Contacts of the strand formed by residues 1036 - 1040 (chain B) in PDB entry 2PDA
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 TYR1036 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035B VAL* 1.3 71.3 - - - +
1037B VAL* 1.3 56.6 + - - +
1038B ALA* 3.6 23.1 - - + -
1052B VAL* 4.0 5.6 - - + +
1055B GLU* 2.7 50.7 + - + +
1056B ALA* 3.9 26.7 - - + -
1059B PHE* 3.6 19.4 - - + -
1062B PRO 2.9 15.9 + - - +
1063B SER* 2.9 5.5 - - - -
1064B LEU 2.6 34.0 + - - -
1100B ARG* 3.1 23.7 - - + +
1101B TYR 3.3 7.4 - - - -
1102B ASP* 3.5 35.4 - - + -
1103B PRO* 3.9 2.9 - - + -
1104B ARG* 3.8 6.5 - - - -
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Residues in contact with VAL1037 (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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1026B ALA* 4.0 20.9 - - + +
1029B VAL* 3.5 25.6 - - + -
1030B MET* 3.6 34.5 - - + -
1035B VAL* 3.0 18.4 - - + +
1036B TYR* 1.3 77.0 - - - +
1038B ALA* 1.3 64.8 + - - +
1064B LEU* 3.7 23.6 - - + -
1099B PHE* 4.6 3.6 - - + -
1100B ARG* 3.4 1.2 + - - -
1101B TYR* 2.7 39.7 + - + +
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Residues in contact with ALA1038 (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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1036B TYR* 3.6 15.9 - - + -
1037B VAL* 1.3 79.0 - - - +
1039B THR* 1.3 65.8 + - - +
1040B VAL* 5.0 0.2 - - - -
1052B VAL* 3.8 18.2 - - + -
1064B LEU 3.0 13.2 + - - +
1065B VAL* 3.4 2.1 - - - -
1066B ILE* 3.2 21.7 + - - +
1099B PHE* 3.4 6.5 - - - +
1100B ARG* 3.5 27.8 - - + -
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Residues in contact with THR1039 (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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1026B ALA* 4.4 9.6 - - + -
1038B ALA* 1.3 78.7 - - - +
1040B VAL* 1.3 72.7 + - - +
1048B GLN* 3.3 14.6 - - - +
1066B ILE* 3.2 22.4 - - + +
1096B TRP* 4.5 11.4 - - + -
1097B PRO 2.9 25.0 + - - +
1098B LEU* 3.4 3.9 - - - +
1099B PHE* 3.3 43.4 + - + +
1159B ARG* 5.3 1.1 - - - +
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Residues in contact with VAL1040 (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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820B TYR* 4.1 2.9 - - + -
1039B THR* 1.3 89.1 - - - +
1041B SER* 1.3 59.4 + - - +
1048B GLN* 3.4 21.3 - - - +
1049B PHE* 3.8 27.6 - - + -
1052B VAL* 3.8 29.6 - - + -
1065B VAL* 4.4 6.7 - - + -
1066B ILE 2.9 9.4 + - - +
1067B ALA* 3.4 26.7 - - + -
1068B TYR 3.2 13.0 + - - -
1096B TRP* 2.8 20.3 + - - -
1098B LEU* 3.5 9.2 - - - +
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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