Contacts of the helix formed by residues 81 - 92 (chain D) in PDB entry 5A15
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 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78D ASP* 3.0 24.5 + - + +
80D PHE* 1.3 73.8 - - + +
82D PHE* 1.3 65.2 + - - +
83D ARG 3.1 3.0 + - - -
84D TYR* 3.2 13.4 + - + -
85D ILE* 3.4 14.0 + - - +
100D PHE* 3.7 31.6 - - + -
102D GLU* 3.6 27.6 - - + +
105D ARG* 3.7 31.2 - - + +
106D LEU* 3.7 19.7 - - + +
109D GLU* 3.8 29.2 - - + -
83E ARG* 4.2 1.1 - - - +
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Residues in contact with PHE 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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29D LEU* 4.0 29.6 - - + -
31D VAL* 3.8 34.8 - - + -
36D TYR* 3.8 16.6 - + + -
43D LEU* 5.0 0.7 - - + -
51D LEU* 4.1 19.3 - - + -
75D ILE* 4.3 9.0 - - + -
78D ASP 3.5 7.1 + - - +
79D GLY 3.9 6.5 - - - +
80D PHE 3.3 1.2 - - - -
81D LEU* 1.3 76.5 - - - +
83D ARG* 1.3 60.3 + - - +
84D TYR 3.2 0.2 - - - -
85D ILE* 4.1 13.0 - - + -
86D LEU* 2.8 53.3 + - + +
113D PHE* 3.7 40.6 - + - -
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Residues in contact with ARG 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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78C ASP* 2.6 42.7 + - - +
80C PHE* 4.2 25.8 - - + +
81C LEU* 4.0 2.4 - - - +
102C GLU* 2.9 42.2 + - - -
105C ARG* 3.4 14.0 - - - +
36D TYR* 3.3 32.4 + - + +
80D PHE 3.6 10.8 - - - +
82D PHE* 1.3 78.0 - - - +
84D TYR* 1.3 86.9 + - + +
86D LEU* 3.5 4.4 + - - +
87D ASP* 3.3 27.5 + - - +
90D ARG* 4.9 1.6 + - - +
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Residues in contact with TYR 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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102C GLU* 4.5 0.2 + - - -
105C ARG* 3.8 25.4 - - - -
80D PHE 3.8 17.0 - - - -
81D LEU* 3.2 16.9 + - + +
82D PHE 3.2 0.4 - - - -
83D ARG* 1.3 107.6 + - + +
85D ILE* 1.3 64.4 + - - +
86D LEU 3.2 1.1 - - - -
87D ASP* 3.6 2.8 + - - +
88D TYR* 3.3 14.7 + - - +
94D VAL* 3.5 26.4 - - + +
95D VAL 4.9 0.2 - - - -
96D LEU* 5.2 1.6 - - + -
97D PRO* 3.6 31.1 - - + +
100D PHE* 3.5 35.8 - + - -
106D LEU* 4.0 23.0 - - + +
118D LEU* 5.0 1.0 - - - +
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Residues in contact with ILE 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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51D LEU* 4.8 6.7 - - + -
81D LEU 3.4 12.7 + - - +
82D PHE* 3.2 24.0 + - + +
84D TYR* 1.3 78.1 - - - +
86D LEU* 1.3 63.4 + - - +
88D TYR* 3.1 16.6 + - - +
89D LEU* 3.2 13.6 + - + +
106D LEU* 3.8 16.2 - - + -
109D GLU* 4.1 7.2 - - + -
110D ALA* 3.8 23.3 - - - +
113D PHE* 4.0 28.7 - - + -
115D LEU* 4.0 14.1 - - + -
118D LEU* 3.6 24.0 - - + -
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Residues in contact with LEU 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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36D TYR* 4.0 28.0 - - + -
37D PHE 4.1 11.2 - - - +
38D THR* 3.7 29.4 - - + +
42D THR* 4.5 4.5 - - + -
43D LEU* 4.8 0.9 - - + -
82D PHE* 2.8 34.8 + - + +
83D ARG 3.7 6.5 - - - +
84D TYR 3.2 0.2 - - - -
85D ILE* 1.3 76.8 - - - +
87D ASP* 1.3 63.8 + - - +
89D LEU* 3.3 20.0 + - + +
90D ARG* 3.2 51.1 + - - +
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Residues in contact with ASP 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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77C ARG* 5.2 2.5 + - - -
78C ASP* 4.4 4.6 - - - +
105C ARG* 2.9 36.2 + - - +
109C GLU* 4.4 12.8 - - - +
83D ARG* 3.3 17.5 + - - +
84D TYR* 4.0 7.5 - - - +
85D ILE 3.3 0.4 - - - -
86D LEU* 1.3 75.0 - - - +
88D TYR* 1.3 65.0 + - - +
90D ARG* 2.8 35.1 + - - +
91D ASP* 3.0 26.4 + - - +
93D GLN 3.5 8.5 - - - +
94D VAL* 4.5 10.8 - - + -
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Residues in contact with TYR 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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46D ILE* 3.4 28.2 - - + +
84D TYR 3.3 5.9 + - - +
85D ILE 3.1 9.9 + - - +
87D ASP* 1.3 79.2 - - - +
89D LEU* 1.3 59.1 + - + +
92D ARG* 2.5 73.8 + - - +
93D GLN* 3.7 5.4 - - - -
94D VAL* 3.4 22.4 - - + +
115D LEU* 4.1 26.6 - - + +
117D ASP* 3.3 28.3 + - + +
118D LEU* 4.0 36.1 + - + -
121D LEU* 4.4 9.0 - - + -
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Residues in contact with LEU 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D THR* 3.5 30.5 - - + +
43D LEU* 4.6 9.9 - - + +
45D SER* 3.8 22.8 + - - +
46D ILE* 3.8 26.7 - - + -
49D SER* 5.7 1.6 - - - +
51D LEU* 3.5 31.6 - - + -
82D PHE* 5.3 0.4 - - + -
85D ILE* 3.2 15.3 + - + +
86D LEU* 3.6 22.7 - - + +
87D ASP 3.3 0.2 - - - -
88D TYR* 1.3 80.2 - - + +
90D ARG* 1.3 62.6 + - - +
92D ARG* 4.3 8.7 - - - +
115D LEU* 4.4 15.0 - - + -
92I ARG* 4.5 5.0 + - - -
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Residues in contact with ARG 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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32C GLY* 4.4 3.0 - - - -
76C ASP* 2.9 42.5 + - - +
77C ARG* 3.7 32.8 + - - +
78C ASP* 3.5 17.8 + - - +
36D TYR* 5.9 0.4 - - - -
37D PHE 3.7 10.1 + - - -
42D THR* 4.2 13.2 - - + +
83D ARG* 4.9 2.2 + - - +
86D LEU* 3.2 44.6 + - - +
87D ASP* 2.8 41.7 + - - +
88D TYR 3.2 0.8 - - - -
89D LEU* 1.3 79.7 - - - +
91D ASP* 1.3 69.7 + - - +
92I ARG* 2.8 23.7 + - - -
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Residues in contact with ASP 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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77C ARG* 2.8 37.4 + - - -
108C ARG* 2.9 40.1 + - - +
112C TYR* 4.7 1.6 - - - -
87D ASP* 3.0 16.1 + - - +
90D ARG* 1.3 78.3 - - - +
92D ARG* 1.3 73.0 + - - +
93D GLN* 3.2 34.1 + - + +
92I ARG* 3.8 14.5 + - - +
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Residues in contact with ARG 92 (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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45D SER* 4.5 11.8 + - - -
46D ILE* 3.7 42.0 - - - +
88D TYR* 2.5 58.2 + - + +
89D LEU 4.3 9.2 - - - +
91D ASP* 1.3 73.6 - - - +
93D GLN* 1.3 57.8 + - - +
117D ASP* 4.8 7.9 + - - -
121D LEU* 4.9 4.2 - - - +
108H ARG* 5.9 0.4 - - - +
45I SER* 6.2 1.4 - - - -
89I LEU 4.7 3.0 + - - -
90I ARG 3.0 29.8 + - - -
91I ASP* 4.2 18.2 + - - +
92I ARG* 3.2 48.2 - - + +
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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