Contacts of the strand formed by residues 943 - 948 (chain B) in PDB entry 4Z02
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 TYR 943 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934B TRP* 4.0 3.6 - - - -
935B ALA* 2.9 35.9 + - - +
941B PRO* 4.0 7.6 - - + +
942B SER* 1.3 76.6 - - - +
944B PRO* 1.4 88.8 - - + +
945B ALA* 3.3 1.6 + - - +
991B PHE* 3.6 14.4 - + + -
992B PHE 4.0 0.2 - - - -
993B ASP* 3.3 48.7 - - + +
994B ASN* 5.5 0.5 + - - -
1031B ALA* 4.1 9.4 + - + +
1032B VAL* 3.9 31.0 - - + -
1035B ALA* 3.4 26.9 - - + +
1038B ARG* 4.6 1.9 + - - -
1101B 4K8 3.6 31.0 - + + -
1102B UNX 4.6 10.3 - - - -
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Residues in contact with PRO 944 (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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933B VAL 3.4 8.3 - - - +
934B TRP* 3.8 15.5 - - + -
942B SER 4.6 0.2 - - - +
943B TYR* 1.4 102.9 - - + +
945B ALA* 1.3 54.6 + - - +
991B PHE* 3.5 1.2 - - - -
992B PHE* 2.8 33.3 + - + -
1009B LEU* 3.6 20.9 - - + -
1032B VAL* 4.2 4.3 - - + +
1035B ALA* 3.6 23.3 - - + +
1036B PHE* 3.6 26.9 - - - +
1039B ALA* 3.8 7.0 - - + -
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Residues in contact with ALA 945 (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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932B VAL* 3.5 5.0 - - - +
933B VAL* 2.9 35.8 + - + +
935B ALA* 3.9 14.1 - - + -
944B PRO* 1.3 74.7 - - - +
946B LEU* 1.3 60.6 + - - +
989B VAL* 3.8 20.2 - - + -
990B LEU 3.3 12.8 - - - +
991B PHE* 3.7 19.1 - - + -
992B PHE* 3.6 9.6 - - - -
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Residues in contact with LEU 946 (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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931B LYS* 3.5 23.1 - - + -
932B VAL* 3.8 17.3 - - + -
945B ALA* 1.3 75.1 - - - +
947B ILE* 1.4 65.2 + - - +
948B ILE* 3.5 26.6 + - + +
989B VAL* 3.2 4.6 - - - -
990B LEU* 2.8 45.5 + - + +
992B PHE* 4.1 10.1 - - + -
1042B HIS* 3.5 38.1 - - + +
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Residues in contact with ILE 947 (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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930B LEU 4.0 14.1 - - - +
931B LYS* 2.9 36.1 + - + +
933B VAL* 3.8 26.5 - - + -
946B LEU* 1.4 74.3 - - - +
948B ILE* 1.3 72.4 + - - +
949B ASP* 4.4 0.7 + - - -
987B PHE* 4.3 23.6 - - + -
988B LEU 3.4 8.7 - - - +
989B VAL* 4.2 3.1 - - + -
1006B MET* 3.8 33.4 - - + -
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Residues in contact with ILE 948 (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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946B LEU* 3.8 39.9 - - + +
947B ILE* 1.3 81.0 - - - +
949B ASP* 1.3 70.8 + - - +
950B PRO* 3.6 7.6 - - - +
965B PRO* 4.9 7.6 - - + +
967B PRO* 3.8 29.8 - - + -
987B PHE* 6.1 0.3 - - - -
988B LEU* 2.7 39.3 + - + +
990B LEU* 4.0 13.7 - - + +
998B TRP* 3.8 18.8 - - + -
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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