Contacts of the helix formed by residues 101 - 112 (chain A) in PDB entry 4FRA
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 ASN 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A TYR* 3.6 30.0 - - - +
72A PRO* 4.9 3.8 - - - +
100A PHE* 1.3 72.0 - - - +
102A ILE* 1.3 63.8 + - - +
103A ASP* 2.9 32.5 + - - +
104A ILE* 3.1 37.4 + - + +
105A LEU* 3.2 15.3 + - - +
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Residues in contact with ILE 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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100A PHE* 3.7 21.6 + - + -
101A ASN* 1.3 74.2 - - - +
103A ASP* 1.3 71.3 + - - +
105A LEU* 3.8 5.6 - - + -
106A ASN* 2.8 51.3 + - - +
219A HIS* 3.5 22.4 - - + +
222A VAL* 4.3 12.3 - - + -
223A GLU* 3.3 27.4 - - - +
403A PEG 3.9 21.5 - - - +
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Residues in contact with ASP 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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69A MET* 3.7 16.2 - - + -
71A TYR* 6.0 2.5 - - + +
101A ASN* 2.9 13.7 + - - +
102A ILE* 1.3 87.4 - - - +
104A ILE* 1.3 63.3 + - - +
106A ASN* 4.0 8.2 + - - +
107A GLU* 3.1 28.3 + - + +
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Residues in contact with ILE 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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66A LEU* 4.7 14.1 - - + -
69A MET* 3.9 20.9 - - + -
71A TYR* 3.7 37.0 - - + +
101A ASN* 3.1 31.4 - - + +
103A ASP* 1.3 77.0 - - - +
105A LEU* 1.3 67.3 + - + +
107A GLU* 3.3 4.5 + - - +
108A GLN* 3.0 38.7 + - + +
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Residues in contact with LEU 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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100A PHE* 3.7 33.0 - - + -
101A ASN 3.2 11.9 + - - +
102A ILE* 3.9 5.8 - - + +
104A ILE* 1.3 80.7 - - + +
106A ASN* 1.3 64.0 + - - +
108A GLN* 3.2 21.4 + - - +
109A PHE* 3.0 40.1 + - + -
222A VAL* 3.8 15.3 - - + -
223A GLU* 3.7 27.6 - - + -
317A LYS* 5.5 5.4 - - - +
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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 ILE* 2.8 44.2 + - - +
103A ASP* 4.0 8.7 + - - +
105A LEU* 1.3 73.9 - - - +
107A GLU* 1.3 58.3 + - + +
109A PHE 3.5 0.3 + - - -
110A ARG* 2.9 38.0 + - + +
143A VAL 5.2 3.8 + - - +
145A HIS* 2.8 32.4 + - + -
219A HIS* 5.5 2.6 - - - -
221A GLY* 6.0 0.2 - - - -
222A VAL* 3.6 11.3 + - - +
403A PEG 5.4 6.5 - - - -
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Residues in contact with GLU 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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66A LEU* 3.5 13.0 - - + -
67A PRO* 3.4 35.6 - - - +
69A MET* 3.8 19.6 - - + +
103A ASP 3.1 18.9 + - - +
104A ILE 3.5 8.1 - - - +
106A ASN* 1.3 77.2 - - + +
108A GLN* 1.3 63.5 + - - +
110A ARG* 3.8 3.5 - - - +
111A LEU* 2.9 39.2 + - - +
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Residues in contact with GLN 108 (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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63A MET* 3.0 37.8 - - + +
66A LEU* 4.1 21.0 - - + +
104A ILE* 3.0 28.5 + - + +
105A LEU* 3.2 32.3 + - - +
107A GLU* 1.3 78.5 - - - +
109A PHE* 1.4 68.2 + - + +
111A LEU 3.5 5.0 + - - -
112A GLN* 3.5 8.3 + - - +
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Residues in contact with PHE 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 LEU* 3.0 41.6 + - + +
108A GLN* 1.4 82.7 - - + +
110A ARG* 1.3 65.3 + - - +
112A GLN* 3.3 9.9 + - + +
114A THR* 2.8 43.0 + - + +
145A HIS* 3.9 6.3 - - - +
206A TYR* 3.9 18.2 - + - -
222A VAL* 3.7 45.1 - - + -
225A LEU* 3.7 41.1 - - + -
317A LYS* 5.1 2.5 - - - -
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Residues in contact with ARG 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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106A ASN* 2.9 23.8 + - + +
107A GLU* 4.1 3.6 - - - +
109A PHE* 1.3 73.5 - - - +
111A LEU* 1.3 62.4 + - + +
113A ASN* 2.9 62.0 + - - +
114A THR 4.6 3.8 + - - +
144A GLY 3.4 26.7 + - - -
145A HIS* 3.5 19.3 - - + +
146A ARG* 4.5 12.1 - - - +
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Residues in contact with LEU 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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63A MET* 4.4 9.2 - - + -
64A VAL* 3.8 34.5 - - + +
65A SER 3.9 19.5 - - - +
66A LEU* 4.0 22.4 - - + -
67A PRO* 4.5 2.5 - - + -
107A GLU* 2.9 33.6 + - - +
108A GLN 3.8 4.9 - - - +
109A PHE 3.3 0.2 - - - -
110A ARG* 1.3 77.4 - - + +
112A GLN* 1.3 65.7 + - - +
113A ASN* 3.4 0.6 + - - +
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Residues in contact with GLN 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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62A PHE 3.8 24.5 + - - +
63A MET* 3.2 34.1 - - + +
64A VAL 4.8 0.7 + - - -
108A GLN 3.6 13.5 - - - +
109A PHE* 3.3 10.5 + - + +
110A ARG 3.1 0.8 - - - -
111A LEU* 1.3 86.3 - - - +
113A ASN* 1.3 67.5 + - - +
114A THR* 3.2 10.2 + - - +
205A ASP* 5.0 2.1 - - - +
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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