Contacts of the helix formed by residues 78 - 91 (chain D) in PDB entry 4OQB
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 ARG 78 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D TYR* 3.0 25.4 + - - +
77D LEU* 1.3 75.3 - - - +
79D TRP* 1.3 67.0 + - - +
80D ASP* 3.3 15.1 + - - +
81D ASP* 3.0 12.4 + - - +
82D GLN* 2.9 20.0 + - - +
242D ASN* 3.7 1.3 - - - -
246D TRP* 3.2 64.5 + - + +
247D ASN* 5.8 1.6 + - - -
250D ASP* 2.7 28.5 + - - +
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Residues in contact with TRP 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ARG* 1.3 71.3 - - - +
80D ASP* 1.3 63.6 + - - +
82D GLN* 3.2 32.7 + - + +
83D GLN* 3.3 37.3 + - + +
86D LYS* 6.3 1.3 - - - -
235D GLU* 3.9 29.2 - - + -
238D LEU* 3.7 29.4 - - + -
239D LYS* 3.6 71.1 - - + +
242D ASN* 2.7 35.6 + - + +
243D ASP* 4.9 7.0 - - + +
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Residues in contact with ASP 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ARG* 3.5 19.9 + - - +
79D TRP* 1.3 78.1 + - - +
81D ASP* 1.3 72.2 + - - +
83D GLN* 3.5 16.1 + - - +
84D LYS* 3.4 19.1 + - - +
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Residues in contact with ASP 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D TYR* 2.6 40.7 + - + +
33D LEU* 4.7 13.1 - - + +
77D LEU* 4.7 3.8 - - + -
78D ARG* 3.0 20.7 + - - +
80D ASP* 1.3 87.5 + - - +
82D GLN* 1.3 65.5 + - - +
84D LYS* 3.3 28.2 + - - +
85D VAL* 3.3 25.7 + - - +
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Residues in contact with GLN 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D PHE* 3.3 58.7 + - + +
75D SER* 3.4 12.0 + - - +
77D LEU* 3.0 30.9 + - + -
78D ARG 2.9 14.1 + - - +
79D TRP* 3.2 26.0 + - + +
81D ASP* 1.3 77.0 - - - +
83D GLN* 1.3 56.5 + - + +
85D VAL* 3.3 1.8 + - - -
86D LYS* 2.9 30.5 + - - +
242D ASN* 3.2 20.4 - - - +
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Residues in contact with GLN 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D TRP* 3.3 41.1 + - + +
80D ASP* 3.7 13.7 - - - +
81D ASP 3.3 0.2 - - - -
82D GLN* 1.3 77.6 - - + +
84D LYS* 1.3 61.5 + - - +
86D LYS* 3.7 15.1 - - + +
87D LYS* 2.9 35.5 + - + +
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Residues in contact with LYS 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 3.7 29.6 - - - +
54D PHE* 4.0 21.9 - - + -
80D ASP 3.4 10.1 + - - +
81D ASP* 3.3 25.4 + - - +
82D GLN 3.3 0.4 - - - -
83D GLN* 1.3 78.6 - - - +
85D VAL* 1.3 56.7 + - - +
87D LYS* 4.3 2.8 - - - +
88D THR* 2.5 40.9 + - - +
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D VAL* 4.7 10.1 - - + -
33D LEU* 4.4 6.5 - - + -
35D MET* 4.8 9.9 - - + -
54D PHE* 3.9 24.5 - - + -
58D TRP* 4.4 14.1 - - + -
67D PRO* 3.8 24.2 - - + -
71D VAL* 5.5 1.8 - - + -
74D PHE* 4.0 8.7 - - + -
77D LEU* 4.3 17.9 - - + -
81D ASP 3.3 14.1 + - - +
82D GLN 3.3 7.5 + - - +
84D LYS* 1.3 76.4 - - - +
86D LYS* 1.3 59.9 + - - +
88D THR* 3.7 0.3 - - - -
89D ALA* 2.8 30.3 + - - +
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Residues in contact with LYS 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D PRO* 4.3 17.1 - - + +
68D ASP* 5.5 8.9 + - - +
74D PHE* 4.0 25.3 - - + -
79D TRP* 6.3 1.4 - - - -
82D GLN* 2.9 16.8 + - - +
83D GLN* 3.7 15.2 - - + +
84D LYS 3.3 0.2 - - - -
85D VAL* 1.3 78.4 - - - +
87D LYS* 1.3 61.8 + - + +
89D ALA* 3.6 11.3 - - - +
90D GLU* 3.9 17.8 + - - +
235D GLU* 4.8 10.7 + - - -
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Residues in contact with LYS 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D GLN* 2.9 18.8 + - + +
84D LYS* 4.3 3.6 - - - +
86D LYS* 1.3 75.3 - - + +
88D THR* 1.3 64.2 + - - +
89D ALA 3.2 0.4 - - - -
90D GLU* 3.2 24.1 + - + +
91D ALA* 3.3 10.7 + - - +
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Residues in contact with THR 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D PHE* 4.0 15.4 - - + -
58D TRP* 3.5 42.0 - - + +
84D LYS* 2.5 30.3 + - - +
85D VAL 4.1 2.0 - - - -
87D LYS* 1.3 72.6 - - - +
89D ALA* 1.3 65.3 + - - +
91D ALA 3.0 30.3 + - - +
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Residues in contact with ALA 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D TRP* 3.8 20.4 - - + -
63D SER* 5.5 4.5 - - - -
64D ILE 3.6 22.5 + - - +
65D ARG 4.9 2.2 - - - +
67D PRO* 3.4 27.1 - - + -
85D VAL 2.8 19.3 + - - +
86D LYS 3.6 7.0 - - - +
88D THR* 1.3 79.2 - - - +
90D GLU* 1.3 60.9 + - + +
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Residues in contact with GLU 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D ARG 5.5 6.1 - - - +
86D LYS* 4.0 17.7 - - - +
87D LYS* 3.2 15.3 + - + +
89D ALA* 1.3 78.6 - - + +
91D ALA* 1.3 63.9 + - + +
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Residues in contact with ALA 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D TRP* 5.2 6.8 - - - +
87D LYS 3.3 7.8 + - - +
88D THR* 3.0 34.5 + - - +
90D GLU* 1.3 82.6 - - + +
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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