Contacts of the strand formed by residues 1299 - 1309 (chain C) in PDB entry 3HS0
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 ALA1299 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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907B LYS* 3.8 3.5 - - - +
908B LEU* 2.8 43.0 + - + +
943B ILE* 4.5 15.5 - - + -
944B GLN 3.5 13.7 - - - +
945B GLY* 4.2 6.7 - - - -
946B ASP* 4.0 5.4 - - - -
1253C LEU* 3.6 19.3 - - + -
1270C ILE* 4.6 2.0 - - + -
1298C LYS* 1.3 77.7 - - - +
1300C THR* 1.3 62.6 + - - +
1301C MET 4.1 0.4 - - - -
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Residues in contact with THR1300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905B ILE* 4.5 15.7 - - + -
906B VAL 4.0 2.7 - - - +
907B LYS* 3.4 30.5 + - + +
942B ILE 3.5 2.6 - - - +
943B ILE* 4.8 0.9 - - - -
944B GLN* 2.9 42.5 + - + +
946B ASP* 4.0 10.3 + - - -
1299C ALA* 1.3 73.0 - - - +
1301C MET* 1.3 63.7 + - - +
1302C THR* 3.8 17.5 + - - +
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Residues in contact with MET1301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904B THR 3.8 0.7 - - - +
905B ILE* 3.6 4.3 - - - +
906B VAL* 2.9 58.1 + - + +
908B LEU* 4.2 9.6 - - + +
923B ILE* 5.9 1.3 - - - -
941B ILE* 3.5 21.5 - - + -
942B ILE 3.5 5.2 - - - +
943B ILE* 3.1 35.4 - - + -
1257C ILE* 3.9 7.2 - - + -
1289C ILE* 6.0 0.2 - - - -
1291C VAL* 3.4 46.4 - - + -
1299C ALA 4.1 1.4 + - - -
1300C THR* 1.3 72.5 - - - +
1302C THR* 1.3 62.3 + - - +
1303C ILE* 3.5 24.7 - - + -
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Residues in contact with THR1302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903B VAL* 4.5 2.9 - - + -
904B THR 3.6 2.0 - - - +
905B ILE* 3.3 27.2 - - + +
940B LYS 3.4 3.6 - - - +
941B ILE* 3.6 1.0 - - - -
942B ILE* 2.8 53.5 + - + +
1300C THR* 3.9 10.9 + - - +
1301C MET* 1.3 73.1 - - - +
1303C ILE* 1.3 65.8 + - - +
1304C LEU* 3.6 28.3 - - + -
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Residues in contact with ILE1303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902B ILE 3.5 1.9 - - - +
904B THR* 2.8 57.7 + - - +
906B VAL* 4.9 3.8 - - + -
923B ILE* 4.8 22.9 - - + -
926B ARG* 4.1 17.3 - - - +
939B THR* 4.3 7.4 - - + -
940B LYS 3.4 2.2 - - - -
941B ILE* 4.4 18.8 - - + -
1289C ILE* 4.9 7.4 - - + -
1301C MET* 3.5 37.7 - - + +
1302C THR* 1.3 73.4 - - - +
1304C LEU* 1.3 68.5 + - - +
1305C THR* 3.8 18.6 - - - +
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Residues in contact with LEU1304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901B SER* 5.5 2.9 - - - +
902B ILE 3.6 2.0 - - - -
903B VAL* 3.6 27.1 - - + -
938B GLU 3.5 1.9 - - - +
939B THR* 3.3 3.2 - - - -
940B LYS* 2.8 46.2 + - + +
942B ILE* 4.0 23.6 - - + -
1302C THR* 3.6 17.7 - - + -
1303C ILE* 1.3 82.1 - - - +
1305C THR* 1.3 62.0 + - - +
1306C PHE* 3.7 30.8 - - + -
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Residues in contact with THR1305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901B SER* 3.0 5.8 - - - -
902B ILE* 2.9 45.3 + - - +
926B ARG* 2.9 38.5 + - - +
928B LEU* 4.3 19.5 - - + -
937B ILE* 4.0 17.7 - - + -
938B GLU 3.6 1.3 - - - -
939B THR* 3.6 16.6 - - - +
1286C ASN* 4.5 4.9 - - - +
1303C ILE* 3.8 3.3 - - - +
1304C LEU* 1.3 72.4 - - - +
1306C PHE* 1.3 64.2 + - - +
1307C TYR* 3.9 3.7 - - + -
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Residues in contact with PHE1306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LEU* 3.3 44.9 - - + -
899B GLN* 4.2 20.2 - - + +
900B LYS 3.7 6.3 - - - +
901B SER* 3.4 24.9 - - - -
936B GLU 5.2 0.2 - - - -
937B ILE* 3.2 8.8 - - - +
938B GLU* 2.6 45.3 + - + +
940B LYS* 4.1 15.9 - - + -
1304C LEU* 3.7 37.2 - - + -
1305C THR* 1.3 73.6 - - - +
1307C TYR* 1.3 63.8 + - - +
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Residues in contact with TYR1307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899B GLN* 3.6 4.9 - - - +
900B LYS* 3.0 62.0 + - + +
901B SER 4.2 0.7 - - - -
902B ILE* 3.8 28.5 - - + +
928B LEU* 3.8 42.5 - - + +
930B ASP* 3.3 39.8 + - + -
931B ARG* 4.1 9.9 - - - -
935B THR* 5.5 0.2 - - - +
936B GLU 4.5 7.6 - - - -
937B ILE* 4.3 10.1 - - + -
1305C THR 3.9 7.4 - - - -
1306C PHE* 1.3 79.3 - - - +
1308C ASN* 1.3 77.7 + - - +
1309C ALA* 4.0 11.4 - - + -
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Residues in contact with ASN1308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895B PRO* 3.3 37.4 + - - +
896B GLU 3.6 21.0 + - - +
897B GLY 4.5 6.1 + - - -
898B VAL 3.6 7.3 - - - +
899B GLN* 4.3 19.7 + - - +
931B ARG* 3.4 8.0 - - - +
932B VAL* 2.8 28.2 + - + +
935B THR* 3.9 19.3 + - - +
936B GLU 4.9 3.9 + - - +
1307C TYR* 1.3 81.3 - - - +
1309C ALA* 1.3 60.9 + - - +
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Residues in contact with ALA1309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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897B GLY* 3.4 8.8 - - - -
898B VAL* 2.9 33.7 + - + +
900B LYS* 4.0 18.8 - - + -
930B ASP* 3.5 27.6 - - + -
932B VAL* 3.5 5.7 - - - +
1307C TYR* 4.0 10.5 + - + -
1308C ASN* 1.3 73.9 - - - +
1310C GLN* 1.3 68.9 + - - +
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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