Contacts of the helix formed by residues 115 - 127 (chain B) in PDB entry 4XDO
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 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A GLU 5.2 1.8 - - - +
166A CYS 3.7 21.4 - - - +
167A GLY* 5.6 1.0 - - - -
324A ARG* 4.9 1.1 - - - +
113B TYR* 3.3 14.3 - - - -
114B LEU* 1.3 80.5 - - - +
116B TYR* 1.3 60.2 + - - +
117B GLU* 3.4 15.2 + - - +
118B ASP* 2.8 51.7 + - - +
119B LEU 2.9 10.6 + - - -
121B ARG* 4.7 1.7 + - - -
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Residues in contact with TYR 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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113B TYR* 4.2 21.8 - + - -
115B ASP* 1.3 76.1 - - - +
117B GLU* 1.3 56.8 + - - +
119B LEU* 3.3 5.4 + - + +
120B GLU* 2.9 30.0 + - - +
207B PRO* 3.5 15.0 - - + +
209B SER* 5.5 1.5 + - - +
263B THR* 3.6 37.2 - - + +
265B GLU* 2.5 30.0 + - - -
281B PHE* 5.5 0.9 - - - -
283B HIS* 3.6 27.9 - + + -
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Residues in contact with GLU 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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115B ASP* 3.2 14.5 - - - +
116B TYR* 1.3 78.1 - - + +
118B ASP* 1.3 64.2 + - - +
120B GLU* 3.4 11.6 + - - +
121B ARG* 3.1 45.8 + - - +
261B LYS* 4.6 16.4 + - - +
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Residues in contact with ASP 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TYR* 3.3 9.5 - - - -
114B LEU* 2.9 36.6 + - + +
115B ASP* 2.8 29.7 + - - +
117B GLU* 1.3 78.4 - - - +
119B LEU* 1.3 61.6 + - - +
121B ARG* 3.2 31.2 + - - +
122B LYS* 3.1 41.5 + - - +
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Residues in contact with LEU 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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110B THR* 4.0 4.0 - - + -
111B PRO* 3.7 25.4 - - + -
113B TYR* 4.0 38.9 - - + +
115B ASP 2.9 12.4 + - - +
116B TYR* 3.7 7.9 - - - +
117B GLU 3.3 0.2 - - - -
118B ASP* 1.3 77.4 - - - +
120B GLU* 1.3 57.5 + - - +
122B LYS* 3.2 5.5 + - + +
123B TYR* 2.9 24.8 + - - +
183B TRP* 3.5 35.0 - - + -
281B PHE* 4.8 3.6 - - + -
283B HIS* 3.6 43.7 - - + +
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TYR 2.9 17.8 + - - +
117B GLU* 3.7 10.2 - - - +
118B ASP 3.3 0.2 - - - -
119B LEU* 1.3 76.4 - - - +
121B ARG* 1.3 63.7 + - + +
123B TYR* 3.3 7.8 + - - +
124B TRP* 3.2 28.5 + - + -
209B SER* 5.9 0.2 - - - +
211B TYR* 2.5 41.9 + - - +
249B PRO* 3.7 10.3 - - - +
261B LYS* 2.6 36.6 + - - +
281B PHE* 3.8 21.6 - - + -
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Residues in contact with ARG 121 (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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114B LEU* 5.8 3.2 - - - +
115B ASP* 4.7 2.0 + - - -
117B GLU* 3.1 37.3 + - - +
118B ASP* 3.2 42.9 + - - +
120B GLU* 1.3 75.8 - - + +
122B LYS* 1.3 59.2 + - + +
124B TRP* 3.3 7.3 + - - +
125B LYS* 3.0 33.3 + - + +
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Residues in contact with LYS 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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111B PRO* 4.0 24.9 - - + -
112B ARG 3.0 28.0 - - - +
113B TYR* 4.6 4.0 - - + +
118B ASP* 3.1 38.9 + - - +
119B LEU* 3.2 9.4 + - - +
121B ARG* 1.3 76.4 - - + +
123B TYR* 1.3 63.2 + - - +
125B LYS* 4.3 14.8 - - - +
126B ASN* 2.9 42.4 + - - +
183B TRP* 4.3 4.2 - - + -
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Residues in contact with TYR 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 LEU 2.9 12.6 + - - +
120B GLU 3.5 7.9 - - - +
122B LYS* 1.3 74.9 - - - +
124B TRP* 1.3 111.1 + + - +
126B ASN 3.3 0.5 + - - -
127B LEU* 3.1 52.3 + - + +
183B TRP* 3.7 15.7 - + + -
184B LYS* 3.7 23.9 - - + +
186B THR* 2.8 36.7 + - - +
246B LEU* 3.9 4.9 - - - +
280B GLY 4.1 3.8 + - - -
281B PHE* 3.4 46.9 - + + -
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Residues in contact with TRP 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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82B GLY* 4.9 0.7 - - - -
84B PHE* 4.0 27.4 - + - -
120B GLU* 3.2 27.3 + - + -
121B ARG* 3.3 8.5 + - - +
123B TYR* 1.3 105.3 - + - +
125B LYS* 1.3 60.8 + - - +
126B ASN 3.5 0.2 + - - -
127B LEU* 3.7 39.4 + - + +
189B TRP* 5.7 0.2 - - - -
211B TYR* 3.0 35.7 + + - -
246B LEU* 4.5 6.5 - - + -
247B ILE 3.8 12.8 - - - -
248B SER* 3.6 34.8 - - - -
249B PRO* 3.5 24.1 - - + +
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Residues in contact with LYS 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 ARG* 3.0 19.6 + - + +
122B LYS* 3.9 18.8 - - - +
124B TRP* 1.3 78.6 - - - +
126B ASN* 1.3 71.1 + - - +
127B LEU 3.7 0.7 - - - -
128B THR* 5.3 1.6 + - - -
129B PHE* 3.7 16.0 - - + -
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Residues in contact with ASN 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 LYS* 2.9 38.3 + - - +
123B TYR 3.3 0.9 + - - -
125B LYS* 1.3 100.7 - - - +
127B LEU* 1.3 57.9 + - - +
128B THR 3.1 4.8 + - - -
129B PHE* 3.1 31.9 + - + +
183B TRP* 5.4 4.0 - - + +
184B LYS* 2.8 38.9 + - + +
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Residues in contact with LEU 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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77B VAL* 3.9 25.5 + - + +
84B PHE* 3.8 16.6 - - + -
123B TYR* 3.1 47.0 + - + +
124B TRP* 3.7 37.4 + - + +
125B LYS 3.7 1.4 - - - -
126B ASN* 1.3 76.9 - - - +
128B THR* 1.3 62.6 + - + +
129B PHE 3.4 1.4 + - - +
130B VAL 4.6 2.6 - - - +
131B ALA* 5.9 0.3 - - - -
132B PRO* 5.4 2.3 - - - +
184B LYS* 4.2 17.4 + - + +
186B THR* 4.0 8.7 - - - +
246B LEU* 3.8 23.1 - - + -
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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