Contacts of the strand formed by residues 1021 - 1026 (chain D) in PDB entry 4OUL
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 LEU1021 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1002D ALA* 3.4 6.6 - - - +
1003D ALA 3.0 30.8 + - - +
1005D THR* 3.5 31.0 - - + +
1019D PHE 3.7 1.2 - - - -
1020D ASP* 1.3 81.7 - - - +
1022D LEU* 1.3 82.5 + - - +
1023D LEU* 3.6 23.6 - - + -
1032D LEU* 3.9 4.5 - - - +
1115D LYS* 3.8 19.7 - - + -
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Residues in contact with LEU1022 (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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1001D SER 3.8 7.6 - - - +
1002D ALA* 4.5 2.0 - - + -
1021D LEU* 1.3 82.7 - - - +
1023D LEU* 1.3 60.2 + - - +
1024D ASN* 3.5 24.0 - - - +
1025D ASN* 4.1 28.7 - - + +
1030D PHE* 4.3 20.6 - - + +
1032D LEU* 3.5 38.4 - - + +
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Residues in contact with LEU1023 (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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1001D SER* 2.7 30.8 + - - +
1002D ALA 3.9 3.1 - - - +
1003D ALA* 3.5 35.2 - - + +
1021D LEU* 3.6 15.9 - - + -
1022D LEU* 1.3 73.9 - - - +
1024D ASN* 1.3 63.5 + - - +
1115D LYS* 4.2 4.5 - - + -
1118D THR* 5.3 1.1 - - + -
1071E LEU* 4.2 17.3 - - + +
1072E VAL* 3.8 27.6 - - + -
1090E ALA* 5.2 1.1 - - + -
1091E ILE 3.9 3.3 - - - +
1092E LEU* 4.1 29.3 - - + +
1093E GLN* 4.8 2.3 + - - +
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Residues in contact with ASN1024 (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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999D ALA* 2.8 27.4 - - - +
1000D PHE* 3.3 1.7 - - - -
1001D SER* 2.9 33.7 + - - +
1022D LEU* 3.3 10.2 - - - +
1023D LEU* 1.3 78.7 - - - +
1025D ASN* 1.3 69.1 + - - +
1026D LEU* 3.0 11.5 + - - +
1044E THR* 3.8 12.1 - - - +
1091E ILE* 3.2 22.3 + - - +
1092E LEU 3.8 1.6 - - - -
1093E GLN* 3.6 45.3 + - - +
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Residues in contact with ASN1025 (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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999D ALA 3.4 4.5 - - - -
1000D PHE* 4.0 4.0 - - - +
1022D LEU* 4.1 23.6 - - + +
1024D ASN* 1.3 76.9 + - - +
1026D LEU* 1.3 60.8 + - - +
1027D GLY 3.1 0.9 + - - -
1028D GLU* 2.8 51.9 + - - +
1029D THR* 3.3 18.0 + - - -
1030D PHE* 3.2 35.8 + - - +
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Residues in contact with LEU1026 (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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996D MET 3.6 17.5 - - - +
997D ARG 3.3 14.5 - - - +
998D VAL* 3.4 4.0 - - - +
999D ALA* 2.8 31.4 + - + +
1024D ASN* 3.0 12.0 + - - +
1025D ASN* 1.3 72.4 - - - +
1027D GLY* 1.3 61.0 + - - +
1028D GLU 3.4 0.6 + - - -
1029D THR* 4.6 2.1 + - - +
1044E THR* 3.6 17.7 - - + +
1093E GLN* 4.0 9.4 - - - +
1125E TYR* 3.3 37.7 - - + -
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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