Contacts of the strand formed by residues 1070 - 1073 (chain A) in PDB entry 5ID6
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 ASN1070 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1069A GLY* 1.3 74.6 - - - +
1071A ARG* 1.3 83.6 + - - +
1072A ILE* 5.4 2.6 - - - +
1088A GLU* 2.8 32.3 + - - -
1089A VAL 3.5 13.7 - - - +
1090A CYS* 3.7 17.0 - - + +
1091A LEU* 4.2 4.9 - - - +
1149A PHE* 4.4 5.4 - - - -
1151A ILE* 4.0 8.2 - - - +
1165A ARG* 4.1 23.7 + - - +
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Residues in contact with ARG1071 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1066A TYR 5.0 0.6 + - - -
1067A SER 4.4 0.4 + - - -
1068A TYR 3.5 14.1 + - - -
1069A GLY 3.8 1.0 - - - -
1070A ASN* 1.3 97.3 + - - +
1072A ILE* 1.3 69.2 + - - +
1073A ARG* 3.8 0.7 + - - -
1088A GLU* 4.0 3.2 - - - +
1089A VAL* 3.1 34.2 + - + +
1091A LEU* 3.5 32.7 - - + +
1133A LEU* 3.3 37.9 + - + +
1134A MSE 3.2 19.8 + - - +
1136A GLN* 3.5 22.1 + - - +
1139A ASN* 3.3 9.4 - - - +
1149A PHE* 4.9 0.7 - - - -
1151A ILE* 3.3 36.6 + - - +
1152A SER 4.4 1.2 - - - -
1153A PRO* 4.1 23.2 - - - +
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Residues in contact with ILE1072 (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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1070A ASN* 5.4 2.0 - - - +
1071A ARG* 1.3 75.6 - - - +
1073A ARG* 1.3 63.7 + - - +
1074A ILE* 4.4 5.0 + - + +
1086A TRP* 3.7 33.9 - - + +
1087A GLU 4.3 1.8 - - - -
1088A GLU* 4.4 16.2 - - + +
1136A GLN* 2.7 30.9 + - - +
1139A ASN* 2.9 16.1 + - + +
1140A SER 3.8 24.7 - - - +
1141A ILE* 4.2 17.3 - - + +
1149A PHE* 3.4 34.5 - - + -
1165A ARG* 5.5 0.7 - - - +
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Residues in contact with ARG1073 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1071A ARG 3.8 1.2 + - - -
1072A ILE* 1.3 76.5 - - - +
1074A ILE* 1.3 71.9 + - + +
1075A PHE* 3.2 66.0 + - + +
1086A TRP* 3.7 4.7 - - - -
1087A GLU 2.7 33.8 + - - +
1088A GLU* 4.4 0.2 - - - +
1089A VAL* 4.0 18.8 - - + +
1129A ALA* 6.0 6.6 - - - +
1133A LEU* 3.4 40.8 - - + +
1136A GLN* 4.8 2.9 - - - +
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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
------------------------------------------------------------
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