Contacts of the helix formed by residues 121 - 127 (chain H) in PDB entry 1HNX
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 121 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100H ILE* 3.8 16.2 - - + +
101H PRO 4.1 7.2 - - - +
102H ARG* 4.8 2.8 - - - +
103H VAL 4.8 5.7 + - - -
106H GLY* 6.1 0.5 - - - -
108H GLY 4.6 6.6 - - - +
109H ILE* 3.6 13.1 - - - +
110H ALA* 3.0 38.2 + - + +
112H LEU* 4.9 1.8 - - - -
120H THR* 1.3 69.2 - - - +
122H ARG* 1.3 82.4 + - - +
124H ALA* 2.9 5.8 + - - +
125H ARG* 2.8 51.7 + - - +
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Residues in contact with ARG 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E LYS* 4.3 25.8 - - - +
106H GLY* 3.5 31.9 + - - -
109H ILE* 6.3 3.0 - - + +
120H THR* 3.4 6.7 + - - +
121H ASP* 1.3 88.5 + - - +
123H GLU* 1.3 55.9 + - - +
125H ARG* 2.9 10.0 + - - +
126H LYS* 2.7 37.6 + - - +
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Residues in contact with GLU 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ILE* 4.6 0.2 - - - +
41H ARG* 2.9 37.3 + - - -
42H GLU* 4.6 3.5 - - - +
118H VAL 4.3 1.7 - - - +
119H LEU* 3.0 33.3 - - + +
120H THR* 3.2 33.8 + - - +
122H ARG* 1.3 79.5 - - + +
124H ALA* 1.3 62.1 + - - +
126H LYS* 3.5 7.1 + - + +
127H LEU* 3.0 33.1 + - + +
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Residues in contact with ALA 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H ILE* 3.9 9.6 - - + -
112H LEU* 4.4 11.4 - - + -
114H THR* 4.9 1.8 - - + -
119H LEU* 3.3 19.7 - - + +
120H THR 2.8 17.2 + - - +
121H ASP* 3.3 9.9 - - - +
123H GLU* 1.3 68.9 - - - +
125H ARG* 1.3 56.7 + - - +
127H LEU* 3.0 3.3 + - - +
128H GLY 2.6 31.4 + - - -
129H VAL* 3.0 31.2 + - + +
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Residues in contact with ARG 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H VAL* 4.2 24.4 - - + +
100H ILE* 3.6 21.9 + - + +
101H PRO 3.3 16.4 + - - -
102H ARG* 3.4 42.0 - - - +
121H ASP* 2.8 50.5 + - - +
122H ARG* 3.4 11.3 - - - +
124H ALA* 1.3 73.7 - - - +
126H LYS* 1.3 57.8 + - - +
128H GLY* 2.7 22.4 + - - +
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Residues in contact with LYS 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122H ARG 2.7 19.6 + - - +
123H GLU* 3.6 8.7 - - + +
125H ARG* 1.3 73.6 - - - +
127H LEU* 1.3 74.2 + - + +
128H GLY 3.3 2.3 + - - -
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Residues in contact with LEU 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116H LYS* 3.2 48.9 + - + +
119H LEU* 4.4 12.3 - - + -
123H GLU* 3.0 23.3 + - + +
124H ALA 3.0 5.2 + - - +
126H LYS* 1.3 97.3 - - + +
128H GLY* 1.3 64.9 + - - +
129H VAL* 3.2 12.3 - - + +
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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