Contacts of the helix formed by residues 103 - 117 (chain A) in PDB entry 1EFA
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 GLY 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A SER* 1.3 79.5 + - - +
104A VAL* 1.3 64.4 + - - -
105A GLU* 3.3 3.4 - - - -
106A ALA* 3.5 5.2 + - - +
107A CYS 3.4 13.2 + - - -
126A TYR* 3.0 23.7 + - - -
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Residues in contact with VAL 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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103A GLY* 1.3 71.6 - - - -
105A GLU* 1.3 63.9 + - + +
107A CYS* 3.3 5.7 + - - +
108A LYS* 2.8 57.3 + - + +
128A LEU* 4.9 8.5 - - + -
132A ASP* 3.0 55.6 - - + +
136A VAL* 4.5 9.6 - - + -
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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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101A ARG* 5.2 0.2 - - - -
103A GLY* 3.3 1.5 - - - -
104A VAL* 1.3 81.8 - - + +
106A ALA* 1.3 52.1 + - - +
108A LYS* 3.1 29.5 + - - +
109A THR* 2.7 40.1 + - - +
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Residues in contact with ALA 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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99A VAL* 3.5 12.9 - - + +
101A ARG* 3.4 61.9 + - + +
102A SER 4.7 1.1 - - - +
103A GLY* 3.5 8.6 + - - +
104A VAL 3.2 0.2 - - - -
105A GLU* 1.3 79.9 - - - +
107A CYS* 1.3 57.2 + - - +
109A THR* 3.2 4.2 + - - -
110A ALA* 3.0 27.0 + - - +
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Residues in contact with CYS 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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67A ALA* 4.8 5.8 - - - -
99A VAL* 4.0 10.0 - - - +
103A GLY 3.4 9.6 + - - +
104A VAL* 3.3 10.7 + - - +
105A GLU 3.2 0.2 - - - -
106A ALA* 1.3 76.8 - - - +
108A LYS* 1.3 60.3 + - - +
110A ALA* 3.4 2.1 + - - +
111A VAL* 3.0 30.8 + - - +
124A ILE* 4.0 26.9 - - - -
126A TYR* 4.0 29.2 - - + -
128A LEU* 4.2 12.8 - - + -
136A VAL* 4.3 9.4 - - + -
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Residues in contact with LYS 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 VAL* 2.8 40.5 + - + +
105A GLU* 3.4 28.7 + - - +
107A CYS* 1.3 75.6 - - - +
109A THR* 1.3 55.9 + - - +
111A VAL* 3.0 8.7 + - - +
112A HIS* 2.8 34.7 + - - +
135A ALA* 4.1 25.8 - - - +
136A VAL* 4.3 14.8 - - + +
139A ALA* 5.7 8.7 - - + -
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Residues in contact with THR 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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101A ARG* 3.5 24.0 + - - +
105A GLU* 2.7 20.4 + - - +
106A ALA 3.3 9.2 - - - -
108A LYS* 1.3 73.1 - - - +
110A ALA* 1.3 62.7 + - - +
112A HIS* 3.1 19.8 + - + +
113A ASN* 3.2 27.7 + - - +
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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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67A ALA* 4.3 7.4 - - + -
97A SER* 3.6 24.0 + - - +
98A MET 5.4 0.9 - - - +
99A VAL* 3.4 33.0 - - + -
106A ALA 3.0 7.4 + - - +
107A CYS 3.4 7.0 - - - +
108A LYS 3.1 0.2 - - - -
109A THR* 1.3 78.6 - - - +
111A VAL* 1.3 61.1 + - - +
113A ASN* 3.5 4.1 + - - +
114A LEU* 3.1 29.1 + - - +
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Residues in contact with VAL 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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67A ALA* 4.6 2.7 - - + -
107A CYS* 3.0 22.7 + - - +
108A LYS* 3.0 9.4 + - - +
110A ALA* 1.3 73.7 - - - +
112A HIS* 1.3 65.6 + - - +
114A LEU* 3.4 3.8 + - - +
115A LEU* 2.9 34.3 + - + +
122A LEU* 3.4 22.9 - - + -
124A ILE* 3.7 28.5 - - + -
136A VAL* 3.8 16.8 - - + -
139A ALA* 4.8 10.5 - - + -
140A CYS* 3.9 13.9 - - - -
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Residues in contact with HIS 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 LYS 2.8 13.0 + - - +
109A THR* 3.2 16.1 - - + +
111A VAL* 1.3 76.9 - - - +
113A ASN* 1.3 63.1 + - - +
115A LEU* 3.0 11.0 + - - +
116A ALA* 2.9 24.5 + - + +
47B TYR 4.8 2.8 + - - -
48B ILE* 3.4 45.7 - - + +
49B PRO* 5.2 3.9 - - + +
51B ARG* 6.0 1.2 + - - -
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Residues in contact with ASN 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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97A SER* 4.4 9.8 + - - +
109A THR* 3.2 29.3 + - - +
110A ALA* 3.9 8.0 - - - +
111A VAL 3.4 0.2 - - - -
112A HIS* 1.3 78.8 + - - +
114A LEU* 1.3 67.7 + - + +
116A ALA* 3.0 20.1 + - - +
117A GLN* 3.1 25.6 + - - +
51B ARG* 4.0 22.2 + - - +
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Residues in contact with LEU 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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65A GLY* 3.8 13.2 - - - -
66A VAL 3.2 36.1 - - - +
67A ALA* 3.7 10.3 - - + +
95A VAL* 4.5 4.0 - - + -
96A VAL 4.4 2.9 - - - -
97A SER* 3.2 36.1 - - - +
110A ALA 3.1 12.4 + - - +
111A VAL* 3.7 5.6 - - - +
113A ASN* 1.3 79.7 - - + +
115A LEU* 1.3 61.5 + - - +
117A GLN* 3.3 23.1 + - - +
119A VAL* 3.1 29.8 + - + +
122A LEU* 3.6 26.2 - - + -
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Residues in contact with LEU 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 VAL* 2.9 26.6 + - + +
112A HIS* 3.2 10.3 - - - +
114A LEU* 1.3 76.6 - - - +
116A ALA* 1.3 55.7 + - - +
118A ARG* 2.7 38.9 + - - -
119A VAL* 4.4 5.8 - - + -
122A LEU* 4.1 18.4 - - + -
139A ALA* 3.3 28.0 - - + +
140A CYS* 4.1 1.8 - - - -
141A THR* 4.1 11.0 - - - +
143A VAL* 3.9 27.6 - - + -
48B ILE* 4.1 24.5 - - + -
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Residues in contact with ALA 116 (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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112A HIS* 2.9 10.4 + - + +
113A ASN* 3.0 10.7 + - - +
115A LEU* 1.3 77.2 - - - +
117A GLN* 1.3 57.6 + - - +
118A ARG* 3.0 22.1 + - - +
48B ILE* 3.6 19.7 - - + +
49B PRO 3.8 5.4 - - - +
50B ASN* 3.8 1.2 - - - -
51B ARG* 3.2 52.8 + - - +
52B VAL 4.4 0.9 + - - -
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Residues in contact with GLN 117 (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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55A GLN* 3.8 8.3 + - - +
63A LEU* 3.7 12.0 - - + +
95A VAL* 3.1 37.3 - - - +
113A ASN* 3.1 24.6 + - - +
114A LEU* 3.7 15.5 - - - +
115A LEU 3.1 1.4 - - - -
116A ALA* 1.3 74.9 - - - +
118A ARG* 1.3 72.1 + - - +
119A VAL* 3.3 7.0 + - + -
51B ARG* 4.4 18.1 - - + +
52B VAL* 4.1 11.7 - - + +
93B SER* 5.5 6.3 + - - -
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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