Contacts of the helix formed by residues 115 - 127 (chain A) in PDB entry 4IX8
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 ALA 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A PRO* 4.8 3.1 - - + +
111A PRO* 4.1 14.9 - - + +
114A GLY* 1.3 72.6 - - - -
116A ASP* 1.3 64.9 + - - +
117A ASN* 3.2 18.3 + - - +
118A LEU* 3.3 3.5 + - + +
119A ARG* 3.1 20.8 + - - +
146A ILE* 4.6 0.2 - - - +
329A GLN* 2.8 31.1 + - + +
330A GLU* 5.9 0.4 - - - +
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Residues in contact with ASP 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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111A PRO* 4.7 10.4 - - - +
114A GLY 3.5 5.2 + - - +
115A ALA* 1.3 70.1 - - - +
117A ASN* 1.3 63.4 + - - +
119A ARG* 3.2 16.0 + - - +
120A GLN* 3.0 40.1 + - - +
141A TRP* 4.3 20.2 - - - -
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Residues in contact with ASN 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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106A PHE* 5.3 2.2 - - - -
115A ALA* 3.4 17.7 - - - +
116A ASP* 1.3 76.0 - - - +
118A LEU* 1.3 72.3 + - - +
120A GLN* 3.2 14.5 + - - +
121A VAL* 2.9 35.2 + - + +
329A GLN 5.1 0.5 - - - +
330A GLU* 2.6 33.4 + - - +
333A ALA* 3.7 13.7 - - + +
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Residues in contact with LEU 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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115A ALA* 3.3 8.0 + - + +
117A ASN* 1.3 81.5 + - - +
119A ARG* 1.3 61.0 + - - +
121A VAL* 3.1 5.3 + - + -
122A VAL* 2.8 47.6 + - + +
146A ILE* 3.7 29.4 - - + -
295A VAL* 4.6 9.9 - - + -
297A TRP* 5.5 1.8 - - + -
329A GLN* 3.8 45.8 - - + +
332A ILE* 3.8 27.4 - - + +
333A ALA* 3.9 18.2 - - + +
336A LEU* 5.0 0.2 - - + -
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Residues in contact with ARG 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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111A PRO* 6.2 0.8 - - - +
113A VAL* 3.5 27.8 - - - +
114A GLY 3.7 20.4 + - - -
115A ALA 3.1 11.6 + - - +
116A ASP* 3.6 14.1 + - - +
118A LEU* 1.3 77.0 - - - +
120A GLN* 1.3 63.5 + - - +
122A VAL* 3.9 0.2 - - - +
123A SER* 3.2 23.6 + - - -
141A TRP* 3.4 40.4 + - + +
142A GLU* 3.0 30.9 + - - +
144A VAL* 2.8 38.3 + - + +
145A ILE* 5.5 0.8 - - - +
146A ILE* 3.8 19.1 - - + -
315A GLU* 5.3 4.8 + - - -
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Residues in contact with GLN 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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116A ASP* 3.0 28.0 + - - +
117A ASN* 3.5 13.3 - - - +
119A ARG* 1.3 76.7 - - - +
121A VAL* 1.3 58.7 + - + +
123A SER* 3.4 4.5 + - - -
124A THR* 3.0 31.6 + - - -
141A TRP* 3.6 54.9 - - + -
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Residues in contact with VAL 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 ASN* 2.9 23.0 + - + +
118A LEU* 3.1 8.3 + - + +
120A GLN* 1.3 77.1 - - + +
122A VAL* 1.3 60.7 + - - +
124A THR* 3.1 8.2 + - - -
125A TYR* 2.8 27.5 + - - +
333A ALA* 3.6 31.2 - - + +
336A LEU* 3.8 30.7 - - + -
337A LEU* 4.0 22.0 - - + +
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Residues in contact with VAL 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 LEU* 2.8 41.8 + - + +
119A ARG 3.9 2.9 - - - +
121A VAL* 1.3 71.6 - - - +
123A SER* 1.3 63.6 + - - +
125A TYR* 3.2 2.1 + - - +
126A TRP* 3.0 23.4 + - + +
144A VAL* 3.9 18.4 - - + -
146A ILE* 4.3 4.9 - - + -
297A TRP* 3.7 57.0 - - + +
299A ILE* 4.0 9.9 - - + -
336A LEU* 4.1 10.3 - - + -
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Residues in contact with SER 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 ARG 3.2 12.8 + - - -
120A GLN 3.4 9.9 - - - -
122A VAL* 1.3 81.1 - - - +
124A THR* 1.3 58.8 + - - +
126A TRP* 3.5 5.8 + - - +
127A ARG* 2.9 32.2 + - - +
139A LEU* 3.3 30.0 + - - +
140A LYS 4.2 0.2 - - - -
141A TRP* 3.6 24.2 + - - -
144A VAL* 4.2 8.5 - - - +
299A ILE* 5.5 1.3 - - - -
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Residues in contact with THR 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 GLN* 3.0 15.9 + - - +
121A VAL* 3.1 9.7 + - - -
123A SER* 1.3 75.4 - - - +
125A TYR* 1.3 64.3 + - - +
127A ARG* 3.2 27.5 - - + +
128A ARG* 4.2 2.9 + - - +
337A LEU* 4.0 25.2 - - + +
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Residues in contact with TYR 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 VAL 2.8 15.9 + - - +
122A VAL 3.2 4.9 + - - +
124A THR* 1.3 77.7 - - - +
126A TRP* 1.3 95.4 + + - +
127A ARG 3.1 0.7 + - - -
128A ARG* 3.1 59.9 + - - +
129A PHE* 4.0 11.3 - + - -
257A ALA* 5.3 1.0 - - - +
258A GLU* 2.8 41.9 + - - +
283A GLY 5.3 0.9 + - - -
287A TYR* 3.8 22.9 + + - -
297A TRP* 4.0 14.8 - + - -
336A LEU* 3.7 33.9 - - + -
337A LEU* 3.9 11.8 - - + +
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Residues in contact with TRP 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 VAL 3.0 14.3 + - - +
123A SER 3.5 1.8 + - - +
125A TYR* 1.3 108.2 - + - +
127A ARG* 1.3 62.6 + - - +
128A ARG 3.1 0.4 - - - -
129A PHE* 3.0 36.8 + + + +
130A CYS* 4.0 1.7 - - - -
139A LEU* 3.6 18.1 - - + +
254A GLU* 3.5 42.2 - - + -
257A ALA* 4.3 5.2 - - + -
266A PHE* 4.7 0.7 - + - -
268A SER* 3.0 20.2 + - - -
270A ALA* 4.0 17.3 - - + -
280A ILE* 3.6 24.1 - - + +
282A GLY* 4.5 6.7 - - - -
283A GLY 5.0 0.7 - - - -
297A TRP* 3.6 30.3 - + - -
299A ILE* 3.8 16.8 - - + -
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Residues in contact with ARG 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 SER* 2.9 30.5 + - - +
124A THR* 3.2 20.4 - - + +
125A TYR 3.1 0.4 - - - -
126A TRP* 1.3 77.5 - - - +
128A ARG* 1.3 55.1 + - - +
129A PHE 3.1 0.9 - - - -
130A CYS* 3.0 28.7 + - - +
136A GLN* 3.1 50.9 + - + +
137A GLU* 4.4 8.7 + - - +
139A LEU* 2.5 40.0 + - + +
140A LYS* 4.7 2.6 - - - +
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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