Contacts of the helix formed by residues 100 - 112 (chain A) in PDB entry 4XQ2
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 TYR 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A GLN* 3.1 24.2 - - - -
99A VAL* 1.3 72.9 - - - +
101A ALA* 1.3 63.9 - - + +
102A GLY* 3.4 20.0 - - - -
103A THR* 2.7 34.7 + - - +
104A ASP 3.1 8.1 + - - -
143A GLU* 2.9 30.9 + - - +
147A ASN 6.1 0.9 - - - -
197A LLP 3.3 50.6 + + + +
46B TYR* 5.4 1.7 - - - -
48B ARG* 2.8 24.9 + - - -
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Residues in contact with ALA 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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99A VAL 3.5 3.7 + - - -
100A TYR* 1.3 81.6 - - + +
102A GLY* 1.3 61.9 + - - +
104A ASP* 3.8 9.1 - - - +
105A GLY* 3.1 18.5 + - - -
338A THR 5.5 6.5 - - - +
339A HIS* 5.8 7.2 - - + +
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Residues in contact with GLY 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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77A GLN* 2.8 40.5 + - - -
100A TYR* 3.0 14.7 + - - -
101A ALA* 1.3 77.9 - - - +
103A THR* 1.3 62.4 + - - +
105A GLY* 3.3 3.2 + - - -
106A LEU* 3.1 16.3 + - - +
48B ARG* 5.6 2.0 - - - -
227B THR* 4.4 1.7 - - - +
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Residues in contact with THR 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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77A GLN* 3.7 3.4 + - - -
80A ALA* 4.9 3.6 - - + +
99A VAL* 3.9 11.6 - - + +
100A TYR* 2.7 32.8 + - - +
102A GLY* 1.3 71.6 - - - +
104A ASP* 1.3 48.7 + - - -
106A LEU* 3.0 16.1 + - + +
107A PHE* 2.7 50.8 + - + -
141A TRP* 3.6 45.2 + - + +
143A GLU* 4.4 1.6 + - - -
172A ASP* 4.5 5.0 + - - -
192A LEU* 5.5 0.2 - - - +
197A LLP 4.8 1.9 - - - -
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Residues in contact with ASP 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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97A ASP 5.3 4.4 - - - +
99A VAL* 4.1 14.3 - - + +
100A TYR 3.1 7.1 + - - +
101A ALA* 4.0 10.5 - - - +
102A GLY 3.3 0.2 - - - -
103A THR* 1.3 74.5 - - - +
105A GLY* 1.3 55.5 + - - +
107A PHE* 3.2 8.8 + - - +
108A ASP* 2.7 49.9 + - - +
119A TYR* 2.8 41.7 + - - -
350A ARG* 5.9 1.1 + - - -
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Residues in contact with GLY 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 ALA 3.1 14.0 + - - -
102A GLY* 3.7 4.0 - - - -
103A THR 3.3 0.2 - - - -
104A ASP* 1.3 75.2 - - - +
106A LEU* 1.3 57.7 + - - +
108A ASP* 3.1 12.3 + - - +
109A LEU* 2.8 30.1 + - - +
227B THR* 3.8 16.4 - - - +
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Residues in contact with LEU 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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77A GLN* 3.5 38.1 - - - +
80A ALA* 3.7 13.9 - - + -
81A ALA* 3.6 31.2 - - + +
84A LEU* 3.2 22.8 - - + +
102A GLY 3.1 11.3 + - - +
103A THR* 3.0 14.2 + - + +
105A GLY* 1.3 74.3 - - - +
107A PHE* 1.3 63.4 + - + +
109A LEU* 3.4 14.3 + - + +
110A ALA 2.9 18.7 + - - -
141A TRP* 5.9 1.1 - - + -
227B THR* 3.6 26.9 - - + +
228B ALA* 4.4 2.5 - - + -
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Residues in contact with PHE 107 (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 LEU* 4.0 18.6 - - + -
93A VAL* 3.9 19.1 - - + -
95A SER* 3.7 33.2 - - - -
99A VAL* 4.2 7.2 - - + -
103A THR* 2.7 40.6 + - + -
104A ASP* 3.4 25.1 - - - +
106A LEU* 1.3 72.0 - - - +
108A ASP* 1.3 52.5 + - - +
110A ALA* 3.3 1.7 + - - +
111A ALA* 2.4 38.9 + - - +
117A VAL* 3.5 36.9 - - + +
119A TYR* 3.8 9.4 - + - +
141A TRP* 3.9 22.9 - + + -
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Residues in contact with ASP 108 (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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104A ASP* 2.7 39.8 + - - +
105A GLY* 3.1 13.1 + - - +
107A PHE* 1.3 70.0 - - - +
109A LEU* 1.3 56.1 + - - +
111A ALA* 3.5 8.4 - - - +
112A ARG* 2.7 44.5 + - - +
119A TYR* 4.3 7.4 + - - -
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Residues in contact with LEU 109 (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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105A GLY 2.8 17.5 + - - +
106A LEU* 3.6 16.6 - - + +
107A PHE 3.4 0.2 - - - -
108A ASP* 1.3 71.7 - - - +
110A ALA* 1.3 64.1 + - - +
112A ARG* 3.1 16.5 + - + +
113A GLN* 3.0 24.6 + - + +
224B TYR* 3.7 38.4 - - + -
227B THR* 4.4 20.6 - - + -
228B ALA* 5.5 0.9 - - + -
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Residues in contact with ALA 110 (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 LEU* 3.6 21.8 - - + +
106A LEU 2.9 17.8 + - - +
107A PHE* 3.5 4.9 - - - +
109A LEU* 1.3 74.2 - - - +
111A ALA* 1.3 59.5 + - - +
113A GLN* 2.9 24.4 + - - +
114A GLY 3.2 0.2 + - - -
115A VAL* 3.2 40.9 + - + +
117A VAL* 5.1 0.9 - - + -
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Residues in contact with ALA 111 (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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107A PHE 2.4 31.3 + - - +
108A ASP* 3.5 12.1 - - - +
110A ALA* 1.3 68.1 - - - +
112A ARG* 1.3 58.4 + - - +
113A GLN 3.0 0.2 - - - -
114A GLY* 3.0 18.7 + - - -
115A VAL 3.5 14.3 - - - +
117A VAL* 4.6 11.6 - - + +
119A TYR* 6.1 0.4 - - - +
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Residues in contact with ARG 112 (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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108A ASP* 2.7 26.2 + - - +
109A LEU* 3.1 11.4 + - + +
111A ALA* 1.3 71.2 - - - +
113A GLN* 1.3 55.6 + - - +
114A GLY 3.5 0.4 - - - -
88B ARG* 2.7 43.4 + - - +
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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