Contacts of the helix formed by residues 121 - 128 (chain B) in PDB entry 2H1H
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 GLU 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B GLY 3.1 8.0 + - - +
96B LEU* 3.2 30.3 - - + +
97B VAL* 2.7 44.6 + - + +
98B LYS 4.4 1.2 + - - -
119B ALA* 3.8 3.4 - - - +
120B ARG* 1.3 80.3 - - - +
122B PRO* 1.3 72.1 - - - +
123B LEU* 3.2 2.2 - - + +
124B ALA* 2.8 22.0 + - - +
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Residues in contact with PRO 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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116B TRP* 3.4 59.2 - - + +
119B ALA* 3.8 11.1 - - + +
120B ARG 3.8 5.8 - - - +
121B GLU* 1.3 84.3 - - - +
123B LEU* 1.3 60.4 + - - +
125B SER* 2.9 29.8 + - - -
136B LYS* 5.9 4.0 - - - +
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Residues in contact with LEU 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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97B VAL* 3.7 19.5 - - + -
116B TRP* 3.8 27.8 - - + -
121B GLU* 2.9 4.0 + - + -
122B PRO* 1.3 76.6 - - + +
124B ALA* 1.3 62.8 + - - +
126B LEU* 3.0 37.4 + - + +
127B PHE* 3.6 8.9 - - + -
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Residues in contact with ALA 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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95B GLY* 3.7 20.2 - - - +
96B LEU 3.7 16.6 - - - +
97B VAL* 3.8 6.2 - - - +
100B ALA* 4.0 2.0 - - + -
119B ALA* 4.8 1.1 - - + -
121B GLU 2.8 16.0 + - - +
123B LEU* 1.3 78.9 - - - +
125B SER* 1.3 61.8 + - - +
127B PHE* 3.1 25.7 + - - +
128B TYR* 3.3 30.9 - - + +
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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
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114B MET 3.3 18.8 + - - -
115B ASP* 3.6 3.8 - - - -
116B TRP* 3.5 33.6 + - - +
119B ALA* 4.8 1.7 - - - +
122B PRO 2.9 19.2 + - - -
124B ALA* 1.3 78.5 - - - +
126B LEU* 1.3 64.5 + - - +
127B PHE 3.0 2.1 + - - -
128B TYR* 3.2 24.5 + - - -
131B LYS* 3.6 22.0 + - - +
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Residues in contact with LEU 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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116B TRP* 4.2 15.9 - - + -
123B LEU* 3.0 36.6 + - + +
125B SER* 1.3 87.0 + - - +
127B PHE* 1.3 65.9 + - + +
128B TYR 3.4 2.8 + - - +
131B LYS* 4.9 8.0 + - - +
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Residues in contact with PHE 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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97B VAL* 4.8 13.7 - - + -
100B ALA* 4.1 20.9 - - + +
101B ALA* 3.8 27.6 - - + -
104B THR* 4.7 0.5 + - - -
105B ARG* 3.8 35.7 - - + +
111B LYS* 3.8 20.6 - - - +
123B LEU* 3.6 19.3 - - + -
124B ALA* 3.1 21.7 + - - +
125B SER 3.0 1.4 - - - -
126B LEU* 1.3 84.2 - - + +
128B TYR* 1.3 64.9 + - + +
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Residues in contact with TYR 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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92B ASP* 3.0 41.7 + - + -
95B GLY* 3.4 20.0 - - - -
100B ALA* 4.2 7.0 - - + -
104B THR* 4.2 12.1 - - + -
111B LYS* 3.8 12.1 - - + +
112B HIS 4.4 2.5 - - - -
113B GLY* 3.2 28.2 - - - +
114B MET* 3.3 26.9 - - + -
119B ALA* 5.3 0.2 - - + -
124B ALA* 3.3 25.4 - - + +
125B SER* 3.2 17.2 + - - +
126B LEU 4.7 2.1 - - - +
127B PHE* 1.3 87.5 - - - +
129B ASN* 1.3 60.8 + - - +
130B ARG 3.8 11.9 - - - +
131B LYS* 2.7 28.1 - - + -
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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