Contacts of the helix formed by residues 113 - 129 (chain A) in PDB entry 6EBT
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 ASP 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A GLY 3.1 6.3 + - - -
112A LEU* 1.3 75.5 - - - +
114A PRO* 1.3 73.1 - - - +
115A LYS* 3.1 28.9 + - - +
116A ILE* 3.1 30.3 + - + +
117A ALA* 2.7 25.1 + - - +
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Residues in contact with PRO 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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108A GLN* 3.6 25.0 - - + +
111A GLY 5.3 0.7 - - - +
112A LEU 3.6 5.8 - - - +
113A ASP* 1.3 92.4 - - - +
115A LYS* 1.3 56.6 + - - +
117A ALA* 4.2 1.1 - - + -
118A ASN* 2.8 34.5 + - - +
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Residues in contact with LYS 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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113A ASP* 3.1 18.5 + - - +
114A PRO* 1.3 78.5 - - - +
116A ILE* 1.3 61.4 + - + +
118A ASN* 4.3 3.9 + - - +
119A ALA* 3.4 19.6 + - - +
165A LEU* 4.1 16.8 - - + +
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Residues in contact with ILE 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 LEU* 4.4 6.3 - - + -
113A ASP* 3.1 29.7 + - + +
115A LYS* 1.3 77.1 - - + +
117A ALA* 1.3 65.6 + - - +
119A ALA* 3.1 4.9 + - - +
120A ILE* 2.9 40.3 + - + +
165A LEU* 4.6 5.8 - - + -
174A PRO* 3.7 36.8 - - + +
175A VAL* 4.1 12.3 - - + -
180A HIS* 3.9 30.5 - - + +
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Residues in contact with ALA 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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104A ALA* 4.0 7.9 - - - +
108A GLN* 3.4 37.7 - - + +
112A LEU* 3.9 21.5 - - + +
113A ASP 2.7 18.1 + - - +
116A ILE* 1.3 73.6 - - - +
118A ASN* 1.3 57.8 + - - +
120A ILE* 3.3 6.9 + - - +
121A MET* 2.9 35.2 + - - +
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Residues in contact with ASN 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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108A GLN* 5.0 1.7 + - - +
114A PRO 2.8 22.3 + - - +
115A LYS* 4.3 4.6 + - - +
117A ALA* 1.3 72.9 - - - +
119A ALA* 1.3 59.0 + - - +
121A MET* 3.3 20.0 + - + +
122A LYS* 2.9 48.7 + - - +
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Residues in contact with ALA 119 (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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115A LYS 3.4 11.8 + - - +
116A ILE 3.1 8.6 + - - +
118A ASN* 1.3 79.4 - - - +
120A ILE* 1.3 60.2 + - - +
122A LYS* 3.3 7.0 + - - +
123A ALA* 2.9 30.0 + - - +
161A ALA* 3.7 22.6 - - + +
164A MET* 3.8 9.3 - - + +
165A LEU* 3.8 27.4 - - + -
175A VAL* 4.9 0.2 - - + -
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Residues in contact with ILE 120 (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 LYS* 4.4 8.3 - - + +
104A ALA* 3.6 20.6 - - + -
112A LEU* 4.7 6.1 - - + -
116A ILE* 2.9 34.2 + - + +
117A ALA* 3.3 9.4 + - - +
119A ALA* 1.3 75.7 - - - +
121A MET* 1.3 53.7 + - - +
123A ALA* 3.4 1.0 + - - +
124A ALA* 2.7 38.2 + - + +
157A ILE* 3.8 19.6 - - + +
161A ALA* 4.3 2.5 - - + -
175A VAL* 3.7 20.9 - - + -
180A HIS* 3.9 18.6 - - + +
181A VAL* 3.8 28.0 - - + +
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Residues in contact with MET 121 (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 48.6 - - - +
104A ALA* 4.0 14.1 - - + -
105A GLU* 4.2 26.5 - - + +
108A GLN* 4.4 11.7 - - - +
117A ALA 2.9 25.5 + - - +
118A ASN* 3.6 15.9 - - - +
120A ILE* 1.3 77.7 - - - +
122A LYS* 1.3 57.6 + - + +
124A ALA* 3.4 4.4 + - - +
125A ASP* 2.9 37.5 + - - +
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Residues in contact with LYS 122 (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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118A ASN* 2.9 39.6 + - - +
119A ALA* 3.7 1.1 - - - +
121A MET* 1.3 76.6 - - + +
123A ALA* 1.3 63.0 + - - +
125A ASP* 3.2 19.9 + - - +
126A GLU* 3.2 16.5 + - - +
164A MET* 3.6 28.3 - - + -
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Residues in contact with ALA 123 (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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119A ALA 2.9 17.2 + - - +
120A ILE 3.8 2.7 - - - +
122A LYS* 1.3 75.3 - - - +
124A ALA* 1.3 63.9 + - - +
126A GLU* 3.0 14.3 + - - +
127A VAL* 3.2 16.9 + - - +
132A LEU* 4.4 1.4 - - + +
157A ILE* 3.6 29.4 - - + +
160A ARG* 3.7 24.7 - - + -
161A ALA 4.0 2.5 - - - +
164A MET* 3.7 9.3 - - + +
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Residues in contact with ALA 124 (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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97A GLY* 3.4 27.5 - - - +
100A LYS* 4.2 3.4 - - + -
101A ARG* 3.6 20.0 - - + +
120A ILE 2.7 22.8 + - - +
121A MET 3.6 4.5 - - - +
123A ALA* 1.3 74.2 - - - +
125A ASP* 1.3 62.1 + - - +
127A VAL* 3.1 5.5 + - - +
128A ALA* 2.9 19.2 + - - +
157A ILE* 4.1 20.1 - - + +
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Residues in contact with ASP 125 (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* 3.2 35.8 + - - +
121A MET* 2.9 21.4 + - - +
122A LYS* 3.2 12.2 + - - +
124A ALA* 1.3 75.1 - - - +
126A GLU* 1.3 59.2 + - + +
128A ALA* 3.2 8.5 + - - +
129A GLU* 2.8 51.4 + - + +
300A LEU* 5.7 0.7 - - - +
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Residues in contact with GLU 126 (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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122A LYS 3.5 11.7 - - - +
123A ALA 3.0 8.3 + - - +
125A ASP* 1.3 77.3 - - + +
127A VAL* 1.3 61.2 + - - +
129A GLU* 3.4 2.4 + - - +
130A GLY 3.3 3.3 + - - -
131A LYS* 2.9 58.0 + - + +
132A LEU* 3.8 19.5 + - + +
160A ARG* 2.8 49.1 + - - +
164A MET* 3.4 12.6 - - - +
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Residues in contact with VAL 127 (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 ILE* 3.4 42.1 - - + +
94A LYS* 3.6 9.7 - - - +
97A GLY* 4.0 10.1 - - - +
123A ALA 3.2 12.7 + - - +
124A ALA 3.1 6.8 + - - +
126A GLU* 1.3 75.8 - - - +
128A ALA* 1.3 62.0 + - - +
130A GLY* 3.0 13.7 + - - -
132A LEU* 3.9 23.1 - - + +
133A ASN* 4.6 3.1 - - - +
136A PHE* 4.1 17.7 - - + -
153A VAL* 5.3 4.7 - - + -
156A VAL* 4.4 2.5 - - + -
157A ILE* 4.1 20.4 - - + -
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Residues in contact with ALA 128 (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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94A LYS* 3.4 43.0 - - - +
97A GLY* 4.0 0.4 - - - -
98A ILE* 3.8 25.4 - - + +
101A ARG* 6.4 0.2 - - + -
124A ALA 2.9 13.5 + - - +
125A ASP* 3.6 12.1 - - - +
127A VAL* 1.3 77.7 - - - +
129A GLU* 1.3 61.0 + - + +
130A GLY 3.4 3.1 + - - -
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Residues in contact with GLU 129 (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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94A LYS* 4.5 4.9 + - - -
125A ASP* 2.8 35.9 + - - +
126A GLU* 3.4 4.2 + - - +
127A VAL 3.2 0.4 - - - -
128A ALA* 1.3 78.5 - - + +
130A GLY* 1.3 61.6 + - - +
131A LYS* 2.5 45.4 + - - +
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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