Contacts of the helix formed by residues 103 - 115 (chain A) in PDB entry 4ORA
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 GLN 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ILE* 3.3 15.7 + - + +
101A HIS* 3.2 9.6 + - - +
102A GLY* 1.3 75.6 - - - +
104A PHE* 1.3 57.4 + - - +
105A PHE 3.2 2.7 - - - -
106A ASP* 2.8 45.9 + - + +
107A LEU* 3.0 10.8 + - - +
132A GLY* 4.7 8.5 - - - +
134A PHE* 5.1 3.4 - - - -
138A CYS* 3.9 5.1 - - - -
317A ALA* 3.6 14.3 - - + +
318A PRO* 3.1 20.7 - - - +
319A ASN 4.6 1.3 - - - +
320A TYR* 3.6 32.1 - - - +
321A LEU* 3.9 11.7 - - - +
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Residues in contact with PHE 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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56A LYS* 4.8 2.5 - - + -
59A LEU* 3.8 32.3 - - + -
60A VAL* 4.0 15.3 - - + -
102A GLY 3.0 5.9 + - - -
103A GLN* 1.3 74.5 - - - +
105A PHE* 1.3 73.4 + + + +
107A LEU* 3.3 5.4 + - + +
108A MET* 3.0 69.4 + - + +
134A PHE* 3.5 30.4 - + + +
137A GLU* 3.7 37.2 - - + -
138A CYS* 3.6 13.6 - - - -
141A TYR* 3.8 15.5 - + + -
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Residues in contact with PHE 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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59A LEU 4.4 5.6 - - - -
60A VAL* 3.3 48.5 - - + -
62A GLU* 4.6 4.3 - - + -
103A GLN 3.1 1.2 + - - -
104A PHE* 1.3 89.1 - + - +
106A ASP* 1.3 62.5 + - - +
108A MET* 3.7 10.7 - - + +
109A LYS* 3.6 12.1 + - - +
134A PHE* 3.9 28.5 - + - -
346A SER* 3.8 17.4 - - - +
347A PRO 3.5 26.0 - - - +
348A HIS* 3.6 19.1 - - + -
349A PRO* 3.4 28.7 - - + -
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Residues in contact with ASP 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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103A GLN* 2.8 36.5 + - + +
105A PHE* 1.3 80.3 - - - +
107A LEU* 1.3 54.0 + - - +
108A MET 3.2 1.3 - - - -
109A LYS* 3.0 7.5 + - - +
110A LEU* 2.7 34.5 + - - +
316A SER 5.2 3.1 - - - +
318A PRO* 3.4 30.9 - - + +
343A PHE* 4.0 5.1 - - + -
344A ASN 4.3 1.0 - - - +
345A CYS* 3.4 9.6 - - - +
346A SER* 3.1 33.8 + - - +
348A HIS* 5.8 3.6 - - - -
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Residues in contact with LEU 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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100A ILE* 4.0 32.2 - - + +
103A GLN 3.0 11.2 + - - +
104A PHE* 3.5 12.6 - - + +
106A ASP* 1.3 74.6 - - - +
108A MET* 1.3 69.0 + - + +
110A LEU* 3.2 9.4 + - + +
111A PHE* 3.1 62.6 + - + -
124A PHE* 4.2 12.1 - - + -
138A CYS* 4.3 22.4 - - + -
141A TYR* 4.2 12.8 - - + -
142A LEU* 4.1 21.3 - - + -
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Residues in contact with MET 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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56A LYS* 3.7 35.9 - - - -
60A VAL* 4.4 8.1 - - + -
104A PHE* 3.0 59.1 + - + +
105A PHE* 3.7 13.9 - - + +
107A LEU* 1.3 83.7 - - + +
109A LYS* 1.3 62.7 + - - +
111A PHE* 3.2 11.7 + - + +
112A GLU* 2.8 25.5 - - - +
141A TYR* 3.6 28.0 - - + -
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Residues in contact with LYS 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 PHE 3.6 4.3 + - - +
106A ASP* 3.0 11.9 + - - +
108A MET* 1.3 77.6 - - - +
110A LEU* 1.3 64.3 + - - +
112A GLU* 3.0 16.7 + - + +
113A VAL* 2.9 41.0 + - + +
343A PHE* 3.9 26.9 - - + -
344A ASN 4.4 7.0 - - - +
346A SER* 3.8 23.6 - - - +
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Residues in contact with LEU 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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97A CYS* 4.1 13.0 - - + -
100A ILE* 4.0 17.7 - - + -
106A ASP 2.7 16.5 + - - +
107A LEU* 3.2 13.4 + - + +
109A LYS* 1.3 74.0 - - - +
111A PHE* 1.3 65.0 + - + +
113A VAL* 3.6 2.4 - - - +
114A GLY* 2.8 26.7 + - - +
122A TYR* 3.9 25.4 - - + -
124A PHE* 4.2 10.1 - - + -
316A SER* 3.9 22.0 - - - +
330A VAL* 3.7 27.3 - - + +
343A PHE* 3.8 19.5 - - + -
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Residues in contact with PHE 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 LEU* 3.1 48.1 + - + -
108A MET* 3.2 7.8 + - + +
110A LEU* 1.3 74.8 - - + +
112A GLU* 1.3 65.5 + - - +
115A GLY* 2.9 32.1 + - - +
116A SER* 4.0 1.3 + - - -
117A PRO* 3.8 30.7 - - + -
122A TYR* 3.6 31.4 - + - -
124A PHE* 3.7 27.1 - + - -
141A TYR* 3.8 28.3 - + - +
142A LEU* 3.9 4.9 - - + -
145A LEU* 3.5 16.8 - - + -
153A LEU* 4.6 1.1 - - + -
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Residues in contact with GLU 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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56A LYS* 4.1 20.3 + - - -
108A MET* 2.8 22.5 - - - +
109A LYS* 3.0 21.0 + - + +
111A PHE* 1.3 82.7 - - - +
113A VAL* 1.3 63.1 + - + +
115A GLY* 4.3 3.1 + - - -
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Residues in contact with VAL 113 (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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109A LYS* 2.9 43.7 + - - +
110A LEU* 3.7 6.3 - - - +
112A GLU* 1.3 81.0 - - - +
114A GLY* 1.3 62.2 + - - +
115A GLY 3.7 0.2 + - - -
330A VAL* 4.7 3.6 - - + -
332A LYS* 4.8 2.8 - - - +
341A ARG* 3.8 58.9 + - + +
342A GLN 4.8 3.4 - - - +
343A PHE* 4.1 24.9 - - + -
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Residues in contact with GLY 114 (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 THR* 3.8 7.6 + - - -
110A LEU 2.8 16.0 + - - -
113A VAL* 1.3 74.8 - - - +
115A GLY* 1.3 55.5 + - - +
120A THR* 3.4 8.0 + - - +
122A TYR* 2.9 19.6 + - - -
330A VAL* 4.8 3.8 - - - +
332A LYS* 2.5 40.1 + - - -
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Residues in contact with GLY 115 (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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111A PHE 2.9 18.4 + - - +
112A GLU 4.3 3.3 + - - -
113A VAL 3.5 3.0 + - - -
114A GLY* 1.3 77.3 - - - +
116A SER* 1.3 67.4 + - - -
117A PRO* 3.4 2.6 - - - +
119A ASN* 6.1 0.2 - - - -
120A THR* 3.5 7.9 - - - -
122A TYR* 2.7 24.8 + - - -
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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