Contacts of the strand formed by residues 983 - 987 (chain B) in PDB entry 2NUP
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 ALA 983 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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948B ARG* 3.7 0.7 - - - +
949B VAL* 3.0 25.7 + - + -
950B ASP* 3.0 16.6 + - + +
982B GLY* 1.3 73.2 - - - +
984B PHE* 1.3 68.2 + - - +
994B LEU* 4.4 6.1 - - + -
995B TRP 3.4 11.2 - - - +
996B VAL* 4.3 5.2 - - - +
1000B CYS* 4.6 0.4 - - - -
1004B PHE* 3.5 40.8 - - + -
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Residues in contact with PHE 984 (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* 3.9 17.9 - - + -
947B TYR 3.5 3.4 - - - -
948B ARG* 3.4 48.7 - - + -
971B LEU* 3.9 15.5 - - + -
977B LYS 3.7 14.6 - - - -
978B LEU* 3.8 15.7 - - + -
979B SER* 3.4 42.4 - - - -
982B GLY* 3.9 1.6 - - - -
983B ALA* 1.3 85.1 - - - +
985B LEU* 1.3 59.3 + - - +
986B MET 4.1 0.3 + - - -
993B MET 4.0 0.7 - - - +
994B LEU* 3.3 3.8 - - - +
995B TRP* 2.7 68.0 + + + +
1065B PHE* 4.2 2.5 - - + -
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Residues in contact with LEU 985 (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* 3.5 3.4 - - - +
947B TYR* 2.8 51.7 + - + -
949B VAL* 3.7 21.6 - - + +
984B PHE* 1.3 72.9 - - - +
986B MET* 1.3 72.7 + - - +
987B ASP* 4.1 2.7 - - - +
992B LEU* 4.0 12.8 - - + +
993B MET 3.7 2.9 - - - -
994B LEU* 3.9 13.0 - - + +
1035B ILE* 5.9 0.7 - - + -
1038B PHE* 4.3 3.8 - - + -
1039B ILE* 4.1 23.8 - - + -
1042B LEU* 3.9 24.9 - - + -
1052B LEU* 3.9 27.4 - - + -
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Residues in contact with MET 986 (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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944B PRO* 3.5 22.0 - - + -
945B SER 3.4 6.7 - - - +
946B LEU* 4.3 6.1 - - + +
973B LEU* 4.2 7.4 - - + -
984B PHE 4.1 0.4 + - - -
985B LEU* 1.3 75.8 - - - +
987B ASP* 1.3 59.8 + - - +
988B ALA* 3.5 4.8 + - + +
992B LEU* 3.4 24.8 - - - -
993B MET* 2.9 18.1 + - + +
1065B PHE* 3.4 50.5 - - + +
1068B ASN* 3.5 38.8 - - + -
1069B MET* 3.7 24.2 - - + -
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Residues in contact with ASP 987 (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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940B LEU* 3.7 11.9 - - - +
944B PRO* 3.2 5.8 - - - +
945B SER* 2.6 41.1 + - - +
947B TYR* 4.1 16.3 + - + -
985B LEU* 4.1 3.9 - - + +
986B MET* 1.3 70.0 - - - +
988B ALA* 1.3 57.9 + - - +
989B GLY* 2.7 30.4 + - - -
992B LEU* 3.2 17.2 - - + +
1042B LEU* 3.6 14.3 - - + +
1046B ARG* 2.5 38.0 + - - -
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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