Contacts of the helix formed by residues 124 - 130 (chain B) in PDB entry 2IHU
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 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A PRO* 4.2 16.7 + - + +
108B GLN* 4.9 0.7 - - - +
116B PRO* 3.7 27.5 - - + +
117B ASN* 5.0 1.2 + - - -
123B LEU* 1.3 69.3 - - - +
125B SER* 1.3 63.6 + - - +
126B VAL* 3.9 5.9 + - - +
127B ALA* 3.4 29.3 + - + +
128B ILE* 3.1 28.5 + - - +
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Residues in contact with SER 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLY 5.1 3.5 + - - -
85B MET* 3.5 31.1 - - - +
106B ALA* 5.8 0.2 - - - -
107B ALA 4.9 4.3 + - - -
108B GLN* 3.8 11.3 + - - +
123B LEU* 2.9 12.4 + - - +
124B ASP* 1.3 71.1 + - - +
126B VAL* 1.3 62.5 + - - +
128B ILE* 3.3 1.1 + - - +
129B VAL* 3.0 29.5 + - - +
165B PHE* 3.7 25.8 - - - -
167B SER* 4.0 13.7 + - - -
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASP* 3.4 5.9 + - - +
125B SER* 1.3 76.0 - - - +
127B ALA* 1.3 58.0 + - - +
130B ALA* 2.8 39.2 + - + +
136B ALA* 3.9 23.1 - - + +
137B VAL* 3.6 34.1 - - - +
138B GLU* 3.7 16.8 - - + +
165B PHE* 4.4 7.6 - - + -
167B SER* 4.3 7.6 - - - -
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Residues in contact with ALA 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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127A ALA 3.8 7.6 - - - +
131A PRO* 3.7 19.5 - - + -
124B ASP* 3.3 31.8 + - - +
126B VAL* 1.3 80.2 - - - +
128B ILE* 1.3 60.9 + - - +
130B ALA* 4.3 3.7 - - - +
131B PRO* 3.2 20.4 - - - +
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Residues in contact with ILE 128 (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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89A SER* 5.9 0.9 - - - +
128A ILE* 3.7 49.6 - - + +
131A PRO* 3.9 13.2 - - + -
132A MET* 3.6 34.8 - - + -
85B MET* 3.9 20.9 - - + -
86B THR* 4.9 1.8 - - + -
89B SER* 5.4 7.2 - - - +
123B LEU* 3.9 21.1 - - + -
124B ASP 3.1 27.6 + - - +
125B SER* 3.7 4.5 - - - +
127B ALA* 1.3 75.1 - - - +
129B VAL* 1.3 61.5 + - + +
131B PRO* 3.4 10.4 - - - +
132B MET* 4.4 2.6 - - - +
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B MET* 3.8 25.8 - - + -
89B SER* 4.8 7.4 - - - -
92B ILE* 3.9 28.7 - - + -
125B SER 3.0 18.5 + - - +
128B ILE* 1.3 78.6 - - + +
130B ALA* 1.3 59.8 + - - +
131B PRO* 3.3 3.4 - - - -
132B MET* 3.0 17.9 + - + +
133B SER* 2.7 29.2 + - - +
136B ALA* 4.8 0.4 - - + -
165B PHE* 3.5 41.5 - - + -
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Residues in contact with ALA 130 (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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126B VAL* 2.8 27.5 + - + +
127B ALA* 4.3 4.3 - - - +
129B VAL* 1.3 72.1 - - - +
131B PRO* 1.4 66.5 - - + +
132B MET 3.2 1.2 + - - -
133B SER* 3.4 22.1 + - - +
136B ALA* 4.0 13.5 - - + +
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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