Contacts of the helix formed by residues 122 - 134 (chain A) in PDB entry 2I3B
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 GLN 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A LEU* 3.9 19.4 - - + +
119A LEU 5.5 2.0 + - - -
120A PHE* 3.1 22.1 + - - +
121A SER* 1.3 76.7 + - - +
123A LEU* 1.3 74.0 + - + +
124A PHE 3.2 3.8 + - - +
125A ILE* 3.8 18.7 + - - +
126A GLN* 4.0 9.3 + - - +
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Residues in contact with LEU 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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84A LEU* 4.3 24.9 - - + +
87A PHE* 6.2 0.4 - - + -
88A GLU* 3.9 37.9 - - + +
92A LEU* 4.1 20.6 - - + -
122A GLN* 1.3 85.2 - - + +
124A PHE* 1.3 54.4 + - - +
126A GLN* 3.4 20.1 + - + +
127A ALA* 2.8 37.8 + - - +
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Residues in contact with PHE 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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35A PHE* 3.7 31.2 - + - -
84A LEU* 5.5 4.1 - - + +
87A PHE* 3.8 35.9 - + - -
95A LEU* 6.3 1.6 - - + -
111A ILE* 3.9 13.0 - - + -
113A GLU 4.1 17.5 - - - -
114A ILE* 4.5 3.4 - - + -
117A MET* 4.0 20.2 - - + -
121A SER* 4.3 12.8 - - - -
122A GLN 4.0 1.1 - - - +
123A LEU* 1.3 74.7 - - - +
125A ILE* 1.3 65.1 + - - +
127A ALA* 4.8 3.1 - - + -
128A VAL* 2.8 49.0 + - + +
153A LEU* 3.4 32.8 - - + -
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Residues in contact with ILE 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 SER* 3.2 43.1 - - - +
122A GLN* 3.9 8.3 - - - +
124A PHE* 1.3 72.7 - - - +
126A GLN* 1.3 64.7 + - + +
128A VAL* 4.4 1.6 - - - +
129A ARG* 3.2 37.8 + - - +
152A ALA 3.7 25.1 - - - +
153A LEU* 3.6 11.1 - - + +
156A GLU* 3.7 28.7 - - + +
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Residues in contact with GLN 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 4.5 7.0 - - - +
123A LEU* 3.4 24.3 + - - +
124A PHE 3.0 0.8 + - - -
125A ILE* 1.3 78.4 - - + +
127A ALA* 1.3 66.9 + - + +
129A ARG* 3.1 13.3 + - - +
130A GLN* 2.9 31.3 + - + +
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Residues in contact with ALA 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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91A ALA 5.1 0.2 - - - +
92A LEU* 4.6 21.5 - - + +
95A LEU* 3.9 29.6 - - + +
123A LEU 2.8 21.2 + - - +
124A PHE* 3.9 3.1 - - + +
126A GLN* 1.3 72.3 - - - +
128A VAL* 1.3 52.7 + - + +
130A GLN* 3.1 11.7 + - - +
131A THR* 2.8 35.2 + - - -
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Residues in contact with VAL 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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95A LEU* 4.8 3.8 - - + -
111A ILE* 3.9 24.2 - - + -
114A ILE* 5.4 4.5 - - + -
124A PHE* 2.8 49.2 + - + +
125A ILE* 4.4 2.2 - - - +
127A ALA* 1.3 71.8 - - + +
129A ARG* 1.3 56.4 + - - +
131A THR* 3.0 12.2 + - - -
132A LEU* 2.8 48.1 + - + +
139A ILE* 5.7 4.5 - - + -
153A LEU* 4.7 5.4 - - + -
156A GLU* 5.3 3.1 - - + -
157A ILE* 4.0 24.7 - - + -
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Residues in contact with ARG 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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125A ILE* 3.2 27.4 + - - +
126A GLN* 3.1 11.7 + - - +
128A VAL* 1.3 74.8 - - - +
130A GLN* 1.3 56.8 + - - +
132A LEU* 3.3 19.6 + - + +
133A SER* 2.9 29.9 + - - -
156A GLU* 4.1 28.5 - - + +
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Residues in contact with GLN 130 (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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96A ARG* 3.0 45.0 + - + +
126A GLN* 2.9 24.4 + - + +
127A ALA* 3.1 11.5 + - - +
129A ARG* 1.3 73.6 - - - +
131A THR* 1.3 62.3 + - - +
133A SER* 3.2 18.0 - - - -
134A THR* 3.2 14.3 + - - -
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Residues in contact with THR 131 (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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3A HIS* 5.9 0.3 - - - -
95A LEU* 3.3 42.8 - - - +
96A ARG* 5.0 2.2 - - - +
109A CYS* 3.9 8.3 - - - -
127A ALA 2.8 21.1 + - - -
128A VAL* 3.2 8.0 + - - -
130A GLN* 1.3 75.9 - - - +
132A LEU* 1.3 57.1 + - - +
134A THR* 3.0 32.6 + - - +
137A THR* 3.6 19.9 - - + +
139A ILE* 3.2 29.0 - - + +
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Residues in contact with LEU 132 (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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3A HIS* 4.2 27.8 + - + +
5A PHE* 5.8 0.2 - - + -
128A VAL* 2.8 39.5 + - + +
129A ARG* 3.8 18.4 - - + +
131A THR* 1.3 68.7 - - - +
133A SER* 1.3 62.7 - - - +
134A THR 3.9 4.9 - - - +
139A ILE* 3.7 28.7 - - + -
156A GLU 4.0 20.4 - - - +
157A ILE* 4.5 13.2 - - + -
160A ARG* 4.6 20.0 - - + -
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Residues in contact with SER 133 (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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129A ARG 2.9 12.6 + - - -
130A GLN* 3.2 15.8 - - - -
131A THR 3.1 0.2 - - - -
132A LEU* 1.3 76.9 - - - +
134A THR* 1.3 63.4 + - - +
135A PRO* 3.5 6.6 - - - +
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Residues in contact with THR 134 (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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3A HIS* 5.3 4.0 - - - -
96A ARG* 3.4 22.8 + - + +
98A ALA 5.8 0.2 - - - +
99A ASP* 3.7 28.8 + - - +
107A ARG* 5.5 2.7 - - - -
130A GLN 3.2 13.2 + - - -
131A THR 3.0 15.7 + - - +
132A LEU* 3.9 5.4 - - - +
133A SER* 1.3 79.0 - - - +
135A PRO* 1.3 71.4 - - + +
136A GLY* 3.7 2.9 - - - +
137A THR* 3.4 38.3 - - - +
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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