Contacts of the strand formed by residues 938 - 945 (chain B) 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 GLU 938 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A LEU* 3.9 30.1 - - + -
936B GLU* 6.1 0.2 - - - +
937B ILE* 1.3 80.7 - - - +
939B THR* 1.3 67.3 + - - +
940B LYS* 4.7 3.4 - - - +
1282C GLU* 3.6 35.0 - - - +
1283C THR 3.8 2.6 - - - +
1284C LYS* 3.1 37.7 + - - +
1306C PHE* 2.6 43.8 + - + +
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Residues in contact with THR 939 (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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926B ARG* 3.2 30.1 + - - +
937B ILE* 4.3 0.9 - - - +
938B GLU* 1.3 73.9 - - - +
940B LYS* 1.3 73.1 + - - +
941B ILE* 4.2 11.7 - - + -
1281C VAL 3.7 0.7 - - - +
1282C GLU* 3.3 6.9 - - - +
1283C THR* 2.9 54.7 + - + +
1285C LEU 3.4 11.6 + - - -
1289C ILE* 4.4 4.9 - - + -
1303C ILE* 4.3 7.9 - - + -
1304C LEU 3.3 8.1 - - - +
1305C THR* 3.6 11.1 - - - +
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Residues in contact with LYS 940 (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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167A PRO* 4.5 5.7 - - - +
169A LEU* 3.3 54.8 + - - +
938B GLU* 4.7 2.7 - - + +
939B THR* 1.3 75.3 - - - +
941B ILE* 1.3 61.6 + - - +
942B ILE* 3.8 18.2 - - + +
1280C THR* 4.8 8.9 - - + +
1281C VAL 3.5 3.6 - - - +
1282C GLU* 2.6 45.8 + - + +
1302C THR 3.4 4.3 - - - +
1303C ILE* 3.4 2.3 - - - -
1304C LEU* 2.8 49.2 + - + +
1306C PHE* 4.1 11.9 - - + -
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Residues in contact with ILE 941 (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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939B THR* 4.2 13.5 - - + +
940B LYS* 1.3 76.3 - - - +
942B ILE* 1.3 60.7 + - - +
943B ILE* 4.8 2.4 - - + +
1257C ILE* 4.1 15.9 - - + -
1259C LEU* 4.0 17.9 - - + -
1268C TYR* 5.8 0.2 - - - -
1279C ARG 3.4 1.7 - - - +
1280C THR* 3.3 5.1 - - - -
1281C VAL* 2.9 43.6 + - + +
1283C THR* 5.4 2.9 - - + -
1289C ILE* 3.7 37.2 - - + -
1301C MET* 3.5 37.7 - - + -
1302C THR 3.6 3.1 - - - +
1303C ILE* 4.4 9.9 - - + -
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Residues in contact with ILE 942 (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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149A ILE* 6.1 0.2 - - + -
940B LYS* 3.8 25.6 - - + +
941B ILE* 1.3 75.4 - - - +
943B ILE* 1.3 63.7 + - - +
944B GLN* 4.2 14.4 - - + +
1278C ALA* 4.1 22.9 - - + -
1279C ARG 3.3 7.2 - - - +
1280C THR* 3.8 18.4 - - + +
1300C THR 3.5 2.6 - - - +
1301C MET* 3.5 2.9 - - - -
1302C THR* 2.8 58.2 + - + +
1304C LEU* 4.0 21.1 - - + -
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Residues in contact with ILE 943 (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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908B LEU* 4.4 4.5 - - + -
941B ILE* 4.9 1.3 - - + +
942B ILE* 1.3 73.7 - - - +
944B GLN* 1.3 63.9 + - - +
945B GLY 4.3 0.2 + - - -
1255C ILE* 4.2 22.7 - - + -
1257C ILE* 4.3 4.3 - - + -
1268C TYR* 4.1 24.5 - - + -
1270C ILE* 3.6 28.8 - - + +
1277C LEU 4.1 1.4 - - - +
1278C ALA* 3.5 5.4 - - - -
1279C ARG* 2.9 42.5 + - + +
1299C ALA* 4.5 8.5 - - + -
1300C THR 3.9 2.0 - - - +
1301C MET* 3.1 47.3 - - + -
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Residues in contact with GLN 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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149A ILE* 3.7 44.0 - - - +
942B ILE* 4.2 11.8 - - + +
943B ILE* 1.3 79.2 - - - +
945B GLY* 1.3 71.3 + - - +
946B ASP* 3.7 2.6 - - - +
1275C ALA 5.2 0.4 - - - -
1276C LEU* 4.7 10.2 - - - +
1277C LEU 5.1 0.4 - - - -
1278C ALA* 4.0 14.1 - - + +
1299C ALA* 4.3 2.7 - - - -
1300C THR* 2.9 45.6 + - + +
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Residues in contact with GLY 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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943B ILE 4.2 1.8 + - - -
944B GLN* 1.3 83.2 - - - +
946B ASP* 1.3 63.0 + - - +
947B PRO* 4.0 4.2 - - - +
1251C LEU* 5.4 1.1 - - - -
1253C LEU* 6.0 0.2 - - - -
1270C ILE* 4.2 23.6 - - - +
1275C ALA* 3.7 27.3 + - - +
1276C LEU* 5.6 0.3 - - - +
1277C LEU 5.0 1.8 + - - -
1298C LYS 4.1 8.1 - - - -
1299C ALA* 4.2 5.4 - - - -
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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