Contacts of the helix formed by residues 115 - 127 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B PRO* 4.8 8.8 - - + +
111B PRO* 4.0 15.5 - - + +
114B GLY* 1.3 73.2 - - - -
116B ASP* 1.3 65.8 + - - +
117B ASN* 3.4 17.9 - - - +
118B LEU* 3.1 11.3 + - + +
119B ARG* 3.1 19.1 + - - +
146B ILE* 4.6 2.4 - - - +
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Residues in contact with ASP 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B PRO* 4.7 10.3 - - - +
114B GLY 3.3 4.4 + - - +
115B ALA* 1.3 70.2 - - - +
117B ASN* 1.3 63.8 + - - +
119B ARG* 3.0 18.6 + - - +
120B GLN* 2.9 39.4 + - - +
141B TRP* 4.0 22.2 - - - -
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Residues in contact with ASN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B PHE* 5.4 10.9 - - - -
115B ALA* 3.4 18.0 - - - +
116B ASP* 1.3 76.9 - - - +
118B LEU* 1.3 66.7 + - - +
120B GLN* 3.2 16.9 + - - +
121B VAL* 2.9 37.8 + - + +
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ALA* 3.1 15.0 + - + +
117B ASN* 1.3 89.0 + - - +
119B ARG* 1.3 57.1 + - - +
121B VAL* 3.3 13.8 + - + -
122B VAL* 2.9 42.3 + - + +
146B ILE* 3.8 37.0 - - + -
295B VAL* 4.6 12.8 - - + -
297B TRP* 5.3 4.9 - - + -
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B PRO* 6.1 0.8 - - - +
113B VAL* 3.4 28.4 - - - +
114B GLY 3.7 18.4 + - - -
115B ALA 3.1 10.4 + - - +
116B ASP* 3.0 16.1 + - - +
118B LEU* 1.3 77.8 - - - +
120B GLN* 1.3 61.9 + - - +
122B VAL* 3.3 2.3 + - - +
123B SER* 3.0 24.3 + - - -
141B TRP* 3.4 39.4 + - + +
142B GLU* 3.1 29.9 + - - +
144B VAL* 2.7 37.7 + - + +
145B ILE* 5.4 0.4 - - - +
146B ILE* 3.9 18.2 - - + -
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Residues in contact with GLN 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ASP* 2.9 35.4 + - - +
117B ASN* 3.5 16.0 - - - +
119B ARG* 1.3 75.2 - - - +
121B VAL* 1.3 65.7 + - + +
123B SER* 3.3 3.8 + - - -
124B THR* 3.0 26.8 + - - +
141B TRP* 3.8 45.2 - - + -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ASN* 2.9 23.6 + - + +
118B LEU* 3.8 16.2 - - + +
120B GLN* 1.3 79.3 - - + +
122B VAL* 1.3 53.3 + - + +
124B THR* 3.1 8.2 + - - -
125B TYR* 2.8 37.3 + - + +
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B LEU* 2.9 35.4 + - + +
119B ARG 3.7 2.9 - - - +
121B VAL* 1.3 76.2 - - + +
123B SER* 1.3 63.4 + - - +
125B TYR* 3.3 8.6 + - + +
126B TRP* 3.0 23.0 + - - +
144B VAL* 3.8 16.2 - - + -
146B ILE* 4.4 3.4 - - + -
297B TRP* 3.4 65.1 - - + +
299B ILE* 4.0 8.7 - - + -
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ARG 3.0 14.0 + - - -
120B GLN 3.4 8.3 - - - -
121B VAL 3.2 0.2 - - - -
122B VAL* 1.3 79.9 - - - +
124B THR* 1.3 61.6 + - - +
126B TRP* 3.5 5.4 + - - -
127B ARG* 3.0 24.7 + - - +
139B LEU* 3.3 32.8 + - - +
140B LYS* 4.0 0.2 - - - -
141B TRP* 3.6 25.2 + - - -
144B VAL* 4.2 9.6 - - - -
299B ILE* 5.7 1.8 - - - -
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Residues in contact with THR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B GLN* 3.0 15.0 + - - +
121B VAL* 3.1 10.2 + - - -
123B SER* 1.3 76.6 + - - +
125B TYR* 1.3 63.5 + - - +
127B ARG* 3.2 28.3 + - + +
128B ARG* 4.2 5.1 + - - +
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Residues in contact with TYR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B VAL* 2.8 24.7 + - + +
122B VAL* 3.6 8.1 - - - +
123B SER 3.3 0.2 - - - -
124B THR* 1.3 74.7 - - - +
126B TRP* 1.3 90.2 + + - +
127B ARG 3.4 0.2 + - - -
128B ARG* 3.1 60.9 + - - +
129B PHE* 4.0 11.7 - + - -
257B ALA* 5.7 0.5 - - - +
258B GLU* 2.6 41.6 + - - +
283B GLY 5.5 0.4 + - - -
287B TYR* 3.6 24.0 + + - -
297B TRP* 4.1 19.7 - + - -
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Residues in contact with TRP 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B VAL 3.0 15.2 + - - +
123B SER* 4.2 0.7 - - - +
124B THR 3.3 0.4 - - - -
125B TYR* 1.3 103.5 - + - +
127B ARG* 1.3 64.4 + - - +
128B ARG 3.1 2.7 - - - -
129B PHE* 3.1 38.3 + + + +
130B CYS* 3.9 2.3 - - - -
139B LEU* 3.6 23.8 - - + +
254B GLU* 3.2 45.0 + - + -
257B ALA* 4.3 6.3 - - + -
266B PHE* 4.8 0.7 - + - -
268B SER* 3.2 18.8 + - - -
270B ALA* 4.1 12.8 - - + -
280B ILE* 3.5 22.3 - - + +
282B GLY* 4.5 6.3 - - - -
283B GLY 5.0 0.9 - - - -
297B TRP* 3.7 29.4 - + - -
299B ILE* 3.9 16.4 - - + -
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Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B SER* 3.0 23.8 + - - +
124B THR* 3.2 18.1 - - + +
125B TYR 3.2 0.4 - - - -
126B TRP* 1.3 77.8 - - - +
128B ARG* 1.3 55.9 + - - +
130B CYS* 2.9 30.2 + - - +
136B GLN* 3.0 51.6 + - + +
137B GLU* 4.2 10.9 + - - +
139B LEU* 2.6 38.1 + - + +
140B 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