Contacts of the helix formed by residues 65 - 74 (chain N) in PDB entry 2D2C
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 ALA 65 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58N TYR* 4.1 20.9 - - + +
59N LYS 3.5 6.3 - - - +
61N THR 3.7 17.0 - - - +
63N THR* 2.2 24.1 + - - +
64N GLU* 1.3 66.0 - - - +
66N TYR* 1.3 55.2 + - - +
67N ALA 3.3 0.2 - - - -
68N SER* 2.3 34.7 + - - -
69N VAL* 2.7 16.9 + - - +
138N LEU 4.3 2.0 - - - +
139N PRO 5.5 0.2 - - - -
140N TRP* 4.3 18.6 - - + -
180N LEU* 5.6 0.2 - - + -
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Residues in contact with TYR 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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63N THR* 3.2 5.2 + - - +
65N ALA* 1.3 76.5 - - - +
67N ALA* 1.3 68.1 - - + +
68N SER 2.8 1.4 + - - -
69N VAL* 2.9 21.8 + - + +
70N GLN* 3.0 52.3 + - + +
139N PRO 4.4 14.4 + - - +
140N TRP* 5.3 2.6 - - + +
62O VAL* 4.8 7.2 - - + +
63O GLY* 3.2 21.2 + - - -
64O GLU 3.1 33.7 + - - -
65O PRO* 3.0 44.4 - - + -
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Residues in contact with ALA 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 THR* 3.8 14.1 + - - +
64N GLU* 4.3 16.6 - - - +
65N ALA 3.3 0.2 - - - -
66N TYR* 1.3 83.0 - - + +
68N SER* 1.3 57.8 + - - +
70N GLN* 3.8 26.1 - - - +
71N TYR* 3.9 6.9 + - - +
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Residues in contact with SER 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57N TYR 4.6 2.7 + - - +
58N TYR* 3.9 7.6 - - - -
59N LYS* 3.7 37.1 + - - +
64N GLU* 3.0 23.3 + - - -
65N ALA* 2.3 28.0 + - - +
67N ALA* 1.3 78.3 - - - +
69N VAL* 1.3 58.1 + - - -
70N GLN 3.2 1.3 - - - -
71N TYR* 2.8 28.2 - - - +
72N ILE* 2.8 11.5 - - - +
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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
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58N TYR* 4.4 9.2 - - + -
65N ALA 2.7 26.2 + - - +
66N TYR* 2.9 10.1 + - + +
68N SER* 1.3 71.3 - - - +
70N GLN* 1.3 67.3 + - - +
71N TYR 2.8 1.8 - - - -
72N ILE* 2.8 23.5 + - + -
73N MET* 3.1 18.5 + - + +
83N ARG* 3.7 28.0 - - - +
139N PRO* 4.4 12.1 - - + +
301N HEM 3.3 28.7 - - - +
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Residues in contact with GLN 70 (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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66N TYR* 3.0 55.2 + - + +
67N ALA* 3.8 20.6 - - - +
69N VAL* 1.3 76.1 - - - +
71N TYR* 1.3 56.5 + - - +
73N MET* 4.8 3.6 - - - +
74N ASN* 2.9 49.4 + - - +
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Residues in contact with TYR 71 (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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57N TYR* 5.9 8.3 - + + +
59N LYS* 4.2 23.8 - - - -
67N ALA 3.9 4.5 + - - +
68N SER* 2.8 20.7 + - - +
69N VAL 2.8 0.2 - - - -
70N GLN* 1.3 78.6 - - - +
72N ILE* 1.3 64.3 + - + +
74N ASN 3.6 10.8 - - - +
75N GLU* 4.1 27.8 - - + -
76N VAL* 3.6 15.3 + - + +
45Q PRO* 3.4 32.7 - - + +
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Residues in contact with ILE 72 (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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54N MET* 5.7 13.9 - - + -
57N TYR* 4.4 32.3 - - + +
58N TYR* 5.1 5.4 - - + +
68N SER* 2.8 33.2 - - - +
69N VAL* 2.8 30.1 + - + +
71N TYR* 1.3 71.8 - - + +
73N MET* 1.3 71.8 + - - +
76N VAL* 2.7 28.9 - - + +
79N GLY* 3.2 32.0 - - - +
82N ILE* 6.0 0.4 - - + -
83N ARG* 4.8 12.1 - - + +
301N HEM 5.3 3.6 - - - +
41Q TYR* 5.4 7.9 - - + +
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Residues in contact with MET 73 (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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69N VAL* 3.1 21.0 + - + +
70N GLN* 4.0 4.7 - - - +
72N ILE* 1.3 88.3 - - - +
74N ASN* 1.3 73.7 + - - +
75N GLU 3.3 6.2 + - - -
76N VAL 3.9 5.9 + - - +
80N TRP* 3.9 46.0 - - + +
83N ARG* 4.0 29.4 - - - +
59O PRO* 5.1 3.4 - - + -
60O ALA* 3.5 39.7 - - + +
61O MET 4.7 5.6 - - - +
62O VAL* 6.4 0.9 - - - -
145P GLY* 5.4 7.0 - - - -
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Residues in contact with ASN 74 (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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70N GLN* 2.9 35.5 + - - +
71N TYR* 3.6 2.4 - - - +
73N MET* 1.3 87.2 - - - +
75N GLU* 1.3 73.3 + - - +
76N VAL 3.9 0.2 - - - -
62O VAL* 6.4 0.2 - - - +
143P HIS* 3.0 55.9 - - + +
144P PHE 4.1 10.9 + - - +
147P TYR* 4.9 4.8 + - - -
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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