Contacts of the strand formed by residues 1289 - 1295 (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 ILE1289 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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921B GLU 3.6 2.4 - - - +
922B VAL* 4.6 1.6 - - - -
923B ILE* 3.0 41.0 + - + +
926B ARG* 3.5 30.3 - - - +
939B THR* 4.4 9.6 - - + -
941B ILE* 3.7 26.9 - - + -
1257C ILE* 4.1 9.4 - - + -
1258C GLU 4.2 2.5 - - - -
1259C LEU* 3.6 27.1 - - + -
1260C PRO* 5.3 0.4 - - + -
1283C THR* 5.2 5.4 - - + -
1287C GLN 3.9 4.9 - - - +
1288C ASP* 1.3 80.3 - - - +
1290C THR* 1.3 62.7 + - - +
1291C VAL* 4.2 11.1 - - + +
1301C MET* 5.7 0.7 - - + -
1303C ILE* 4.9 10.5 - - + -
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Residues in contact with THR1290 (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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920B LEU* 3.8 28.5 - - + -
921B GLU 3.6 5.4 - - - +
922B VAL* 4.2 20.1 - - + +
1256C THR 3.6 0.7 - - - +
1257C ILE* 3.5 5.2 - - - +
1258C GLU* 3.1 59.8 + - - +
1288C ASP* 5.3 1.7 - - - +
1289C ILE* 1.3 73.0 + - - +
1291C VAL* 1.3 63.3 + - - +
1292C THR* 4.2 1.1 - - - +
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Residues in contact with VAL1291 (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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908B LEU* 4.4 16.5 - - + +
919B GLN 3.5 3.5 - - - +
920B LEU* 3.7 2.3 - - - +
921B GLU* 2.9 47.8 + - + +
923B ILE* 5.6 4.0 - - + -
1255C ILE* 4.3 13.5 - - + -
1256C THR 3.3 8.3 - - - +
1257C ILE* 4.6 2.7 - - + -
1289C ILE* 4.2 17.0 - - + +
1290C THR* 1.3 79.2 - - - +
1292C THR* 1.3 66.5 + - - +
1293C ALA 4.0 0.2 - - - -
1301C MET* 3.4 47.6 - - + -
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Residues in contact with THR1292 (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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918B THR* 3.8 26.2 - - + -
919B GLN 3.6 2.0 - - - +
920B LEU* 3.6 22.2 - - + +
1254C ASP 3.4 4.9 - - - +
1255C ILE* 4.5 0.4 - - - -
1256C THR* 2.8 48.4 + - - +
1258C GLU* 3.6 19.1 + - - -
1290C THR* 4.5 1.0 - - - +
1291C VAL* 1.3 76.9 - - - +
1293C ALA* 1.3 59.9 + - - +
1294C SER* 5.3 1.7 + - - +
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Residues in contact with ALA1293 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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908B LEU* 4.2 30.0 - - + +
910B PRO* 3.6 14.4 - - + +
918B THR* 4.6 1.1 - - - -
919B GLN* 2.8 40.5 + - - +
1253C LEU* 4.9 2.5 - - + -
1254C ASP 3.3 6.3 - - - +
1255C ILE* 4.2 20.4 - - + +
1291C VAL* 4.0 1.0 - - + -
1292C THR* 1.3 73.4 - - - +
1294C SER* 1.3 61.1 + - - +
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Residues in contact with SER1294 (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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910B PRO* 3.7 4.9 - - - -
917B GLY 3.6 8.7 - - - -
918B THR* 3.6 26.7 - - - -
1253C LEU* 3.7 2.6 - - - -
1254C ASP* 2.9 45.7 + - - +
1292C THR* 4.2 2.2 + - - +
1293C ALA* 1.3 74.6 - - - +
1295C GLY* 1.3 58.4 + - - +
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Residues in contact with GLY1295 (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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910B PRO* 3.5 20.8 - - - +
911B ARG* 4.4 4.7 + - - +
917B GLY* 3.8 6.5 + - - +
1252C ASN* 3.2 11.4 - - - -
1253C LEU* 4.0 1.6 - - - -
1294C SER* 1.3 76.3 - - - +
1296C ASP* 1.3 70.3 + - - +
1297C GLY 3.9 0.2 - - - -
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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