* 2.6 31.5 + - - +
86C LEU* 2.8 13.1 + - - +
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Residues in contact with LEU 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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65C ALA* 4.8 4.5 - - + -
79C ALA 5.5 0.7 - - - +
80C LEU* 3.5 43.1 - - + +
82C ALA* 1.3 79.6 - - + +
84C SER* 1.3 58.1 + - - +
86C LEU* 3.0 3.3 + - - +
87C HIS* 2.4 50.9 + - + +
136C LEU* 4.0 24.5 - - + -
142C HEM 4.0 57.4 - - + +
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Residues in contact with SER 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 LEU 3.6 2.0 + - - -
81C SER* 3.4 11.4 + - - -
82C ALA 3.1 0.8 - - - -
83C LEU* 1.3 79.8 - - - +
85C ASP* 1.3 57.7 + - - +
87C HIS 4.6 0.4 - - - +
88C ALA* 2.8 39.2 + - - +
135C VAL 3.3 19.0 + - - -
136C LEU* 3.1 27.1 + - - +
137C THR* 3.9 8.0 - - - -
138C SER* 4.0 11.4 + - - -
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Residues in contact with ASP 85 (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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81C SER 3.2 9.3 + - - +
82C ALA* 2.6 21.7 + - - +
84C SER* 1.3 78.2 - - - +
86C LEU* 1.3 55.0 + - - +
89C HIS* 2.9 60.0 + - - +
90C LYS* 3.8 7.3 - - - +
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Residues in contact with LEU 86 (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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82C ALA 2.8 10.8 + - - +
83C LEU* 3.7 6.7 - - - +
85C ASP* 1.3 81.1 - - - +
87C HIS* 1.3 88.2 + - + +
90C LYS* 2.4 57.8 - - + +
91C LEU* 3.8 10.6 - - + +
142C HEM 3.3 54.3 - - + +
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Residues in contact with HIS 87 (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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83C LEU* 2.4 50.2 + - + +
84C SER* 4.6 2.9 - - - +
86C LEU* 1.3 98.2 - - + +
88C ALA* 1.3 60.5 + - - +
90C LYS 3.6 5.9 - - - +
91C LEU* 5.1 1.6 - - + -
92C ARG* 4.2 3.5 - - - -
93C VAL* 3.4 40.6 + - + +
95C PRO* 5.7 3.4 - - + +
136C LEU* 5.0 16.7 - - + +
142C HEM 3.0 68.2 + + + -
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Residues in contact with ALA 88 (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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84C SER* 2.8 26.7 + - - +
87C HIS* 1.3 80.3 - - - +
89C HIS* 1.3 57.9 + - + +
90C LYS 3.2 7.0 + - - +
92C ARG* 4.9 9.5 - - - +
136C LEU 5.2 2.9 - - - +
137C THR* 5.7 5.4 - - - +
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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