Contacts of the helix formed by residues 85 - 96 (chain A) in PDB entry 5AM8
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 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLU* 3.4 14.4 + - - +
18A GLN* 2.9 27.9 + - - +
83A PHE* 3.4 0.9 - - - +
84A THR* 1.3 79.2 + - - +
86A PRO* 1.3 65.5 - - - +
87A GLN* 3.0 23.4 + - - +
88A LEU* 3.3 16.9 + - + +
89A ARG* 3.1 29.4 + - - +
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Residues in contact with PRO 86 (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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84A THR 3.5 10.0 - - - +
85A ASP* 1.3 87.9 - - - +
87A GLN* 1.3 70.0 + - + +
89A ARG* 3.4 29.7 + - - +
90A ARG* 3.1 34.6 + - - +
549A SER 4.9 6.1 - - - +
550A ARG* 6.6 0.4 - - + -
551A PRO* 6.0 4.7 - - + -
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Residues in contact with GLN 87 (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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85A ASP* 3.0 11.4 + - - +
86A PRO* 1.3 78.5 - - + +
88A LEU* 1.3 60.6 + - - +
90A ARG* 3.2 7.3 + - - +
91A ILE* 3.0 36.0 + - + +
375A LEU* 5.2 6.1 - - - +
376A PRO* 5.2 6.3 - - - +
379A LEU* 3.8 21.0 - - + +
549A SER* 3.7 35.7 + - - +
550A ARG* 5.9 1.2 - - - +
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Residues in contact with LEU 88 (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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14A GLU* 3.6 39.0 - - + +
17A ALA* 3.5 26.5 - - + +
18A GLN* 3.5 29.8 - - - +
21A ALA* 3.9 13.9 - - + -
83A PHE* 3.6 17.9 - - + -
85A ASP* 3.3 22.1 + - + +
87A GLN* 1.3 76.2 - - - +
89A ARG* 1.3 59.3 + - - +
91A ILE* 3.2 8.2 + - + +
92A ILE* 2.9 42.3 + - + +
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Residues in contact with ARG 89 (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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80A TRP* 3.2 39.5 - - + +
81A GLN* 3.2 29.4 + - - +
83A PHE* 2.6 39.1 + - + -
84A THR* 4.3 5.3 + - - +
85A ASP 3.1 14.5 + - - +
86A PRO* 3.5 37.2 - - - +
87A GLN 3.3 0.2 - - - -
88A LEU* 1.3 76.3 - - - +
90A ARG* 1.3 54.7 + - + +
92A ILE* 4.7 1.3 - - - -
93A GLY 2.8 29.5 + - - -
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Residues in contact with ARG 90 (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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80A TRP* 5.5 0.2 - - - -
86A PRO* 3.1 17.0 + - - +
87A GLN* 3.6 6.7 - - - +
88A LEU 3.2 0.2 - - - -
89A ARG* 1.3 75.4 - - + +
91A ILE* 1.3 61.3 + - - +
93A GLY* 3.9 1.5 - - - +
94A ALA* 3.0 29.5 + - - +
203A ASN* 5.3 10.9 + - - +
378A SER* 5.0 0.3 - - - +
379A LEU* 3.8 13.0 - - + +
381A ARG* 5.6 6.0 + - - +
383A ALA 5.1 5.7 + - - -
548A SER* 2.7 28.9 + - - -
549A SER* 3.3 18.1 + - - +
550A ARG* 3.6 18.5 + - - +
551A PRO* 3.6 33.7 - - - +
552A TRP* 4.7 2.0 - - - +
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Residues in contact with ILE 91 (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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18A GLN* 6.0 0.7 - - - +
21A ALA* 3.9 33.7 - - + +
24A TYR* 5.0 4.7 - - + -
87A GLN* 3.0 27.5 + - + +
88A LEU* 3.2 10.1 + - + +
90A ARG* 1.3 72.5 - - - +
92A ILE* 1.3 69.3 + - + +
94A ALA* 3.3 3.6 + - - +
95A VAL* 3.0 30.2 + - + +
376A PRO* 3.9 28.3 - - + -
378A SER* 3.9 23.7 + - - +
379A LEU* 4.0 18.8 - - + -
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Residues in contact with ILE 92 (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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17A ALA* 4.3 16.2 - - + +
20A PHE* 3.8 33.4 - - + -
21A ALA* 4.7 4.7 - - + -
72A ALA* 4.8 9.1 - - + +
76A TYR* 4.3 15.3 - - + -
80A TRP* 3.5 36.1 - - + -
83A PHE* 4.5 10.5 - - + -
88A LEU* 2.9 34.2 + - + +
89A ARG* 4.0 3.1 - - - +
91A ILE* 1.3 77.3 - - + +
93A GLY* 1.3 63.9 + - - +
95A VAL* 3.2 4.4 + - - +
96A ARG* 3.0 24.8 + - + +
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Residues in contact with GLY 93 (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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80A TRP* 3.6 25.0 - - - -
89A ARG 2.8 21.8 + - - -
90A ARG* 3.9 2.0 - - - -
91A ILE 3.2 0.2 - - - -
92A ILE* 1.3 74.0 - - - +
94A ALA* 1.3 58.7 + - - +
96A ARG* 3.0 24.1 - - - +
97A THR* 3.5 8.8 + - - -
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Residues in contact with ALA 94 (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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90A ARG 3.0 18.1 + - - +
91A ILE 3.6 4.3 - - - +
93A GLY* 1.3 75.5 - - - +
95A VAL* 1.3 62.1 + - - +
97A THR* 3.1 25.3 + - - +
378A SER* 4.3 22.4 - - - +
381A ARG* 5.4 6.5 - - - +
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Residues in contact with VAL 95 (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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20A PHE* 4.2 11.0 - - + -
24A TYR* 3.9 39.9 - - + +
65A ALA* 4.7 1.9 - - - +
68A TRP* 3.7 36.8 - - + +
69A GLY* 3.2 14.3 - - - +
72A ALA* 3.9 10.3 - - + -
91A ILE* 3.0 23.0 + - + +
92A ILE* 3.2 6.3 + - - +
94A ALA* 1.3 75.2 - - + +
96A ARG* 1.3 61.0 + - - +
97A THR 3.1 6.0 + - - +
98A LEU* 4.5 0.5 - - - +
378A SER* 4.3 4.5 - - - +
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Residues in contact with ARG 96 (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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69A GLY 4.3 9.9 - - - -
72A ALA* 4.4 7.3 - - + +
73A LYS* 3.6 35.5 + - + +
77A GLU* 3.3 33.6 + - - +
80A TRP* 3.8 24.7 - - + +
92A ILE* 3.0 17.0 + - + +
93A GLY* 3.0 24.9 + - - +
95A VAL* 1.3 75.0 - - - +
97A THR* 1.3 80.4 + - - +
98A LEU* 3.4 16.6 + - - +
188A GLN 4.9 0.8 + - - -
189A ASP* 3.4 38.3 + - - +
191A PHE* 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