Contacts of the helix formed by residues 81 - 92 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78F ASP* 3.6 22.4 + - + +
79F GLY 3.4 0.2 - - - -
80F PHE* 1.3 78.2 - - + +
82F PHE* 1.3 64.3 + - - +
83F ARG 3.1 3.6 + - - -
84F TYR* 3.3 15.3 + - + -
85F ILE* 3.5 8.4 + - - +
100F PHE* 4.0 24.5 - - + -
102F GLU* 3.5 25.4 - - - +
105F ARG* 3.4 35.2 - - + +
106F LEU* 3.7 20.6 - - + +
109F GLU* 3.9 30.1 - - + +
83G ARG* 3.8 8.5 - - - +
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Residues in contact with PHE 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F LEU* 5.4 7.2 - - + -
31F VAL* 3.7 25.1 - - + -
36F TYR* 3.7 28.9 - + + -
38F THR* 6.2 0.2 - - + -
43F LEU* 5.4 4.0 - - + -
51F LEU* 4.3 18.8 - - + -
75F ILE* 5.6 1.8 - - + -
78F ASP 3.7 10.6 + - - +
79F GLY 3.4 13.0 + - - +
80F PHE 3.2 1.0 - - - -
81F LEU* 1.3 76.8 - - - +
83F ARG* 1.3 59.6 + - - +
84F TYR 3.1 0.4 - - - -
85F ILE* 3.6 20.9 - - + -
86F LEU* 2.8 54.5 + - + +
89F LEU* 5.5 0.2 - - + -
109F GLU* 5.8 0.2 - - - +
113F PHE* 3.4 43.7 - + - -
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Residues in contact with ARG 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F TYR* 3.5 28.1 + - + +
80F PHE* 3.5 17.8 + - + +
81F LEU 3.1 0.4 - - - -
82F PHE* 1.3 78.5 - - - +
84F TYR* 1.3 68.4 + - + +
86F LEU* 3.6 5.2 + - - +
87F ASP* 3.0 31.8 + - - +
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Residues in contact with TYR 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F PHE* 4.2 25.1 - + - -
81F LEU* 3.3 18.0 + - - +
82F PHE 3.1 0.4 - - - -
83F ARG* 1.3 80.9 - - + +
85F ILE* 1.3 64.7 + - - +
86F LEU 3.2 1.3 - - - -
87F ASP* 3.7 14.1 - - - -
88F TYR* 3.2 5.7 + - - +
94F VAL* 3.2 31.4 - - + +
95F VAL 4.5 12.8 - - - -
96F LEU* 4.7 7.2 - - + -
97F PRO* 3.2 41.6 - - + +
100F PHE* 3.5 30.8 - + - -
106F LEU* 4.0 26.7 - - + -
118F LEU* 5.2 1.5 - - - +
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Residues in contact with ILE 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F LEU* 4.7 7.6 - - + -
81F LEU 3.5 13.4 + - - +
82F PHE* 3.1 34.4 + - + +
84F TYR* 1.3 76.2 - - - +
86F LEU* 1.3 62.2 + - - +
88F TYR* 3.3 15.5 + - - +
89F LEU* 3.4 14.4 + - + +
106F LEU* 3.8 18.6 - - + -
109F GLU* 4.1 7.0 - - + -
110F ALA* 3.9 30.5 - - - +
113F PHE* 3.9 24.2 - - + -
115F LEU* 4.4 11.2 - - + -
118F LEU* 3.9 12.8 - - + -
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Residues in contact with LEU 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F TYR* 4.1 34.8 - - + -
37F PHE 4.2 14.4 - - - +
38F THR* 3.7 33.2 - - + +
42F THR* 4.7 3.4 - - + -
43F LEU* 4.8 1.3 - - + -
82F PHE* 2.8 31.6 + - + +
83F ARG* 3.7 6.5 - - - +
85F ILE* 1.3 80.0 - - - +
87F ASP* 1.3 61.3 + - - +
89F LEU* 3.5 25.8 + - + +
90F ARG* 3.5 21.1 + - - +
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Residues in contact with ASP 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F ARG* 3.0 18.7 + - - +
84F TYR* 3.7 20.0 - - + +
85F ILE 3.2 0.4 - - - -
86F LEU* 1.3 77.6 - - - +
88F TYR* 1.3 63.0 + - - +
90F ARG* 2.6 40.6 + - - +
91F ASP* 3.2 17.8 + - - +
93F GLN 3.5 7.9 - - - +
94F VAL* 3.8 12.3 - - + -
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Residues in contact with TYR 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F ILE* 3.4 27.3 - - + +
84F TYR 3.2 8.3 + - - +
85F ILE 3.6 9.0 - - - +
86F LEU 3.3 0.2 - - - -
87F ASP* 1.3 75.8 - - - +
89F LEU* 1.3 61.7 + - - +
92F ARG* 2.5 80.0 + - - -
93F GLN* 3.7 8.5 - - - -
94F VAL* 3.4 14.1 - - + +
115F LEU* 3.8 25.9 - - + +
117F ASP* 3.4 26.2 - - - +
118F LEU* 3.9 41.7 + - + -
121F LEU* 4.5 9.4 - - + -
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Residues in contact with LEU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F THR* 3.4 35.9 - - + +
43F LEU* 4.4 18.4 - - + +
45F SER* 3.7 22.0 + - - -
46F ILE* 3.9 29.4 - - + -
49F SER* 5.6 1.8 - - - +
51F LEU* 3.6 31.6 - - + -
82F PHE* 5.5 0.2 - - + -
85F ILE* 3.4 16.7 + - + +
86F LEU* 3.8 12.8 - - + +
87F ASP 3.4 0.2 - - - -
88F TYR* 1.3 77.9 - - - +
90F ARG* 1.3 61.9 + - - +
92F ARG* 4.5 5.4 - - - +
115F LEU* 4.2 20.6 - - + -
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Residues in contact with ARG 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F THR* 5.0 6.5 - - - +
42F THR* 3.6 26.5 - - + +
86F LEU* 3.5 12.0 + - - +
87F ASP* 2.6 44.9 + - - +
88F TYR 3.2 0.8 - - - -
89F LEU* 1.3 79.8 - - - +
91F ASP* 1.3 92.3 + - - +
92F ARG* 5.1 2.3 - - - +
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Residues in contact with ASP 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F ASP 3.2 9.6 + - - +
90F ARG* 1.3 115.6 + - - +
92F ARG* 1.3 73.5 + - - +
93F GLN* 3.1 35.1 + - + +
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Residues in contact with ARG 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F SER* 4.7 10.5 + - - +
46F ILE* 3.4 47.4 - - - +
47F PRO* 6.1 0.4 - - - +
88F TYR* 2.5 56.7 + - + +
89F LEU 4.5 7.4 - - - +
90F ARG 5.1 2.2 - - - +
91F ASP* 1.3 74.9 - - - +
93F GLN* 1.3 59.6 + - - +
117F ASP* 3.8 19.6 + - - -
121F LEU* 5.2 3.6 - - - +
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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