Contacts of the helix formed by residues 102 - 117 (chain A) in PDB entry 1EUQ
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 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ARG* 4.0 4.7 - - - -
97A ARG* 3.6 15.8 + - + +
98A TYR 3.6 14.4 - - - -
99A SER* 2.7 15.1 + - - +
101A ASP* 1.3 87.4 - - + +
103A PHE* 1.3 63.6 + - - -
104A ASP 3.4 2.0 - - - -
105A GLN* 3.0 19.4 - - + +
106A LEU* 2.8 35.5 + - + +
218A SER* 3.4 32.8 - - - +
221A LEU* 4.5 22.9 - - + -
222A GLU* 2.6 45.4 + - + +
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Residues in contact with PHE 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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67A ASP 3.9 17.3 - - - -
68A THR* 4.3 11.9 - - + -
99A SER 4.0 3.6 - - - -
100A SER* 3.1 38.5 + - - +
101A ASP 3.4 1.6 - - - -
102A TYR* 1.3 75.0 - - - +
104A ASP* 1.3 67.5 + - - +
106A LEU* 2.9 24.3 + - + +
107A HIS* 3.0 10.4 + - - +
191A TYR* 3.6 5.1 + - - +
198A HIS* 4.2 5.8 - + - -
201A THR* 4.1 6.1 - - + -
205A TRP* 3.1 43.7 - + + +
208A TYR* 3.7 37.9 - + - -
209A PRO* 3.7 25.8 - - + -
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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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100A SER 5.4 0.7 - - - +
101A ASP 4.6 7.1 - - - +
103A PHE* 1.3 76.4 + - - +
105A GLN* 1.3 65.2 + - - +
107A HIS* 3.0 9.3 + - + +
108A ALA* 3.0 23.6 + - - +
204A LYS* 2.9 29.7 + - - -
205A TRP* 3.7 15.0 - - + -
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Residues in contact with GLN 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 ASP 5.9 0.6 + - - -
102A TYR* 3.0 29.3 + - + +
104A ASP* 1.3 80.9 - - - +
106A LEU* 1.3 59.8 + - + +
108A ALA* 3.3 9.8 + - - +
109A TYR* 3.1 37.4 + - + -
221A LEU* 3.3 34.9 - - + +
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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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99A SER 4.4 3.1 - - - +
102A TYR* 2.8 46.4 + - + +
103A PHE* 2.9 17.2 + - + +
105A GLN* 1.3 73.2 - - - +
107A HIS* 1.3 53.0 + - - +
109A TYR* 3.2 3.2 + - - -
110A ALA* 2.8 31.7 + - - +
191A TYR* 3.3 17.0 - - + +
209A PRO* 4.3 8.1 - - + -
213A PHE* 3.3 23.3 - - + -
214A THR* 4.4 22.0 - - + +
217A ILE* 3.5 44.0 - - + -
218A SER* 5.2 0.9 - - - +
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Residues in contact with HIS 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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103A PHE 3.0 9.7 + - - +
104A ASP* 3.0 15.8 + - + +
106A LEU* 1.3 74.2 - - - +
108A ALA* 1.3 68.1 + - - +
110A ALA* 3.0 16.3 + - - +
111A ILE* 3.0 34.1 + - + +
157A PHE* 3.4 34.2 - + - -
158A GLU* 4.7 8.4 + - - -
161A ARG* 4.2 30.8 + - + +
191A TYR* 3.4 8.4 + - - +
205A TRP* 4.2 16.5 - + + -
207A ILE* 4.8 2.8 - - - +
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Residues in contact with ALA 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 3.0 11.5 + - - +
105A GLN* 3.6 15.5 - - - +
107A HIS* 1.3 77.0 - - - +
109A TYR* 1.3 62.5 + - + +
111A ILE* 3.0 15.9 + - - +
112A GLU* 2.8 25.2 + - - +
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Residues in contact with TYR 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 GLN* 3.1 27.0 + - + -
106A LEU 3.5 7.9 - - - +
108A ALA* 1.3 81.6 - - + +
110A ALA* 1.3 65.7 + - - +
112A GLU* 3.0 31.0 + - + +
113A LEU* 3.0 25.0 + - - +
213A PHE* 3.9 13.0 - - + -
217A ILE* 4.0 31.0 - - + -
221A LEU* 4.4 13.3 - - + +
247A ILE* 3.6 26.9 - - + -
248A THR 2.9 25.0 + - - -
249A ILE* 3.7 21.5 - - + +
250A PRO* 5.4 0.3 - - - +
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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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106A LEU 2.8 16.9 + - - +
107A HIS 3.0 9.2 + - - +
109A TYR* 1.3 71.4 - - - +
111A ILE* 1.3 58.6 + - - +
113A LEU* 3.1 10.9 + - - +
114A ILE* 2.9 31.7 + - - +
119A ALA* 4.4 0.9 - - - +
157A PHE* 3.8 14.8 - - + -
172A LEU* 3.8 23.1 - - + -
190A LEU* 5.2 0.9 - - + -
191A TYR* 4.0 11.0 - - + -
213A PHE* 3.6 11.8 - - + -
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Residues in contact with ILE 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 HIS* 3.0 42.7 + - + +
108A ALA* 3.0 13.1 + - - +
110A ALA* 1.3 73.1 - - - +
112A GLU* 1.3 68.0 + - - +
114A ILE* 2.9 9.3 + - + -
115A ASN* 2.8 45.3 + - - +
154A LEU* 4.8 13.7 - - + -
157A PHE* 4.2 17.3 - - + -
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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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108A ALA 2.8 13.6 + - - +
109A TYR* 3.0 29.9 + - + +
111A ILE* 1.3 75.7 - - - +
113A LEU* 1.3 58.2 + - - +
115A ASN* 3.8 5.1 - - - +
116A LYS* 2.8 53.5 + - - +
247A ILE* 3.9 7.6 - - + -
248A THR* 2.5 49.2 + - - -
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Residues in contact with LEU 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 TYR 3.0 14.9 + - - +
110A ALA 3.5 6.5 - - - +
112A GLU* 1.3 75.2 - - - +
114A ILE* 1.3 58.6 + - - +
116A LYS* 3.1 6.1 + - - -
117A GLY 2.7 10.2 + - - -
118A LEU* 2.7 33.3 + - + +
119A ALA* 3.7 11.7 - - + -
190A LEU* 3.2 34.3 - - + -
213A PHE* 3.9 15.0 - - + -
242A TRP* 4.2 22.7 - - + -
243A VAL* 4.9 3.4 - - + +
246A ASN* 3.0 38.4 - - + +
247A ILE* 3.4 13.0 - - + -
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Residues in contact with ILE 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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110A ALA 2.9 19.5 + - - +
111A ILE* 2.9 10.8 + - + +
113A LEU* 1.3 75.5 - - - +
115A ASN* 1.3 55.3 + - - +
117A GLY* 2.6 26.9 + - - -
119A ALA* 3.7 24.9 - - + +
150A VAL* 3.7 8.7 - - + +
153A ASN* 3.3 32.7 - - + +
154A LEU* 3.3 22.2 - - + +
157A PHE* 3.7 31.4 - - + -
172A LEU* 3.6 27.4 - - + -
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Residues in contact with ASN 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 ILE* 2.8 40.9 + - - +
112A GLU* 3.8 5.7 - - - +
114A ILE* 1.3 67.1 - - - +
116A LYS* 1.3 59.7 + - - +
117A GLY 2.8 8.8 + - - -
150A VAL* 3.5 32.3 - - - +
154A LEU* 3.7 19.3 - - - +
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Residues in contact with LYS 116 (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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112A GLU* 2.8 49.2 + - - +
113A LEU* 3.5 6.1 - - - +
115A ASN* 1.3 76.1 - - - +
117A GLY* 1.3 61.4 + - - +
118A LEU* 3.3 24.4 + - + +
246A ASN* 3.6 31.1 + - - +
247A ILE* 4.0 4.8 - - - +
248A THR* 4.5 2.8 + - - -
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Residues in contact with GLY 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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113A LEU 2.7 1.4 + - - -
114A ILE 2.6 25.0 + - - -
115A ASN 2.8 2.9 - - - -
116A LYS* 1.3 71.4 - - - +
118A LEU* 1.3 59.9 + - - +
119A ALA 3.4 6.7 - - - -
150A VAL* 4.7 8.7 - - - -
153A ASN* 6.1 0.2 - - - -
175A LYS* 3.5 31.6 + - - +
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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