Contacts of the helix formed by residues 116 - 128 (chain A) in PDB entry 6CNB
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 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A LEU 4.8 0.9 - - - -
115A LEU* 1.3 84.3 - - - +
117A GLU* 1.3 106.4 + - - +
119A ASP* 3.3 2.3 - - - +
120A LYS* 3.0 19.3 + - - +
151A GLN* 4.9 3.8 + - - +
155A LEU* 3.6 28.7 - - - -
336O LEU* 4.1 19.4 - - - +
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Residues in contact with GLU 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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115A LEU* 5.7 0.5 - - - +
116A SER* 1.3 113.5 + - - +
118A THR* 1.3 70.2 + - - +
119A ASP* 3.1 27.4 - - + +
120A LYS* 3.4 16.3 + - - +
121A ARG 3.8 0.7 + - - -
155A LEU* 5.3 0.4 - - - +
73O ARG* 3.6 18.0 + - - +
212O GLU* 3.7 24.7 - - + +
216O GLN* 4.5 14.8 - - - +
336O LEU* 5.2 3.5 - - - +
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Residues in contact with THR 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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117A GLU* 1.3 78.0 - - - +
119A ASP* 1.3 52.3 + - - -
120A LYS 3.1 1.3 - - - -
121A ARG* 2.8 27.6 + - + +
122A GLN* 2.5 41.9 + - + +
73O ARG* 4.5 7.4 + - - +
212O GLU* 4.2 7.0 + - - -
213O ASP* 4.4 12.6 + - - -
216O GLN* 5.3 7.2 - - - +
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Residues in contact with ASP 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 LEU* 3.8 24.8 - - + +
116A SER 3.3 3.6 - - - +
117A GLU* 3.1 28.7 - - + +
118A THR* 1.3 76.9 - - - +
120A LYS* 1.3 58.5 + - - +
122A GLN* 2.9 25.5 + - - +
123A PHE* 3.0 25.9 + - - -
147A GLN* 4.9 6.1 + - - +
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Residues in contact with LYS 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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113A ILE* 3.6 31.6 + - + +
115A LEU* 3.8 29.8 - - + +
116A SER* 3.0 15.1 + - - +
117A GLU 3.5 11.0 - - - +
118A THR 3.1 0.2 - - - -
119A ASP* 1.3 76.7 - - - +
121A ARG* 1.3 60.2 + - - +
123A PHE* 3.5 8.0 + - - +
124A LEU* 3.3 23.4 + - + +
155A LEU* 5.6 2.8 - - - +
237A ALA* 5.4 7.8 - - - +
238A ASP* 5.7 2.0 - - + +
241A LEU* 3.2 25.3 - - + +
73O ARG* 3.8 26.2 - - - +
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Residues in contact with ARG 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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117A GLU 3.8 0.6 + - - -
118A THR* 2.8 35.2 + - + +
120A LYS* 1.3 79.0 - - - +
122A GLN* 1.3 57.5 + - - +
124A LEU* 3.0 15.9 + - + +
125A HIS* 2.8 68.5 + - - +
128A ARG* 5.9 2.8 - - - +
73O ARG* 3.1 43.0 - - + +
78O GLU* 5.5 2.2 + - - -
119O TYR* 3.7 39.7 + - - -
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Residues in contact with GLN 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 THR* 2.5 21.0 + - - +
119A ASP* 3.1 19.7 - - - +
121A ARG* 1.3 72.6 - - - +
123A PHE* 1.3 60.3 + - - +
125A HIS* 3.7 17.2 + - - +
126A GLU* 2.8 35.1 + - + +
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Residues in contact with PHE 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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115A LEU* 2.8 31.4 - - + -
119A ASP* 3.0 31.7 + - - -
120A LYS* 3.5 8.5 - - - +
122A GLN* 1.3 76.6 - - + +
124A LEU* 1.3 56.3 + - - +
126A GLU* 3.6 5.7 + - + +
127A LEU* 2.7 38.0 + - + +
140A ILE* 4.4 13.7 - - + -
143A LYS* 3.8 23.6 - - + -
144A ILE* 3.1 50.5 - - + -
147A GLN* 3.8 17.9 - - + -
241A LEU* 3.8 13.9 - - + -
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Residues in contact with LEU 124 (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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120A LYS* 3.3 20.6 + - + +
121A ARG* 3.0 23.9 + - + +
123A PHE* 1.3 73.6 - - - +
125A HIS* 1.3 57.9 + - - +
126A GLU 3.0 1.1 - - - -
127A LEU* 2.6 32.2 + - + +
128A ARG* 3.1 50.7 + - - +
237A ALA 5.7 4.5 - - - +
238A ASP* 5.1 2.0 - - - +
240A GLU* 3.9 15.0 - - + +
241A LEU* 3.5 27.8 - - + -
71O LEU 5.5 4.3 - - - +
73O ARG* 4.9 15.0 - - + +
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Residues in contact with HIS 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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121A ARG* 2.8 55.1 + - - +
122A GLN* 3.8 18.3 + - - +
124A LEU* 1.3 70.6 - - - +
126A GLU* 1.3 65.0 + - - +
128A ARG* 4.2 8.6 - - - +
129A ARG* 3.8 23.0 + - + +
119O TYR* 5.3 3.6 - - - -
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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 GLN* 2.8 21.8 + - + +
123A PHE* 3.6 7.2 - - + +
124A LEU 3.0 0.2 + - - -
125A HIS* 1.3 81.3 + - - +
127A LEU* 1.3 70.9 + - - +
129A ARG* 3.3 32.5 + - - +
132A VAL* 3.8 5.9 - - - +
136A ARG* 3.4 21.5 + - - +
140A ILE* 3.1 50.2 - - + +
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Residues in contact with LEU 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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123A PHE* 2.7 32.4 + - + +
124A LEU* 2.6 18.3 + - + +
126A GLU* 1.3 79.6 + - - +
128A ARG* 1.3 62.2 + - + +
129A ARG 2.9 7.2 + - - +
132A VAL* 3.2 24.6 - - + +
137A ARG* 4.2 30.4 - - - +
140A ILE* 3.5 30.1 - - + -
141A LEU* 5.4 7.6 - - + -
240A GLU* 4.1 33.2 - - + +
241A LEU* 5.1 8.1 - - + +
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Residues in contact with ARG 128 (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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121A ARG* 5.9 3.0 - - - +
124A LEU* 3.1 51.9 + - - +
125A HIS* 3.9 6.5 + - - +
126A GLU 3.5 0.4 - - - -
127A LEU* 1.3 75.7 - - + +
129A ARG* 1.3 65.3 + - - +
130A PRO* 3.2 9.0 - - - +
240A GLU* 2.3 37.1 + - - +
71O LEU* 3.3 29.3 + - - +
73O ARG 4.9 5.0 + - - -
78O GLU* 3.1 28.0 + - - +
82O LYS* 4.9 9.8 - - - +
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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