Contacts of the helix formed by residues 135 - 140 (chain A) in PDB entry 5U7Z
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 ILE 135 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 5.3 3.8 - - + -
105A LEU* 3.8 29.2 - - + -
108A PHE* 4.2 16.4 - - + -
116A MET* 5.9 0.4 - - - -
131A ILE* 3.0 22.7 + - + +
132A SER* 3.9 2.5 - - - +
134A ASN* 1.3 84.0 - - + +
136A PHE* 1.3 64.4 + - - +
137A TYR 3.1 3.7 + - - -
138A GLU* 3.2 10.5 + - - +
139A LEU* 3.1 40.9 + - + +
236B ILE* 5.6 1.6 - - + -
248B TRP* 3.5 44.6 - - + -
251B PHE* 5.1 4.0 - - + -
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Residues in contact with PHE 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 5.5 11.4 - - + -
132A SER* 3.2 19.3 + - - -
133A PHE* 3.6 20.6 + + + +
134A ASN 3.5 2.8 - - - -
135A ILE* 1.3 78.4 - - - +
137A TYR* 1.3 51.7 + - - +
139A LEU* 3.4 14.7 - - + -
140A PHE* 2.5 54.8 + - - -
163B PHE* 3.6 33.8 - + + -
166B PHE* 4.2 40.8 - + + -
207B TYR* 5.2 2.9 - - + -
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Residues in contact with TYR 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ASN 5.4 0.6 + - - +
135A ILE 3.1 0.8 - - - -
136A PHE* 1.3 77.5 - - - +
138A GLU* 1.3 74.1 + - - +
140A PHE* 2.9 34.7 + + - +
163B PHE* 6.4 1.3 - - - -
207B TYR* 4.8 14.7 + - - +
211B LEU* 5.8 2.9 - - + -
223B LEU* 4.4 20.2 - - + -
224B ASN 4.2 4.0 - - - -
225B GLU* 3.5 37.3 - - + -
226B ARG 3.0 17.2 + - - -
249B ILE* 3.9 27.8 - - + -
250B GLY 5.6 0.9 - - - +
277B ALA* 4.0 7.2 - - + -
278B PRO 2.5 30.1 + - - -
279B ALA* 3.1 13.6 - - + +
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Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ASN 5.2 0.2 - - - +
135A ILE* 3.2 14.8 + - - +
137A TYR* 1.3 86.6 + - - +
139A LEU* 1.3 59.7 + - - +
140A PHE* 4.2 4.9 - - - -
232B GLY* 3.8 21.4 - - - +
233B TYR* 4.3 2.8 - - - -
236B ILE* 3.8 22.5 - - + +
248B TRP* 3.4 34.1 - - + +
249B ILE* 2.7 44.9 + - - +
250B GLY 5.1 1.6 + - - -
276B LEU* 4.1 14.2 - - + +
277B ALA* 4.0 17.9 - - + -
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A SER* 3.9 28.9 - - - +
135A ILE* 3.1 31.1 + - + +
136A PHE* 3.6 17.5 - - + +
138A GLU* 1.3 74.9 - - - +
140A PHE* 1.3 71.8 + - - +
233B TYR* 3.3 36.6 + - + +
236B ILE* 4.2 17.5 - - + -
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Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PHE* 2.5 43.5 + - - -
137A TYR* 2.9 35.5 + + - +
138A GLU 4.3 5.8 - - - -
139A LEU* 1.3 78.9 - - - +
163B PHE* 4.6 9.0 - - - -
166B PHE* 5.1 10.0 - - - +
225B GLU* 2.9 39.1 - - + +
226B ARG 3.5 26.0 - - - -
227B PHE* 4.4 17.7 - + + -
228B SER* 4.9 13.0 - - - -
231B GLY 5.6 0.2 - - - -
232B GLY* 4.3 24.2 - - - -
233B TYR* 5.1 7.6 - + - -
277B ALA* 5.0 0.9 - - + -
278B PRO* 4.8 9.6 - - + -
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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