Contacts of the helix formed by residues 135 - 141 (chain D) in PDB entry 6UZA
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 ASN 135 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103D LEU* 4.3 3.1 - - - -
126D VAL 4.5 6.1 + - - -
127D ASN* 4.2 20.0 + - + +
128D CYS 3.3 21.3 - - - +
129D VAL* 4.4 4.2 - - + +
133D GLY 4.0 1.6 + - - -
134D GLN* 1.3 77.8 - - - +
136D ALA* 1.3 65.5 + - - +
137D LEU* 4.1 11.5 - - - +
138D GLN* 2.9 29.2 + - - +
139D LEU* 3.1 20.1 + - - +
158D LEU* 4.8 3.6 - - - +
159D SER* 3.4 32.3 + - - +
160D ARG* 4.3 7.7 - - - +
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Residues in contact with ALA 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D PHE* 3.7 31.6 - - + -
103D LEU* 4.2 9.3 - - + +
106D ALA* 3.7 23.1 - - + +
126D VAL 4.4 5.3 + - - +
128D CYS 4.4 0.6 + - - -
135D ASN* 1.3 79.4 - - - +
137D LEU* 1.3 58.3 + - - +
139D LEU* 3.8 2.4 - - - +
140D ALA* 2.9 30.7 + - - +
152D LEU* 3.9 16.8 - - + +
158D LEU* 6.1 0.2 - - + -
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Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D ASN* 3.3 13.4 - - - +
136D ALA* 1.3 79.5 - - - +
138D GLN* 1.3 58.1 + - - +
140D ALA* 3.8 1.2 - - - +
141D VAL* 2.9 38.0 + - + +
149D THR* 4.1 28.5 - - + +
152D LEU* 4.2 16.4 - - + +
153D LEU* 4.5 11.4 - - + -
158D LEU* 3.8 33.8 - - + +
159D SER 4.4 1.6 - - - +
160D ARG 3.4 24.9 - - - +
161D VAL* 4.2 12.1 - - + -
164D ALA* 3.8 15.9 - - + -
180D ILE* 5.5 1.1 - - + -
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Residues in contact with GLN 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D GLY 3.9 5.7 - - - +
134D GLN* 3.5 36.9 - - + +
135D ASN* 2.9 26.0 + - - +
136D ALA 3.4 0.2 - - - -
137D LEU* 1.3 76.8 - - + +
139D LEU* 1.3 59.9 + - - +
140D ALA 3.6 0.2 - - - -
141D VAL* 4.3 6.5 - - - +
142D ALA* 3.4 22.6 + - - +
160D ARG* 3.5 34.3 - - + +
163D ASP* 2.4 38.8 + - - +
164D ALA* 5.0 6.3 - - + +
167D LEU* 4.0 6.6 - - + +
209D TYR* 3.6 12.2 - - - +
215D ARG* 4.0 7.1 - - - +
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Residues in contact with LEU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D LEU* 4.0 35.7 - - + +
106D ALA 4.1 4.0 - - - +
107D GLU* 4.2 34.1 - - + +
130D ASP* 4.6 15.7 - - + +
134D GLN* 4.1 28.5 - - + +
135D ASN 3.1 19.4 + - - +
136D ALA* 3.9 5.6 - - - +
137D LEU 3.2 0.2 - - - -
138D GLN* 1.3 79.9 - - - +
140D ALA* 1.3 60.1 + - - +
141D VAL 3.5 0.4 - - - -
142D ALA* 4.1 3.4 - - + -
143D ASN* 2.6 34.2 + - - +
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Residues in contact with ALA 140 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106D ALA 3.9 8.3 + - - +
136D ALA 2.9 18.2 + - - +
137D LEU* 4.0 4.5 - - - +
139D LEU* 1.3 77.7 - - - +
141D VAL* 1.3 61.2 + - - +
143D ASN 4.0 0.2 - - - -
144D GLU 3.5 2.3 + - - -
145D HIS* 3.0 36.4 + - + +
148D ILE* 3.9 28.9 - - + -
149D THR* 3.8 16.1 + - - +
152D LEU* 4.7 1.8 - - + -
176D ILE* 4.4 0.2 - - - +
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Residues in contact with VAL 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D LEU* 2.9 23.6 + - + +
138D GLN* 4.7 0.2 - - - -
140D ALA* 1.3 76.2 - - - +
142D ALA* 1.3 63.8 + - - +
143D ASN 3.2 1.9 + - - -
144D GLU* 3.4 3.1 + - - -
149D THR* 4.0 13.7 - - + +
164D ALA* 3.5 30.5 - - + +
167D LEU* 4.2 13.0 - - + -
168D ALA* 3.8 23.1 - - + +
171D LYS* 4.6 0.5 - - - +
173D TYR* 3.3 22.2 - - - -
176D ILE* 3.9 21.9 - - + +
180D ILE* 4.0 14.1 - - + -
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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