Contacts of the helix formed by residues 134 - 140 (chain G) in PDB entry 1P8J
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 VAL 134 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G TYR 5.2 0.4 + - - +
124G LEU* 3.5 47.2 + - + +
126G GLY 4.9 1.2 + - - -
132G LEU* 4.1 15.9 - - + -
133G ASN* 1.3 71.4 - - - +
135G LYS* 1.3 61.9 + - - +
137G ALA* 2.8 25.7 + - - +
138G TRP* 2.9 42.5 + - + +
215G VAL* 4.1 18.4 - - + -
377G ILE* 4.5 4.5 - - + -
380G LEU* 4.8 1.1 - - + -
431G ALA* 3.6 20.2 - - + -
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Residues in contact with LYS 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G TYR* 3.8 18.8 + - + +
112G GLU* 2.8 30.7 + - + +
118G PHE* 3.8 21.2 - - - -
124G LEU 3.8 11.4 + - - +
125G SER* 2.8 32.7 + - - +
126G GLY* 4.9 1.8 + - - +
127G VAL* 5.1 17.3 - - + -
133G ASN 3.3 1.1 - - - -
134G VAL* 1.3 80.2 - - - +
136G GLU* 1.3 56.7 + - - +
138G TRP* 3.2 18.7 + - + +
139G ALA* 2.9 32.2 + - - +
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Residues in contact with GLU 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G VAL* 3.6 25.4 - - + +
133G ASN* 3.2 24.8 + - + +
134G VAL 3.0 0.2 + - - -
135G LYS* 1.3 80.6 - - - +
137G ALA* 1.3 59.7 + - - +
139G ALA* 3.7 6.2 + - - +
140G GLN* 3.4 40.1 + - - +
430G ASP* 4.0 6.1 - - - +
432G GLY* 2.9 30.3 - - - -
433G ALA 3.9 1.6 + - - -
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Residues in contact with ALA 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134G VAL 2.8 16.0 + - - +
136G GLU* 1.3 74.9 - - - +
138G TRP* 1.3 64.3 + - - +
140G GLN* 3.2 12.3 + - - +
141G GLY 3.5 0.2 + - - -
142G PHE* 3.1 23.6 + - - +
380G LEU* 3.8 24.0 - - + -
431G ALA* 4.2 15.3 - - + +
432G GLY* 4.5 2.7 - - - -
435G VAL* 4.0 24.5 - - + -
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Residues in contact with TRP 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G TYR* 3.6 40.0 - + + +
113G PRO* 3.8 21.3 - - + -
118G PHE* 3.9 18.4 - + - -
124G LEU* 4.3 3.8 - - + -
134G VAL* 2.9 37.6 + - + +
135G LYS* 3.5 15.5 - - + +
137G ALA* 1.3 76.8 - - - +
139G ALA* 1.3 57.2 + - - +
141G GLY* 2.8 22.7 + - - -
142G PHE 3.3 20.8 + - - -
143G THR* 3.7 17.7 - - + +
213G VAL* 3.8 20.2 - - + -
214G GLY 3.8 6.7 - - - -
215G VAL* 2.8 30.4 + - - -
217G TYR* 3.4 21.9 - + - -
380G LEU* 4.2 7.0 - - + +
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Residues in contact with ALA 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G TYR* 3.7 32.1 - - + +
135G LYS 2.9 16.4 + - - +
136G GLU* 3.8 8.3 - - - +
138G TRP* 1.3 76.9 - - - +
140G GLN* 1.3 60.1 + - + +
141G GLY* 3.1 4.5 + - - -
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Residues in contact with GLN 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G GLU* 3.4 30.8 + - - +
137G ALA* 3.2 8.8 + - - +
138G TRP 3.2 1.2 - - - -
139G ALA* 1.3 77.1 - - + +
141G GLY* 1.3 58.9 + - - +
142G PHE* 3.5 21.9 - - + -
432G GLY 4.9 8.1 + - - -
435G VAL* 3.9 17.7 - - - +
436G ALA* 5.2 6.6 - - - +
439G GLN* 4.2 9.5 + - - +
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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