Contacts of the helix formed by residues 135 - 139 (chain A) in PDB entry 6AF6
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 ASP 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A ASP 5.1 2.6 - - - +
132A ALA* 3.3 16.3 - - - +
133A GLY 3.2 3.2 - - - +
134A SER* 1.3 75.3 - - - +
136A ILE* 1.3 63.8 + - - +
137A TYR* 3.2 3.0 + - - +
138A ASN* 3.2 36.8 + - + +
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Residues in contact with ILE 136 (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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127A ALA* 3.6 31.0 - - + +
128A THR* 3.7 3.4 - - - -
132A ALA* 3.6 22.4 - - + +
133A GLY 3.4 10.1 - - - +
134A SER 3.0 3.3 + - - +
135A ASP* 1.3 76.1 - - - +
137A TYR* 1.3 92.3 + - + +
138A ASN 3.2 0.2 - - - -
139A MET* 3.1 38.4 + - + +
237A PHE* 4.0 17.9 - - + -
506A PRO* 3.7 34.8 - - - +
507A GLY* 4.6 1.6 - - - +
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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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135A ASP* 3.2 3.8 + - - +
136A ILE* 1.3 96.3 - - + +
138A ASN* 1.3 53.9 + - - +
139A MET* 3.2 10.8 - - + -
173A LYS* 2.9 25.8 + - - +
179A GLY* 3.6 7.9 - - - -
180A PHE* 3.4 58.4 - + + +
183A VAL* 4.4 12.8 - - + -
234A GLY* 3.5 27.2 + - - -
237A PHE* 3.7 17.1 - + + -
238A HIS* 4.0 5.7 + - - +
507A GLY* 3.5 20.2 + - - -
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Residues in contact with ASN 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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131A ASP* 3.3 27.5 + - - +
132A ALA* 3.8 4.2 - - - +
135A ASP* 3.2 37.1 + - - +
136A ILE 3.2 1.2 - - - -
137A TYR* 1.3 73.3 - - - +
139A MET* 1.3 67.1 + - - +
140A GLN* 2.9 25.7 + - - +
173A LYS* 4.0 2.9 - - - +
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Residues in contact with MET 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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127A ALA* 4.0 10.3 - - + +
129A GLU* 3.2 19.1 - - + +
132A ALA* 3.5 12.5 - - + +
136A ILE* 3.1 37.5 + - + +
137A TYR* 3.2 5.3 - - + -
138A ASN* 1.3 77.3 - - - +
140A GLN* 1.3 61.0 + - - +
141A ALA 5.0 0.9 - - - +
156A LYS* 3.6 2.9 - - - +
171A TYR* 3.6 48.0 - - + +
172A ALA* 4.0 6.1 - - - -
173A LYS* 2.9 45.8 + - + +
183A VAL* 4.2 17.0 - - + -
237A PHE* 5.9 1.6 - - + -
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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