Contacts of the helix formed by residues 90 - 99 (chain A) in PDB entry 5DPW
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 THR 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A GLN 3.4 17.9 - - - +
53A GLU* 4.7 8.3 - - - +
54A LEU 3.3 8.1 - - - +
55A THR* 4.3 12.3 - - + +
88A SER 4.7 2.0 - - - +
89A ALA* 1.3 78.1 - - - +
91A MET* 1.3 67.2 + - - +
92A ALA* 3.1 6.2 + - - +
93A GLU* 3.2 28.2 + - - +
94A ILE* 3.2 13.0 + - - +
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Residues in contact with MET 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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27A ILE* 4.0 14.6 - - + +
29A VAL* 4.9 4.7 - - - -
50A VAL* 3.6 20.6 - - + -
51A PRO 3.4 25.4 - - - +
52A GLN 3.8 1.1 + - - +
54A LEU* 2.8 25.5 + - + +
55A THR 3.7 6.1 - - - +
56A MET* 3.6 51.8 - - + +
59A PHE* 4.3 20.6 - - + -
90A THR* 1.3 73.1 - - - +
92A ALA* 1.3 52.1 + - - +
94A ILE* 3.7 6.3 - - + +
95A TYR* 2.7 36.4 + - - +
105A VAL* 6.1 1.3 - - - +
107A MET* 4.6 7.9 - - + -
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Residues in contact with ALA 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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27A ILE* 4.6 5.8 - - + -
52A GLN* 4.0 29.7 + - + +
90A THR* 3.1 8.8 + - - +
91A MET* 1.3 78.0 - - - +
93A GLU* 1.3 60.1 + - - +
95A TYR* 3.2 9.3 + - - +
96A ARG* 2.8 30.4 + - - +
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Residues in contact with GLU 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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86A SER* 5.6 1.9 - - - -
89A ALA* 3.2 30.5 - - + +
90A THR* 3.2 18.0 + - - +
92A ALA* 1.3 75.9 - - - +
94A ILE* 1.3 63.9 + - + +
96A ARG* 3.0 16.9 - - + +
97A ASP* 2.8 48.7 + - - +
112E GLN* 5.5 2.3 - - - +
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Residues in contact with ILE 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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56A MET* 4.2 18.2 - - + -
79A VAL* 4.1 24.2 - - + -
85A VAL* 3.8 23.8 - - + -
89A ALA* 3.8 21.8 - - + -
90A THR 3.2 15.4 + - - +
91A MET* 3.8 8.7 - - + +
93A GLU* 1.3 78.7 - - + +
95A TYR* 1.3 58.4 + - - +
98A TYR* 2.8 55.4 + - + +
105A VAL* 4.3 8.3 - - + +
107A MET* 4.6 10.8 - - + -
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Residues in contact with TYR 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 ARG* 4.3 22.4 + - - +
27A ILE* 3.5 39.5 - - + -
28A PRO* 4.4 6.1 - - + -
91A MET 2.7 20.4 + - - +
92A ALA* 3.3 6.7 - - - +
94A ILE* 1.3 75.6 - - - +
96A ARG* 1.3 68.9 + - + +
99A LYS* 3.0 65.0 + - + +
103A GLY* 3.5 24.4 + - - -
105A VAL* 3.7 17.2 - - + +
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Residues in contact with ARG 96 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A ALA 2.8 18.5 + - - +
93A GLU* 3.0 28.9 - - - +
95A TYR* 1.3 81.9 - - + +
97A ASP* 1.3 82.7 + - - +
99A LYS* 4.4 15.3 + - - +
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Residues in contact with ASP 97 (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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93A GLU* 2.8 38.9 + - - +
96A ARG* 1.3 108.2 + - - +
98A TYR* 1.3 90.1 + - + +
99A LYS 3.6 0.9 + - - +
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Residues in contact with TYR 98 (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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79A VAL* 3.7 21.9 - - + +
80A ASN* 3.7 29.8 + - - +
83A SER* 3.5 25.1 + - - -
85A VAL* 3.5 23.8 - - + +
94A ILE* 2.8 52.9 + - + +
95A TYR 3.8 1.8 - - - -
97A ASP* 1.3 98.0 + - + +
99A LYS* 1.3 63.1 + - - +
100A ASP 3.3 2.4 + - - -
105A VAL* 4.1 13.3 - - + +
112E GLN* 4.8 8.0 + - - -
114E THR* 4.8 7.4 + - + -
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Residues in contact with LYS 99 (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 ASN* 5.9 0.2 - - - -
95A TYR* 3.0 62.1 + - + +
96A ARG* 4.4 14.2 + - - +
97A ASP 3.6 2.6 + - - -
98A TYR* 1.3 75.1 - - - +
100A ASP* 1.3 76.1 + - - +
103A GLY* 4.0 16.4 - - - +
104A PHE 3.9 3.4 - - - +
105A VAL* 4.3 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