Contacts of the helix formed by residues 134 - 142 (chain I) in PDB entry 5U07
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 HIS 134 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I ILE* 3.3 17.4 + - + +
131I ALA 4.0 3.6 + - - +
132I ASP 3.1 2.1 - - - -
133I GLU* 1.3 94.3 + - + +
135I ARG* 1.3 61.9 + - - +
136I ASP 3.4 2.7 - - - -
137I ALA* 3.3 16.9 + - + +
138I VAL* 3.1 27.6 + - + +
150I ILE* 5.7 5.5 - - + +
151I LEU* 3.3 36.6 - - + -
152I PRO* 4.1 19.6 - - + +
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Residues in contact with ARG 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76I ARG 4.6 9.1 + - - -
77I GLY 4.9 6.9 + - - -
78I TRP* 3.5 59.7 - - + +
82I LEU* 5.6 6.3 - - + -
132I ASP* 3.4 16.6 + - - +
133I GLU 3.5 3.6 + - - -
134I HIS* 1.3 75.4 - - - +
136I ASP* 1.3 58.5 + - - +
138I VAL* 3.3 2.9 + - - +
139I ALA* 2.8 29.1 + - + +
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Residues in contact with ASP 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134I HIS 3.4 0.6 - - - -
135I ARG* 1.3 75.8 - - - +
137I ALA* 1.3 67.8 + - - +
139I ALA* 3.2 9.3 + - - +
140I LYS* 2.9 40.4 + - - +
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Residues in contact with ALA 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134I HIS* 3.3 21.3 + - + +
136I ASP* 1.3 77.8 - - - +
138I VAL* 1.3 58.1 + - + +
140I LYS* 3.1 28.1 - - - +
141I GLU* 2.8 32.7 + - - +
150I ILE* 4.0 29.2 - - + -
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Residues in contact with VAL 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I TRP* 3.9 22.0 - - + -
82I LEU* 4.1 10.3 - - + +
85I ALA* 4.6 5.3 - - + +
86I GLY* 4.0 32.3 - - - +
89I GLN* 4.9 13.7 - - + -
131I ALA* 4.4 12.1 - - + +
134I HIS* 3.1 20.7 + - + +
135I ARG 3.6 7.0 - - - +
136I ASP 3.2 0.2 - - - -
137I ALA* 1.3 75.1 - - + +
139I ALA* 1.3 64.3 + - - +
141I GLU* 3.9 4.7 - - - +
142I ALA* 2.9 24.3 + - - +
150I ILE* 5.8 2.5 - - + -
151I LEU* 5.4 6.5 - - + -
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Residues in contact with ALA 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I LEU* 4.2 21.5 - - + +
135I ARG* 2.8 23.0 + - + +
136I ASP* 3.2 10.7 + - - +
138I VAL* 1.3 74.9 - - - +
140I LYS* 1.3 62.6 + - - +
142I ALA* 3.8 8.5 + - - +
143I ALA* 4.5 4.3 + - - +
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Residues in contact with LYS 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136I ASP* 2.9 25.0 + - - +
137I ALA* 3.1 43.9 - - - +
139I ALA* 1.3 78.9 - - - +
141I GLU* 1.3 63.6 + - + +
142I ALA 3.5 0.5 + - - -
143I ALA* 3.7 15.1 + - - +
144I LYS* 4.1 8.2 + - - +
150I ILE* 5.8 1.0 - - - +
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Residues in contact with GLU 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89I GLN* 2.5 31.7 + - + +
137I ALA 2.8 22.4 + - - +
138I VAL* 3.9 4.3 - - - +
140I LYS* 1.3 78.9 - - + +
142I ALA* 1.3 63.3 + - - +
143I ALA 3.2 1.2 + - - -
144I LYS* 3.1 35.2 + - - +
147I PRO* 2.8 15.6 - - - +
148I LYS* 3.0 27.9 + - - +
150I ILE* 3.3 24.2 - - + -
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Residues in contact with ALA 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81I ASP 6.4 0.2 - - - -
82I LEU* 4.7 10.8 - - + -
85I ALA* 4.0 26.5 - - + -
89I GLN* 6.1 0.2 - - - +
138I VAL 2.9 16.8 + - - +
139I ALA 4.2 5.6 - - - +
140I LYS 3.4 1.0 - - - -
141I GLU* 1.3 77.0 - - - +
143I ALA* 1.3 61.9 + - - +
144I LYS 3.6 6.3 + - - +
147I PRO* 5.6 2.4 - - - +
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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
------------------------------------------------------------
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