Contacts of the helix formed by residues 98 - 106 (chain A) in PDB entry 5PIU
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 VAL 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ILE* 3.5 28.9 - - + +
67A SER* 3.4 3.8 + - - -
69A ILE* 2.8 29.0 + - + +
71A ILE* 4.1 7.4 - - + -
97A THR* 1.3 72.4 - - - +
99A GLY* 1.3 53.9 + - - +
101A TYR* 3.6 6.0 - - + +
102A ARG* 2.8 36.8 + - - +
182A PHE* 3.5 54.3 - - + -
287A PHE* 4.4 14.6 - - + -
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Residues in contact with GLY 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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67A SER* 3.1 30.4 + - - +
97A THR* 3.1 3.9 - - - -
98A VAL* 1.3 77.1 - - - +
100A GLU* 1.3 61.2 + - - +
102A ARG* 3.5 16.0 + - - +
103A HIS* 3.1 22.9 + - - +
413A SO4 4.8 1.6 + - - -
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Residues in contact with GLU 100 (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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95A ALA 4.6 1.0 - - - +
96A MET* 3.3 21.3 - - + +
97A THR* 2.9 41.7 + - - +
99A GLY* 1.3 76.1 - - - +
101A TYR* 1.3 58.2 + - - +
103A HIS* 3.3 6.9 + - - +
104A LEU* 2.9 29.1 + - - +
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Residues in contact with TYR 101 (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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71A ILE* 3.7 21.3 - - + -
74A PRO* 5.5 0.9 - - + -
96A MET* 3.5 21.0 - - + -
97A THR 2.9 16.0 + - - +
98A VAL* 3.3 4.7 + - - +
100A GLU* 1.3 77.4 - - - +
102A ARG* 1.3 57.2 + - - +
104A LEU* 3.2 5.4 + - + +
105A ALA* 2.8 25.1 + - - +
135A ILE* 2.7 42.3 + - + -
136A TYR* 3.9 0.2 - - - -
137A GLY* 4.1 9.0 - - - -
182A PHE* 3.1 27.2 + + + -
183A GLY* 3.0 38.4 - - - -
184A MET* 3.2 17.3 + - + +
287A PHE* 3.8 17.9 - + - -
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Residues in contact with ARG 102 (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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66A ILE* 4.6 14.1 - - - +
67A SER* 3.0 32.5 + - - +
98A VAL* 2.8 24.6 + - - +
99A GLY* 3.8 12.3 + - - +
101A TYR* 1.3 69.7 - - - +
103A HIS* 1.3 66.1 + - - +
105A ALA* 3.2 2.4 + - - +
106A ASN* 3.0 35.5 + - - +
206A LEU* 6.0 1.6 - - - +
287A PHE* 3.7 46.1 - - + -
408A EDO 3.9 10.1 + - - -
413A SO4 3.0 24.7 + - - +
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Residues in contact with HIS 103 (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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99A GLY 3.1 15.1 + - - +
100A GLU* 3.5 10.3 + - - +
102A ARG* 1.3 78.6 - - - +
104A LEU* 1.3 62.8 + - - +
106A ASN* 3.3 4.4 + - + +
107A SER* 3.2 22.7 + - - -
413A SO4 3.1 34.9 + - - +
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Residues in contact with LEU 104 (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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96A MET* 4.1 22.7 - - + -
100A GLU 2.9 13.8 + - - +
101A TYR* 3.2 7.2 + - - +
103A HIS* 1.3 80.0 + - - +
105A ALA* 1.3 60.5 + - - +
107A SER* 2.7 30.6 + - - +
110A TYR* 3.4 37.1 - - + +
135A ILE* 3.9 28.3 - - + -
184A MET* 4.2 12.1 - - + -
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Residues in contact with ALA 105 (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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101A TYR* 2.8 17.2 + - + +
102A ARG* 3.5 9.2 - - - +
104A LEU* 1.3 73.3 - - - +
106A ASN* 1.3 59.2 + - - +
110A TYR* 3.5 4.3 - - - +
111A GLN* 3.2 28.1 + - - -
184A MET* 3.7 36.5 - - + +
185A TRP 5.7 0.3 + - - -
287A PHE* 4.0 26.5 + - + +
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Residues in contact with ASN 106 (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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102A ARG* 3.0 26.9 + - - +
103A HIS 3.6 2.9 - - - +
104A LEU 3.1 0.4 - - - -
105A ALA* 1.3 78.5 - - - +
107A SER* 1.3 59.2 + - - +
111A GLN* 3.0 25.9 + - - +
287A PHE* 4.3 14.3 + - - +
413A SO4 3.3 32.9 + - - +
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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