Contacts of the helix formed by residues 113 - 121 (chain B) in PDB entry 2W5X
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 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B SER* 3.3 17.3 - - - -
93B CYS* 3.8 13.9 - - - -
111B VAL 4.6 0.9 - - - -
112B LYS* 1.3 74.6 - - - +
114B ILE* 1.3 60.2 + - - +
115B VAL* 3.4 9.5 + - - +
116B GLU* 3.0 36.9 + - - +
117B ILE* 2.9 30.9 + - - +
140B SER 4.7 5.2 - - - -
141B PHE 4.1 7.1 + - - -
142B TYR* 5.5 1.0 - - - -
144B HIS* 4.6 5.3 - - - -
364B PHE* 4.2 2.9 - - - -
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Residues in contact with ILE 114 (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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91B PHE 4.8 1.6 - - - +
92B SER* 2.8 21.3 + - - +
113B SER* 1.3 72.3 - - - +
115B VAL* 1.3 60.7 + - - +
117B ILE* 3.7 11.8 - - + +
118B ALA* 2.8 29.3 + - - +
141B PHE* 4.1 18.4 - - + -
250B PHE* 3.9 30.6 - - + -
364B PHE* 3.8 21.7 - - + +
367B ILE* 4.0 31.6 - - + -
368B LEU* 4.5 12.3 - - + +
373B TRP* 4.2 20.9 - - + -
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Residues in contact with VAL 115 (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 SER* 3.2 2.6 + - - +
114B ILE* 1.3 78.7 - - - +
116B GLU* 1.3 61.0 + - + +
118B ALA* 3.6 6.3 - - - +
119B ALA* 3.0 27.0 + - - +
125B THR* 3.7 25.5 - - - +
126B GLY 6.0 0.2 - - - +
127B VAL* 5.1 1.6 - - + -
141B PHE* 2.9 44.4 - - + +
142B TYR* 5.3 2.7 - - + -
161B SER* 6.1 0.2 - - - -
162B ASP* 4.9 6.1 - - + +
163B LEU* 4.1 21.5 - - + +
250B PHE* 4.2 23.1 - - + -
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Residues in contact with GLU 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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112B LYS* 3.5 18.9 - - + +
113B SER* 3.0 36.1 + - - +
115B VAL* 1.3 79.0 - - + +
117B ILE* 1.3 64.8 + - - +
119B ALA* 3.6 5.7 + - - +
120B LEU* 3.2 29.7 + - + +
142B TYR* 5.1 5.0 - - - +
144B HIS* 2.6 35.2 + - - -
162B ASP* 5.5 11.9 - - + +
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Residues in contact with ILE 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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112B LYS* 3.6 31.2 - - + +
113B SER 2.9 18.5 + - - +
114B ILE* 3.7 7.0 - - + +
116B GLU* 1.3 74.3 - - - +
118B ALA* 1.3 66.6 + - - +
120B LEU* 3.1 4.3 + - - -
121B ASN* 2.9 32.0 + - - +
364B PHE* 3.6 32.5 - - + -
368B LEU* 4.1 28.3 - - + -
373B TRP* 4.1 11.0 - - + -
374B ASN 3.4 20.0 - - - +
375B GLN* 4.2 8.7 - - + -
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Residues in contact with ALA 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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114B ILE 2.8 21.8 + - - +
115B VAL* 3.6 1.1 - - - +
116B GLU 3.4 0.2 - - - -
117B ILE* 1.3 72.2 - - - +
119B ALA* 1.3 63.7 + - - +
121B ASN* 2.9 11.8 + - - -
123B ILE* 2.9 44.7 + - + +
125B THR* 3.4 26.0 - - + -
250B PHE* 4.5 4.5 - - + -
373B TRP* 4.3 13.0 - - + -
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Residues in contact with ALA 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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115B VAL 3.0 14.5 + - - +
116B GLU 3.8 5.8 - - - +
118B ALA* 1.3 74.2 - - - +
120B LEU* 1.3 59.7 + - + +
122B ASN* 3.0 19.9 + - - -
123B ILE 3.9 10.9 + - - +
125B THR* 4.5 1.5 - - + +
162B ASP* 3.5 43.1 - - + +
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Residues in contact with LEU 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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112B LYS* 3.5 36.8 - - - +
116B GLU* 3.2 11.4 + - + +
117B ILE* 3.1 7.4 + - - +
119B ALA* 1.3 77.9 - - + +
121B ASN* 1.3 62.9 + - - +
122B ASN 3.3 1.5 + - - -
374B ASN* 5.7 0.6 - - - +
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Residues in contact with ASN 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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117B ILE* 2.9 28.6 + - - +
118B ALA 2.9 8.4 + - - +
120B LEU* 1.3 79.2 - - - +
122B ASN* 1.3 71.8 + - - +
123B ILE* 3.2 19.3 + - + +
373B TRP* 3.5 17.6 - - + -
374B ASN* 2.8 61.6 + - - +
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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