Contacts of the helix formed by residues 97 - 105 (chain A) in PDB entry 1DQU
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 SER 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A GLY* 4.9 1.8 - - - -
78A CYS 5.5 0.2 + - - -
95A TYR* 3.7 24.2 + - - -
96A VAL* 1.3 73.7 - - - +
98A GLY* 1.3 53.0 + - - +
99A TRP* 3.0 11.8 + - - +
100A GLN* 2.9 31.6 + - - +
101A SER* 2.7 34.9 + - - -
123A VAL* 5.3 0.7 - - - -
168A ASP* 4.2 0.4 - - - -
457A THR* 4.2 17.9 - - - +
458A LEU* 3.9 6.6 - - - +
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Residues in contact with GLY 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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97A SER* 1.3 70.9 + - - +
99A TRP* 1.3 60.8 + - - +
101A SER* 4.2 4.9 - - - -
102A SER* 2.9 29.7 + - - -
114A ASP* 4.2 6.0 - - - +
118A TYR* 3.5 23.8 + - - -
123A VAL* 4.5 3.4 - - - -
168A ASP* 3.2 30.0 + - - +
170A ASP* 4.9 1.1 - - - -
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Residues in contact with TRP 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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97A SER* 3.0 8.1 + - - +
98A GLY* 1.3 75.6 - - - +
100A GLN* 1.3 78.3 + - + +
102A SER* 3.0 11.6 + - - -
103A SER* 3.1 27.9 + - - -
113A PRO* 6.4 1.3 - - + -
114A ASP* 3.2 47.0 + - + +
168A ASP* 4.5 2.0 + - - -
458A LEU* 3.6 34.8 - - + +
461A LEU* 3.6 35.4 - - + -
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Residues in contact with GLN 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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77A GLY* 3.2 30.5 + - - -
78A CYS 4.2 4.9 + - - -
79A LEU* 3.7 21.3 - - + +
97A SER* 2.9 18.1 + - - +
99A TRP* 1.3 88.2 - - + +
101A SER* 1.3 54.5 + - - +
103A SER* 2.5 28.3 + - - -
104A THR* 2.9 15.5 + - - +
457A THR 3.4 8.6 - - - +
458A LEU* 3.3 21.0 - - + -
460A GLY 3.4 5.0 + - - -
461A LEU* 2.9 42.6 + - + -
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Residues in contact with SER 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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96A VAL* 4.3 10.6 - - - +
97A SER 2.7 19.8 + - - -
98A GLY* 4.2 3.5 - - - -
100A GLN* 1.3 75.9 - - - +
102A SER* 1.3 62.9 + - - +
104A THR* 4.1 1.3 - - - -
105A ALA* 3.1 46.4 + - - +
106A SER* 3.6 2.8 + - - -
118A TYR* 4.6 2.1 - - - -
122A THR* 4.1 19.7 - - - +
123A VAL* 4.2 12.1 - - - +
126A LYS* 4.4 7.6 - - - +
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Residues in contact with SER 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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98A GLY 2.9 21.5 + - - -
99A TRP* 3.3 8.7 - - - -
100A GLN 2.8 0.4 + - - -
101A SER* 1.3 81.0 - - - +
103A SER* 1.3 61.3 + - - +
104A THR 3.8 0.2 + - - -
106A SER* 3.9 5.6 + - - -
110A GLU 5.1 0.2 - - - +
111A PRO* 3.9 6.8 - - - +
112A SER* 3.1 48.3 + - - -
113A PRO 3.3 7.7 + - - -
114A ASP* 4.4 7.0 - - - -
115A LEU 3.7 8.5 + - - -
118A TYR* 3.7 15.2 - - - -
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Residues in contact with SER 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 TRP* 3.1 32.4 + - - -
100A GLN 2.5 16.2 + - - -
102A SER* 1.3 73.2 - - - +
104A THR* 1.3 69.5 + - - +
111A PRO* 4.8 13.2 - - - +
112A SER 4.0 10.6 + - - -
113A PRO* 5.6 0.7 - - - +
461A LEU* 5.0 3.4 - - - -
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Residues in contact with THR 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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79A LEU* 3.7 34.7 + - + +
100A GLN 2.9 13.3 + - - +
101A SER* 4.1 0.5 - - - -
102A SER 3.5 0.6 + - - -
103A SER* 1.3 89.5 - - - +
105A ALA* 1.3 68.2 + - - +
106A SER* 4.1 1.1 + - - -
126A LYS* 5.4 1.4 + - - -
461A LEU* 4.4 13.9 - - + -
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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 SER* 3.1 29.8 + - - -
104A THR* 1.3 86.1 - - - +
106A SER* 1.3 63.3 + - - +
107A SER 3.4 2.8 + - - -
109A ASP* 5.5 1.3 - - - -
122A THR* 3.8 15.6 - - + +
126A LYS* 3.9 29.6 - - + +
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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