Contacts of the helix formed by residues 134 - 140 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124H LEU* 3.5 32.3 + - + +
132H LEU* 4.1 19.1 - - + -
133H ASN* 1.3 71.1 - - - +
135H LYS* 1.3 65.4 + - + +
136H GLU 3.0 2.5 - - - -
137H ALA* 2.8 21.5 + - - +
138H TRP* 2.9 50.3 + - + +
215H VAL* 4.0 22.2 - - + -
377H ILE* 4.4 2.9 - - + -
380H LEU* 4.8 1.1 - - + -
431H ALA* 3.6 21.3 - - + -
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Residues in contact with LYS 135 (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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110H TYR* 4.4 15.5 - - + -
112H GLU* 3.1 33.3 + - + +
118H PHE* 4.8 0.9 - - + -
124H LEU 4.3 1.3 + - - +
125H SER* 2.9 36.6 + - - +
133H ASN* 3.5 1.2 - - - +
134H VAL* 1.3 81.6 - - - +
136H GLU* 1.3 56.7 + - - +
138H TRP* 3.2 27.4 + - + +
139H ALA* 2.9 31.9 + - - +
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Residues in contact with GLU 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H ASN* 3.3 45.2 + - - +
134H VAL 3.0 0.6 - - - -
135H LYS* 1.3 78.7 - - - +
137H ALA* 1.3 60.2 + - - +
139H ALA* 3.7 7.3 + - - +
140H GLN* 3.3 33.7 + - - +
432H GLY* 3.7 14.9 - - - -
433H ALA 4.6 0.3 + - - -
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Residues in contact with ALA 137 (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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133H ASN 4.2 0.6 + - - -
134H VAL 2.8 10.0 + - - +
136H GLU* 1.3 78.0 - - - +
138H TRP* 1.3 64.6 + - - +
140H GLN* 3.2 15.1 + - - +
141H GLY 3.5 0.2 + - - -
142H PHE* 3.1 23.7 + - - +
380H LEU* 3.8 24.2 - - + -
431H ALA* 4.1 17.0 - - + +
432H GLY* 4.5 2.9 - - - -
435H VAL* 4.1 20.4 - - + -
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Residues in contact with TRP 138 (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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110H TYR* 3.1 44.6 - - + +
113H PRO* 3.7 19.1 - - + -
118H PHE* 3.8 27.8 - + - -
124H LEU* 4.1 3.8 - - + -
134H VAL* 2.9 36.0 + - + +
135H LYS* 3.6 25.4 - - + +
137H ALA* 1.3 75.8 - - - +
139H ALA* 1.3 55.0 + - - +
141H GLY* 2.7 26.7 + - - -
142H PHE 3.2 19.9 + - - -
143H THR* 3.6 17.3 - - + +
213H VAL* 3.9 11.9 - - + -
214H GLY 3.8 6.1 - - - -
215H VAL* 2.8 31.7 + - - -
217H TYR* 3.4 17.4 - + - -
380H LEU* 4.2 7.2 - - + +
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Residues in contact with ALA 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H TYR* 3.7 33.2 - - + +
135H LYS* 2.9 16.4 + - - +
136H GLU* 3.7 8.5 - - - +
138H TRP* 1.3 77.7 - - - +
140H GLN* 1.3 58.7 + - + +
141H GLY* 3.1 4.9 + - - -
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Residues in contact with GLN 140 (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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136H GLU* 3.3 25.0 + - + +
137H ALA* 3.2 9.2 + - - +
138H TRP 3.1 1.0 - - - -
139H ALA* 1.3 76.4 - - + +
141H GLY* 1.3 59.0 + - - +
142H PHE* 3.5 19.9 - - + -
432H GLY* 4.2 12.3 + - - -
435H VAL* 3.9 18.5 - - - +
436H ALA* 4.8 8.3 - - - +
439H GLN* 3.5 19.4 + - - -
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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
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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