Contacts of the helix formed by residues 103 - 118 (chain A) in PDB entry 4YET
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 SER 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A ILE* 4.3 6.2 - - - +
98A GLU* 4.4 7.5 - - - +
101A PHE* 3.1 5.7 + - - +
102A GLY* 1.3 77.4 - - - +
104A PHE* 1.3 64.5 + - - +
105A SER* 3.5 9.6 + - - -
106A ALA* 3.0 25.8 + - - +
107A PHE* 3.1 19.6 + - - +
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Residues in contact with PHE 104 (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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87A GLY 3.9 24.2 - - - -
88A GLU* 3.3 34.8 - - + +
89A PRO* 3.4 24.2 - - + -
97A ILE* 4.2 9.0 - - + +
98A GLU* 4.8 6.6 + - + +
103A SER* 1.3 71.2 - - - +
105A SER* 1.3 62.9 + - - +
107A PHE* 3.1 25.8 + + - -
108A LYS* 2.8 49.1 + - + +
180A TRP* 3.9 20.0 - + + -
185A TRP* 3.7 21.5 - + - -
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Residues in contact with SER 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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103A SER* 3.5 8.9 + - - -
104A PHE* 1.3 81.8 - - - +
106A ALA* 1.3 60.7 + - - +
108A LYS* 3.3 7.8 + - - +
109A THR* 3.1 29.2 + - - -
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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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101A PHE* 3.2 25.1 - - + +
103A SER* 3.0 17.0 + - - +
105A SER* 1.3 72.7 - - - +
107A PHE* 1.3 61.5 + - - +
109A THR* 3.3 7.2 + - - -
110A ASP* 2.9 38.2 + - - +
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Residues in contact with PHE 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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97A ILE* 4.0 17.3 - - + -
101A PHE* 3.4 40.7 - + + +
103A SER 3.1 10.8 + - - +
104A PHE* 3.1 27.9 + + - +
106A ALA* 1.3 79.4 - - - +
108A LYS* 1.3 56.0 + - - +
110A ASP 3.2 0.2 + - - -
111A PHE* 2.8 42.8 + + + +
126A LEU* 3.8 30.1 - - + -
136A ILE* 3.6 25.1 - - + -
155A LEU* 6.0 1.3 - - + -
179A TRP* 6.5 0.2 - + - -
180A TRP* 3.5 27.6 - + - -
185A TRP* 4.1 14.6 - + - -
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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 PHE* 2.8 44.4 + - + +
105A SER* 3.6 7.6 - - - +
106A ALA 3.3 0.2 - - - -
107A PHE* 1.3 73.2 - - - +
109A THR* 1.3 56.3 + - - +
112A SER* 2.6 38.6 + - - +
177A ASN* 5.0 8.0 + - - +
180A TRP* 3.5 56.6 - - + +
181A ASN* 5.6 2.2 + - - -
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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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105A SER* 3.1 16.5 + - - -
106A ALA* 3.6 9.8 - - - -
107A PHE 3.3 0.2 - - - -
108A LYS* 1.3 76.5 - - - +
110A ASP* 1.3 63.6 + - - +
112A SER* 3.8 3.6 - - - -
113A ASN* 2.9 53.0 + - - +
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Residues in contact with ASP 110 (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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101A PHE* 3.5 24.5 - - + +
106A ALA* 2.9 23.3 + - - +
107A PHE 3.8 3.1 - - - +
109A THR* 1.3 83.9 - - - +
111A PHE* 1.3 59.1 + - - +
113A ASN* 3.4 8.5 + - - +
114A LEU* 3.1 25.6 + - - +
136A ILE* 3.7 18.7 - - + +
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Residues in contact with PHE 111 (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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107A PHE* 2.8 34.8 + + + +
110A ASP* 1.3 70.2 - - - +
112A SER* 1.3 65.0 + - - +
114A LEU* 3.2 16.4 + - + +
115A LEU* 2.9 50.8 + - + +
124A GLY 3.6 23.3 - - - -
125A TRP* 3.6 31.2 - - - -
126A LEU* 4.1 5.2 - - + -
136A ILE* 3.4 26.2 - - + +
155A LEU* 5.2 1.6 - - + -
157A CYS* 4.6 2.2 - - + -
179A TRP* 3.8 22.7 - + - -
180A TRP* 3.7 30.1 - + + -
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Residues in contact with SER 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* 2.6 29.3 + - - +
109A THR* 3.8 4.7 - - - -
111A PHE* 1.3 77.3 - - - +
113A ASN* 1.3 59.4 + - - +
115A LEU* 3.4 2.7 + - - +
116A ALA* 2.8 31.8 + - - +
173A LEU* 5.6 6.5 - - - -
176A ILE* 3.7 20.8 - - - +
177A ASN* 4.9 3.4 + - - -
180A TRP* 2.8 25.6 + - - -
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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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109A THR* 2.9 40.9 + - - +
110A ASP* 3.7 9.1 + - - +
112A SER* 1.3 74.0 - - - +
114A LEU* 1.3 66.7 + - - +
116A ALA* 3.9 5.7 - - - +
117A GLY* 3.0 21.3 + - - -
173A LEU* 6.1 1.4 - - - +
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Residues in contact with LEU 114 (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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110A ASP 3.1 14.4 + - - +
111A PHE* 3.2 16.8 + - + +
113A ASN* 1.3 77.6 - - - +
115A LEU* 1.3 67.4 + - - +
117A GLY* 3.3 9.8 + - - -
118A HIS* 3.3 14.0 + - + +
123A TRP 5.3 0.2 - - - -
124A GLY* 3.8 28.9 - - - -
136A ILE* 4.0 22.7 - - + +
137A VAL* 3.8 33.4 - - - +
138A GLN* 4.0 27.4 - - + +
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Residues in contact with LEU 115 (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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111A PHE* 2.9 47.4 + - + +
112A SER 3.8 0.9 - - - +
114A LEU* 1.3 77.2 - - + +
116A ALA* 1.3 58.9 - - - +
117A GLY 3.4 0.3 + - - -
118A HIS* 3.6 4.9 + - - +
124A GLY* 3.6 33.4 - - - +
157A CYS* 3.7 30.1 - - + -
159A VAL* 3.9 16.2 - - + +
172A ARG* 2.8 27.2 + - - -
176A ILE* 3.5 35.7 - - + -
179A TRP* 4.7 5.4 - - + -
180A TRP* 5.2 0.7 - - + -
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Residues in contact with ALA 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 SER 2.8 18.6 + - - +
113A ASN* 4.0 6.5 - - - +
115A LEU* 1.3 76.9 - - - +
117A GLY* 1.3 61.2 + - - +
118A HIS 4.5 0.2 - - - +
172A ARG* 3.5 15.9 + - + +
173A LEU* 3.9 28.9 - - + -
176A ILE* 3.5 9.3 - - + +
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Residues in contact with GLY 117 (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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113A ASN 3.0 17.4 + - - -
114A LEU* 3.3 2.7 + - - -
115A LEU 3.2 0.2 - - - -
116A ALA* 1.3 78.6 - - - +
118A HIS* 1.3 62.4 + - - +
119A PHE* 3.2 7.3 + - - +
138A GLN* 5.2 0.9 - - - -
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Residues in contact with HIS 118 (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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114A LEU* 3.3 7.8 + - + +
115A LEU* 4.0 6.5 - - - +
116A ALA 3.4 3.1 - - - +
117A GLY* 1.3 75.7 - - - +
119A PHE* 1.3 68.9 + - - +
120A GLY 3.6 13.0 - - - +
121A SER 3.4 4.2 + - - -
122A GLY* 3.6 14.5 - - - -
123A TRP 4.9 2.2 + - - +
138A GLN* 2.8 38.8 + - + +
139A THR 3.3 23.3 - - - -
140A HIS* 2.8 30.4 + - + -
159A VAL* 4.1 10.3 - - + -
172A ARG* 2.8 39.3 + - - +
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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