Contacts of the helix formed by residues 77 - 84 (chain A) in PDB entry 3DZ8
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 ASP 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A LYS* 5.4 2.1 - - - +
36A THR* 4.7 0.3 + - - -
58A ASP 4.3 2.1 - - - +
59A PHE* 4.0 5.0 - - + -
60A LYS* 3.0 51.9 + - - +
62A LYS* 3.1 24.1 + - - -
75A ILE* 3.8 12.2 - - - +
76A TRP* 1.3 75.3 - - + +
78A THR* 1.3 66.4 + - - +
79A ALA* 5.1 1.3 - - + -
80A GLY* 3.0 20.9 + - - +
81A GLN* 3.1 10.6 + - - +
201A GDP 5.3 1.7 + - - -
501A UNX 3.9 14.4 - - - -
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Residues in contact with THR 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 5.7 0.2 - - - -
29A GLY 2.5 26.8 + - - +
30A ASN* 4.7 1.3 - - - +
31A SER* 3.7 24.0 - - - +
35A LYS* 3.8 9.2 + - - +
76A TRP 3.4 1.8 + - - -
77A ASP* 1.3 71.1 - - - +
79A ALA* 1.3 63.4 + - - +
81A GLN* 3.1 23.1 + - + +
82A GLU* 3.2 33.3 + - + +
116A TRP* 3.6 27.3 - - + -
501A UNX 3.8 3.2 - - - -
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A SER* 4.2 3.5 + - - +
59A PHE* 3.7 27.1 - - + -
77A ASP* 3.3 1.5 - - + -
78A THR* 1.3 78.6 - - - +
80A GLY* 1.3 61.0 + - - +
82A GLU* 3.5 22.5 + - - +
83A ARG* 3.5 10.4 + - - +
501A UNX 3.4 16.2 - - - -
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Residues in contact with GLY 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PHE* 3.5 18.4 - - - -
76A TRP* 3.3 31.5 - - - -
77A ASP* 3.0 10.4 + - - +
79A ALA* 1.3 77.6 - - - +
81A GLN* 1.3 59.7 + - - +
83A ARG* 3.0 2.2 + - - -
84A TYR* 3.0 29.6 + - - -
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Residues in contact with GLN 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ILE 5.6 0.4 + - - -
28A ILE* 4.5 7.1 - - - +
35A LYS* 6.1 0.6 - - - +
76A TRP* 2.9 41.0 + - + +
77A ASP 3.1 9.6 + - - +
78A THR* 3.4 15.5 + - + +
80A GLY* 1.3 76.2 - - - +
82A GLU* 1.3 62.2 + - + +
83A ARG 3.4 0.5 + - - -
84A TYR 4.0 4.9 + - - +
85A ARG* 5.3 0.7 - - - -
88A THR* 3.1 29.6 + - + +
91A TYR* 3.9 10.7 + - - -
92A TYR* 2.6 36.9 + - - -
116A TRP* 3.4 21.4 - - + -
119A GLN* 4.9 2.1 + - - +
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A SER* 5.3 1.2 + - - -
78A THR* 3.2 28.6 + - + +
79A ALA* 3.6 17.4 - - - +
80A GLY 3.1 0.6 - - - -
81A GLN* 1.3 79.6 - - + +
83A ARG* 1.3 56.7 + - - +
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Residues in contact with ARG 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PHE* 4.2 16.3 - - + -
79A ALA 3.5 10.0 + - - +
80A GLY 3.0 7.7 + - - +
82A GLU* 1.3 79.0 - - - +
84A TYR* 1.3 109.2 + - + +
85A ARG 4.0 2.0 + - - -
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A VAL* 3.8 15.7 - - + -
56A GLY* 3.3 22.9 - - - -
59A PHE* 3.7 22.2 - + - -
76A TRP* 3.8 12.6 - + + -
80A GLY 3.0 17.2 + - - +
81A GLN 4.0 2.7 + - - -
82A GLU 3.8 0.4 - - - -
83A ARG* 1.3 124.5 + - + +
85A ARG* 1.3 61.6 + - - +
86A THR* 3.5 0.9 - - - +
87A ILE* 4.0 30.5 - - + +
88A THR* 2.6 31.6 + - - -
503A UNX 4.6 2.5 - - - -
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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