Contacts of the helix formed by residues 135 - 140 (chain P) in PDB entry 1E33
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 LEU 135 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124P TRP* 4.1 1.6 - - + +
127P GLY 4.0 10.8 - - - +
128P VAL* 4.2 9.6 - - + -
132P GLY* 3.0 31.2 + - - +
133P ALA 3.4 0.2 - - - -
134P PHE* 1.3 83.6 - - - +
136P PRO* 1.3 84.3 - - + +
137P PRO* 3.2 9.4 - - + -
138P HIS* 3.0 17.5 + - - +
139P GLN* 3.9 1.9 + - - +
144P PHE* 4.4 1.3 - - + -
148P PRO* 3.9 27.8 - - + -
182P LEU* 3.5 27.8 - - + -
184P ASN 4.3 2.9 - - - +
185P LEU* 4.2 23.8 - - + +
487P ILE* 5.4 2.0 - - + -
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Residues in contact with PRO 136 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120P MET* 4.1 3.8 - - - -
124P TRP* 3.7 38.1 - - + -
134P PHE 3.8 0.2 - - - -
135P LEU* 1.3 100.5 - - + +
137P PRO* 1.3 57.5 - - + +
139P GLN* 2.5 31.4 + - - -
140P GLY 3.5 4.5 + - - -
141P PHE* 3.7 25.0 + - + -
144P PHE* 3.3 39.5 - - + -
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Residues in contact with PRO 137 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135P LEU* 3.4 10.5 - - + -
136P PRO* 1.3 96.8 - - + +
138P HIS* 1.3 63.8 + - + +
139P GLN 3.7 0.5 + - - -
140P GLY* 4.1 5.7 + - - -
141P PHE 3.8 18.4 - - - +
142P HIS 5.8 0.7 - - - +
144P PHE* 3.9 11.2 - - + -
184P ASN* 3.6 38.4 - - + +
185P LEU* 3.7 17.0 - - + -
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Residues in contact with HIS 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102P LEU* 3.9 16.3 - - + +
109P GLU* 3.5 9.4 - - - +
132P GLY 3.1 29.3 + - - -
133P ALA* 3.2 26.1 + - - +
135P LEU 3.0 8.3 + - - +
136P PRO 2.8 4.0 + - - -
137P PRO* 1.3 76.8 - - + +
139P GLN* 1.3 58.2 + - - +
140P GLY 3.4 4.4 + - - -
185P LEU* 4.2 29.3 - - + +
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Residues in contact with GLN 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100P LEU* 3.3 20.7 + - - +
101P PRO 2.7 29.5 + - - -
102P LEU* 3.4 22.4 - - + +
104P GLU 3.5 3.9 + - - +
106P THR* 2.8 40.2 + - + +
108P ALA* 4.0 2.9 - - - +
109P GLU* 3.0 33.8 - - - +
124P TRP* 4.2 28.3 - - + -
134P PHE 4.4 6.7 - - - +
135P LEU 4.5 0.2 - - - +
136P PRO 2.5 19.0 + - - +
138P HIS* 1.3 74.0 - - - +
140P GLY* 1.4 57.6 + - - +
141P PHE* 3.6 5.3 + - + -
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Residues in contact with GLY 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108P ALA* 3.7 16.7 - - - +
109P GLU* 3.9 17.3 + - - +
112P ALA* 4.3 7.9 - - - +
118P THR* 2.9 15.4 + - - +
136P PRO 3.5 0.2 + - - -
137P PRO 4.1 3.9 + - - -
138P HIS 3.4 3.6 - - - -
139P GLN* 1.4 80.4 - - - +
141P PHE* 1.3 61.3 - - - +
142P HIS* 3.8 3.4 + - - -
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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