Contacts of the helix formed by residues 102 - 113 (chain A) in PDB entry 1WFG
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 THR 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A GLY* 3.5 6.7 - - - -
65A LEU* 4.3 10.3 - - + -
100A GLY 4.2 5.6 - - - +
101A ALA* 1.3 77.5 - - - +
103A PHE* 1.3 64.8 + - - +
104A GLU* 3.4 12.5 + - - +
105A GLU* 3.1 38.0 + - + +
106A VAL* 2.9 22.9 + - - +
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Residues in contact with PHE 103 (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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53A LYS* 6.0 5.4 - - - -
54A VAL 5.8 0.9 - - - -
55A VAL* 5.0 17.9 - - + -
56A GLY* 3.5 32.9 + - - +
57A GLY* 3.1 10.0 - - - +
102A THR* 1.3 74.9 - - - +
104A GLU* 1.3 75.9 + - + +
106A VAL* 4.0 2.6 - - - +
107A TYR* 3.3 40.1 + + - +
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Residues in contact with GLU 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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102A THR* 3.1 9.5 + - - +
103A PHE* 1.3 90.9 - - + +
105A GLU* 1.3 56.9 + - + +
107A TYR* 2.9 7.3 + - - +
108A ASN* 2.5 47.5 + - - +
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Residues in contact with GLU 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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96A ARG* 5.6 3.5 + - - -
97A LEU 5.5 1.0 - - - +
101A ALA* 3.7 16.6 - - + +
102A THR* 3.1 44.4 + - + +
104A GLU* 1.3 77.7 - - + +
106A VAL* 1.3 64.0 + - - +
108A ASN* 3.1 14.0 + - - +
109A ILE* 3.0 31.7 + - + +
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Residues in contact with VAL 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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54A VAL* 3.9 31.0 - - + +
56A GLY* 3.7 27.6 - - - +
67A ALA* 4.0 2.0 - - + -
98A LEU* 3.9 27.5 - - + +
101A ALA* 3.7 20.9 - - + +
102A THR 2.9 18.6 + - - +
103A PHE 4.0 2.0 - - - +
105A GLU* 1.3 76.1 - - - +
107A TYR* 1.3 64.2 - - - +
109A ILE* 3.2 23.6 + - - +
110A ILE* 3.4 14.1 + - + +
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Residues in contact with TYR 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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49A MET* 5.8 9.4 - - + -
53A LYS* 5.3 11.9 - - - -
54A VAL 6.1 0.7 - - - -
103A PHE* 3.3 33.6 + + + +
104A GLU* 2.9 12.3 + - - +
106A VAL* 1.3 77.2 - - - +
108A ASN* 1.3 68.2 + - - +
109A ILE 3.2 0.3 + - - -
110A ILE* 3.3 13.0 + - + +
111A LEU* 2.9 44.5 + - + -
114A LYS* 4.8 16.3 + - - -
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Residues in contact with ASN 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 GLU* 2.5 28.7 + - - +
105A GLU* 3.3 17.2 - - - +
107A TYR* 1.3 74.1 - - - +
109A ILE* 1.3 51.9 + - + +
111A LEU* 2.7 21.1 + - - +
112A GLU* 2.6 45.4 + - + +
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Residues in contact with ILE 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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93A TRP* 3.0 36.8 - - + +
96A ARG* 3.5 48.5 - - + +
97A LEU 4.4 5.6 - - - +
98A LEU* 3.0 33.0 - - + -
101A ALA* 4.9 2.5 - - + -
105A GLU* 3.0 24.2 + - + +
106A VAL* 3.3 9.6 - - + +
108A ASN* 1.3 77.4 - - + +
110A ILE* 1.3 55.1 + - - +
111A LEU 2.5 12.5 + - - -
112A GLU* 2.6 21.9 + - - +
113A SER* 2.7 15.0 + - - +
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Residues in contact with ILE 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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48A ALA 4.0 11.4 - - - +
49A MET* 4.4 23.3 - - + -
54A VAL* 4.4 15.9 - - + +
93A TRP* 3.2 59.0 - - + +
98A LEU* 5.7 0.7 - - + -
106A VAL* 3.4 33.4 + - + +
107A TYR* 3.3 10.0 + - + +
109A ILE* 1.3 78.8 - - - +
111A LEU* 1.3 51.3 + - - +
113A SER 3.1 1.3 - - - -
114A LYS* 2.7 52.9 + - - +
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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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107A TYR* 2.9 38.6 + - + +
108A ASN* 2.7 26.8 + - - +
109A ILE 2.5 4.6 + - - -
110A ILE* 1.3 68.4 - - - +
112A GLU* 1.3 55.0 + - + +
113A SER 2.8 4.3 - - - -
114A LYS* 2.7 48.9 + - + +
115A PRO* 3.2 6.6 - - - +
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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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96A ARG* 3.3 28.1 + - - +
108A ASN* 2.6 28.0 + - + +
109A ILE* 2.6 9.7 + - - +
111A LEU* 1.3 72.7 - - + +
113A SER* 1.3 60.7 + - - +
114A LYS 3.5 0.4 - - - -
115A PRO* 4.1 8.4 - - - +
116A GLU* 4.4 6.2 - - - +
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Residues in contact with SER 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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35A LYS* 4.6 0.5 + - - -
48A ALA 5.5 0.2 - - - +
50A LEU* 5.9 0.5 - - - +
93A TRP* 3.8 16.1 + - - -
94A ASN* 3.2 35.8 + - - +
96A ARG* 5.8 1.6 - - - +
109A ILE* 2.7 14.9 + - - +
110A ILE 3.1 4.7 - - - +
112A GLU* 1.3 83.6 + - - +
114A LYS* 1.3 61.2 + - - +
115A PRO 3.5 0.9 - - - -
116A GLU* 3.4 25.5 + - - +
119A VAL* 4.0 13.2 - - - +
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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