Contacts of the strand formed by residues 1043 - 1048 (chain A) in PDB entry 1WUF
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 HIS1043 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1007A ARG* 4.5 4.4 + - - -
1035A GLU* 2.7 29.1 + - + +
1036A LEU 3.4 3.8 - - - +
1037A ILE* 3.4 36.7 - - + +
1041A GLY* 3.3 18.4 + - - -
1042A ILE* 1.3 75.5 - - - +
1044A GLY* 1.3 58.9 + - - +
1045A TYR* 3.5 24.8 - - + +
1110A ASP* 3.5 0.7 - - - +
1114A LYS* 3.0 33.9 - - - +
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Residues in contact with GLY1044 (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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1034A ILE 3.4 0.7 - - - +
1035A GLU* 3.3 5.4 - - - -
1036A LEU* 2.6 41.1 + - - +
1042A ILE 4.0 0.8 + - - -
1043A HIS* 1.3 73.5 - - - +
1045A TYR* 1.3 62.3 + - - -
1107A ALA* 3.5 20.4 - - - -
1110A ASP* 3.3 6.7 - - - -
1111A ALA* 4.0 12.6 - - - +
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Residues in contact with TYR1045 (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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1033A ILE* 4.4 7.2 - - + -
1034A ILE 3.4 1.8 - - - +
1035A GLU* 3.4 44.6 + - + -
1043A HIS* 3.5 26.0 - - + +
1044A GLY* 1.3 77.7 - - - -
1046A GLY* 1.3 59.5 + - - +
1107A ALA* 3.7 7.6 - - - -
1110A ASP* 2.9 23.1 + - - +
1114A LYS* 4.6 8.7 - - - -
1297A VAL* 3.7 18.8 - - + +
1301A HIS* 2.9 27.7 + - - -
1348A ILE* 4.3 13.2 - - + -
1350A VAL 5.4 5.4 - - - -
1351A THR* 6.2 3.8 - - + +
1352A LEU* 3.8 34.5 - - + +
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Residues in contact with GLY1046 (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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1033A ILE* 3.5 10.2 - - - +
1034A ILE* 2.8 32.3 + - - -
1045A TYR* 1.3 76.0 - - - +
1047A GLU* 1.3 62.3 + - - +
1103A ALA 3.3 22.2 - - - -
1106A LEU* 4.5 2.5 - - - -
1107A ALA* 3.6 7.0 - - - +
1297A VAL* 4.0 4.9 - - - -
1301A HIS* 4.5 3.8 - - - -
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Residues in contact with GLU1047 (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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1029A LYS* 3.7 5.9 + - - -
1031A PHE* 4.1 10.8 - - + -
1032A TYR 3.4 14.8 - - - +
1033A ILE* 4.1 6.1 - - + +
1046A GLY* 1.3 75.2 - - - +
1048A LEU* 1.3 62.1 + - - +
1049A GLU* 2.4 43.8 + - - +
1099A MET 5.2 0.2 - - - +
1102A ALA* 5.1 0.9 - - - +
1103A ALA* 3.6 16.5 + - - +
1106A LEU* 5.4 7.0 - - - +
1265A ALA* 5.7 1.2 - - - +
1295A ALA* 2.9 39.6 + - - +
1297A VAL* 3.5 10.3 - - + +
1298A GLY* 2.6 36.7 + - - +
1301A HIS* 5.6 1.2 + - - -
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Residues in contact with LEU1048 (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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1031A PHE* 3.4 25.5 - - - +
1032A TYR* 3.0 31.7 + - + -
1034A ILE* 4.4 2.4 - - + +
1047A GLU* 1.3 70.4 - - - +
1049A GLU* 1.3 62.3 + - - +
1050A ALA* 3.9 7.4 + - + +
1061A LEU* 3.4 41.8 - - + +
1064A ALA* 3.8 18.6 - - + -
1065A ILE* 3.8 18.2 - - + +
1068A ILE* 4.3 2.0 - - + -
1099A MET 3.2 26.9 - - - +
1100A ALA* 4.0 5.6 - - - -
1103A ALA* 3.6 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