Contacts of the strand formed by residues 1106 - 1110 (chain B) in PDB entry 2ASL
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 GLU1106 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005B PHE* 3.4 21.6 - - + -
1006B VAL 3.5 4.0 - - - -
1007B ASP* 3.6 5.4 - - - +
1089B MET* 3.8 4.9 - - - +
1101B ILE* 3.6 2.3 - - - -
1102B ALA* 2.9 39.9 + - + +
1103B SER* 3.2 28.6 + - - +
1105B ASP* 1.3 87.7 - - - +
1107B ALA* 1.3 62.8 + - - +
1108B TYR* 4.5 0.9 + - - -
1152B LYS* 2.6 31.0 + - - +
1415B CA 3.0 19.0 - - - -
1813H G 4.8 1.6 - - - +
1814H DOC 3.2 12.0 + - - +
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Residues in contact with ALA1107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004B LEU 3.9 1.2 - - - +
1005B PHE* 3.2 5.6 - - - -
1006B VAL 2.8 36.8 + - - +
1089B MET* 3.8 13.2 - - + +
1092B LEU* 3.5 31.9 - - + -
1099B ILE* 4.3 13.2 - - + -
1100B GLU 3.3 9.0 - - - +
1101B ILE* 4.4 1.1 - - + -
1106B GLU* 1.3 76.0 - - - +
1108B TYR* 1.3 63.6 + - - +
1109B LEU* 4.0 2.3 - - + +
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Residues in contact with TYR1108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003B VAL* 4.2 5.4 - - + -
1004B LEU 3.9 2.5 - - - -
1005B PHE* 3.2 34.0 - + + +
1099B ILE* 3.4 8.7 - - - +
1100B GLU* 2.9 47.4 + - + +
1102B ALA* 3.7 25.4 - - + -
1106B GLU* 4.5 0.9 + - - -
1107B ALA* 1.3 72.3 - - - +
1109B LEU* 1.3 61.2 + - - +
1148B LYS* 3.2 56.7 + - + +
1149B VAL* 5.5 0.5 - - - -
1152B LYS* 3.3 29.1 - - + +
1184B PRO* 5.5 0.9 - - - +
1237B ILE* 3.9 19.7 - - + +
1240B ARG* 4.5 9.3 + - - -
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Residues in contact with LEU1109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003B VAL* 3.5 2.5 - - - +
1004B LEU* 2.8 56.9 + - + +
1006B VAL* 4.0 17.7 - - + -
1092B LEU* 3.8 39.5 - - + +
1095B TYR* 4.2 16.8 - - + -
1096B SER* 4.2 13.0 - - - -
1098B LYS 3.8 4.5 - - - +
1099B ILE* 4.9 6.3 - - + -
1107B ALA* 4.0 12.1 - - + +
1108B TYR* 1.3 77.6 - - - +
1110B ASP* 1.3 63.2 + - - +
1111B ILE* 3.2 17.1 + - + +
1128B ILE* 4.5 13.0 - - + -
1237B ILE* 4.3 2.5 - - - -
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Residues in contact with ASP1110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002B ILE 3.5 6.8 - - - +
1003B VAL* 4.8 1.6 - - - +
1096B SER* 2.8 26.2 + - - -
1098B LYS* 3.2 38.0 + - + +
1109B LEU* 1.3 70.2 - - - +
1111B ILE* 1.3 58.5 + - - +
1112B SER* 2.6 34.8 + - - -
1113B ASP* 5.4 1.0 + - - -
1114B LYS* 4.9 1.0 - - - +
1236B PRO* 6.0 0.3 - - - +
1237B ILE* 3.7 30.8 + - + +
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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