Contacts of the strand formed by residues 1040 - 1045 (chain A) in PDB entry 5W0N
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 THR1040 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1030A GLU* 3.8 5.3 - - + +
1033A ILE* 3.7 18.1 - - + +
1034A ARG* 2.9 36.3 + - - +
1037A PHE* 2.8 31.3 + - - +
1038A PRO 3.2 0.4 + - - -
1039A GLY* 1.3 76.9 - - - +
1041A LYS* 1.3 61.7 + - - +
1042A LEU* 4.0 24.2 - - + -
1063A MET* 3.3 33.4 - - + +
1064A THR 3.5 5.4 - - - -
1065A ILE* 4.7 3.6 - - - +
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Residues in contact with LYS1041 (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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1030A GLU* 3.4 9.6 - - - +
1034A ARG* 5.0 2.9 - - - +
1039A GLY 3.5 0.2 + - - -
1040A THR* 1.3 74.5 - - - +
1042A LEU* 1.3 70.5 + - - +
1043A SER* 3.6 19.2 + - - +
1062A CYS 3.4 1.6 - - - +
1063A MET* 3.3 4.3 - - - +
1064A THR* 2.8 53.8 + - - +
1066A ASN* 3.8 20.9 - - - +
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Residues in contact with LEU1042 (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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1026A ARG* 3.0 38.6 + - + +
1029A LEU* 3.5 22.2 - - + +
1030A GLU* 3.0 48.0 + - + +
1033A ILE* 4.2 12.8 - - + -
1040A THR* 4.0 11.9 - - + -
1041A LYS* 1.3 78.6 - - - +
1043A SER* 1.3 64.2 + - - +
1061A VAL* 3.8 25.1 - - + -
1062A CYS 3.4 2.0 - - - -
1063A MET* 3.8 27.6 - - + -
1120A ILE* 4.8 3.8 - - + -
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Residues in contact with SER1043 (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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1026A ARG* 4.3 2.5 - - - +
1041A LYS* 3.6 24.8 + - - +
1042A LEU* 1.3 76.2 + - - +
1044A LEU* 1.3 65.2 + - - +
1061A VAL* 3.5 2.9 - - - -
1062A CYS* 2.7 46.7 + - - +
1064A THR* 5.2 2.4 + - - +
1128A LEU* 4.0 25.1 - - - +
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Residues in contact with LEU1044 (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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1022A ARG* 4.1 23.8 - - + +
1023A GLU* 4.2 15.7 - - + +
1026A ARG* 3.9 24.5 - - + +
1043A SER* 1.3 74.8 - - - +
1045A PHE* 1.3 64.7 + - - +
1048A SER* 4.5 10.5 - - - -
1049A LYS* 3.8 37.5 - - + +
1059A LEU* 3.7 32.1 - - + -
1060A ASP 3.4 12.6 - - - +
1061A VAL* 3.9 11.2 - - + -
1128A LEU* 3.7 9.7 - - - +
1131A THR* 5.2 0.5 - - - +
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Residues in contact with PHE1045 (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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1044A LEU* 1.3 74.9 - - - +
1046A GLY* 1.3 81.4 + - - +
1047A SER 3.8 0.5 + - - -
1048A SER* 4.0 12.0 + - - -
1049A LYS* 4.4 2.0 - - - -
1060A ASP* 3.0 42.0 + - + +
1061A VAL 3.5 30.5 - - - -
1062A CYS* 3.7 20.4 - - + -
1119A ASP 5.3 1.1 - - - -
1121A SER* 3.8 8.3 - - - -
1124A ASN* 3.7 18.8 - - + -
1127A ALA* 3.5 31.6 - - + +
1128A LEU* 3.8 15.7 - - + -
1130A ASN* 5.9 0.2 - - - -
1131A THR* 3.4 21.1 - - - +
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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