Contacts of the strand formed by residues 924 - 932 (chain B) in PDB entry 3PT6
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 ARG 924 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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920B GLU* 3.1 7.2 - - - +
921B VAL 2.8 39.8 + - - +
922B ASP* 4.4 6.1 - - + +
923B GLY* 1.3 82.6 - - - +
925B VAL* 1.3 57.8 + - - +
926B TYR* 3.6 19.3 + - + -
1004B HIS* 3.7 25.5 + - + -
1005B CYS* 2.8 24.3 - - - +
1006B GLY* 2.5 41.0 - - - +
1007B LYS* 5.1 2.0 - - - +
1016B ASP* 2.8 32.7 + - - -
1018B LYS* 4.1 20.0 - - - +
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Residues in contact with VAL 925 (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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917B GLN* 5.7 8.5 - - + +
919B GLU 3.5 7.4 - - - +
920B GLU* 4.3 6.3 - - + +
924B ARG* 1.3 71.3 - - - +
926B TYR* 1.3 63.8 + - - +
927B CYS* 3.3 3.9 + - - -
1005B CYS* 2.6 56.5 + - - +
1007B LYS* 4.8 10.8 - - + +
1012B VAL* 4.8 11.0 - - + -
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Residues in contact with TYR 926 (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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917B GLN* 3.8 2.8 - - - +
918B ILE* 2.8 43.4 + - + -
919B GLU* 2.8 25.8 + - + +
921B VAL* 4.8 13.9 - - + -
924B ARG* 3.6 18.1 + - + -
925B VAL* 1.3 70.0 - - - +
927B CYS* 1.3 54.7 + - - +
1002B GLU* 3.5 37.3 + - + -
1003B ILE 3.3 9.4 - - - -
1004B HIS* 3.4 31.6 + + + +
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Residues in contact with CYS 927 (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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914B VAL* 3.3 31.6 - - + -
916B GLU 3.3 13.0 - - - +
917B GLN* 4.9 5.8 - - - -
918B ILE* 3.6 13.4 - - - +
925B VAL* 3.5 15.7 - - - -
926B TYR* 1.3 75.9 - - - +
928B SER* 1.3 62.0 + - - +
930B ILE* 4.1 7.9 - - + -
939B LEU* 4.3 2.4 - - - +
1003B ILE* 2.6 44.4 + - + +
1005B CYS* 3.7 19.1 - - - -
1017B ILE* 6.0 0.2 - - - -
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Residues in contact with SER 928 (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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916B GLU* 3.0 24.3 + - - +
917B GLN 5.0 0.7 + - - -
918B ILE* 3.7 23.0 - - - +
927B CYS* 1.3 75.0 - - - +
929B SER* 1.3 61.4 + - - +
938B ARG* 3.4 8.1 - - - +
939B LEU* 3.3 40.9 + - - +
1003B ILE* 3.8 6.0 - - - +
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Residues in contact with SER 929 (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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914B VAL* 3.6 0.3 - - - -
915B LEU* 2.6 54.0 + - - +
916B GLU* 3.0 27.2 + - - +
928B SER* 1.3 82.9 + - - +
930B ILE* 1.3 60.3 + - - +
936B VAL* 4.2 0.2 - - - +
937B TYR 3.8 4.0 - - - -
938B ARG* 4.1 20.5 - - - +
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Residues in contact with ILE 930 (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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913B LYS 3.5 10.3 - - - +
914B VAL* 3.9 17.9 - - + -
915B LEU* 4.0 5.4 - - - +
927B CYS* 4.1 5.2 - - + -
928B SER 4.4 0.2 - - - -
929B SER* 1.3 80.6 + - - +
931B THR* 1.3 62.9 + - - +
936B VAL* 3.6 4.3 - - - +
937B TYR* 2.9 43.5 + - + +
1003B ILE* 4.0 29.6 - - + -
1017B ILE* 3.8 28.9 - - + -
1019B LEU* 4.3 7.4 - - + -
1056B PHE* 4.1 31.2 - - + -
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Residues in contact with THR 931 (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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909B LYS 5.3 0.5 + - - -
911B MET 5.4 0.4 - - - -
912B PRO* 3.6 2.1 - - - +
913B LYS* 2.9 41.0 + - + +
915B LEU* 3.5 32.3 - - + -
930B ILE* 1.3 74.4 - - - +
932B LYS* 1.3 70.7 + - - +
933B ASN 4.4 0.2 + - - -
934B GLY* 4.2 8.5 + - - -
935B VAL 3.2 16.1 + - - -
936B VAL* 4.2 11.8 - - + +
937B TYR* 4.7 0.9 - - - -
1056B PHE* 3.6 7.9 - - - -
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Residues in contact with LYS 932 (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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909B LYS 4.5 0.7 - - - -
910B GLU 4.0 14.8 - - - +
911B MET 5.1 1.1 - - - -
912B PRO* 4.4 14.1 - - + -
931B THR* 1.3 75.5 + - - +
933B ASN* 1.3 76.4 + - + +
934B GLY 3.4 0.7 - - - -
935B VAL* 3.1 19.0 + - - +
937B TYR* 4.1 10.9 + - + -
1056B PHE* 3.1 53.7 + - + +
1057B SER* 3.2 23.1 + - - -
1059B VAL* 2.7 36.9 + - - -
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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