Contacts of the strand formed by residues 1500 - 1506 (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 TYR1500 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1498C VAL* 4.0 1.6 - - - +
1499C ASP* 1.3 92.8 - - + +
1501C VAL* 1.3 72.2 + - - +
1502C TYR* 3.2 51.6 - + + +
1527C LYS* 3.4 12.6 - - - +
1529C GLY* 4.1 7.6 - - - -
1531C ASP* 6.3 0.4 - - + -
1541C TYR* 2.5 28.8 + - - -
1561C ILE* 4.1 4.9 - - + -
1562C TRP* 3.3 15.6 - - - +
1563C GLY* 3.4 37.3 + - - +
1564C SER 4.1 1.3 - - - -
1577C TYR* 3.5 48.4 - + - -
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Residues in contact with VAL1501 (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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1493C ALA* 4.7 11.4 - - + +
1498C VAL* 4.8 0.2 - - + -
1500C TYR* 1.3 81.8 - - - +
1502C TYR* 1.3 75.1 + - - +
1526C ILE* 3.0 34.0 + - + -
1527C LYS* 3.2 43.8 + - + +
1560C LEU* 3.5 28.5 - - + -
1561C ILE 3.5 2.9 - - - -
1562C TRP* 3.9 20.2 - - + -
1609C PHE* 4.6 7.0 - - + -
1613C LEU* 5.7 3.4 - - + -
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Residues in contact with TYR1502 (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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1500C TYR* 3.2 52.9 - + + +
1501C VAL* 1.3 91.6 - - - +
1503C LYS* 1.3 60.7 + - - +
1504C THR* 4.0 12.6 - - + +
1522C VAL* 3.5 31.2 - - + -
1524C GLU 3.8 3.1 - - - -
1525C VAL* 4.0 24.0 - - + -
1526C ILE* 4.0 6.3 - - - -
1527C LYS 4.6 0.7 - - - -
1529C GLY* 4.9 3.3 + - - -
1531C ASP* 4.0 18.7 + - - +
1534C PRO* 3.8 23.2 - - + +
1539C HIS* 4.5 18.3 - + - -
1541C TYR* 5.0 5.6 - + - -
1559C TYR 3.4 0.7 - - - +
1560C LEU* 3.5 8.7 - - - +
1561C ILE* 2.8 38.3 + - + +
1577C TYR* 5.3 2.3 + + - -
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Residues in contact with LYS1503 (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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1502C TYR* 1.3 73.6 - - - +
1504C THR* 1.3 61.1 + - - +
1522C VAL* 3.3 6.6 - - - +
1523C LEU* 2.8 59.4 + - + +
1524C GLU* 3.2 31.1 + - - +
1526C ILE* 4.0 3.5 - - + +
1558C ASP* 4.3 14.3 + - + -
1559C TYR 3.2 5.2 - - - +
1588C TRP* 3.3 64.6 - - + +
1589C PRO 5.5 0.4 + - - -
1590C HIS 5.5 3.4 + - - -
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Residues in contact with THR1504 (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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1502C TYR* 4.0 13.5 - - + -
1503C LYS* 1.3 80.6 - - - +
1505C LYS* 1.3 59.8 + - - +
1520C MET* 3.6 21.0 - - + -
1521C ASP 3.5 15.3 - - - +
1522C VAL* 3.8 19.3 - - + -
1523C LEU* 4.5 3.1 - - - +
1539C HIS* 6.2 0.4 - - + -
1541C TYR* 5.9 3.4 - - + -
1557C ASP 3.4 1.2 - - - +
1558C ASP* 3.1 6.1 - - - -
1559C TYR* 2.8 44.9 + - - +
1561C ILE* 3.9 26.3 - - + +
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Residues in contact with LYS1505 (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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1504C THR* 1.3 72.9 - - - +
1506C LEU* 1.3 62.7 + - - +
1507C LEU* 3.0 37.9 + - + +
1520C MET* 3.3 13.1 - - - +
1521C ASP 3.2 9.1 + - - +
1523C LEU* 3.9 22.1 - - + +
1556C ASN* 4.2 31.2 + - - +
1557C ASP 3.2 4.5 - - - -
1558C ASP* 3.6 20.2 + - - +
1590C HIS* 3.7 22.6 + - - -
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Residues in contact with LEU1506 (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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1505C LYS* 1.3 70.2 - - - +
1507C LEU* 1.3 65.0 + - - +
1508C ARG 3.4 24.5 - - - +
1509C ILE* 4.3 8.5 - - + -
1518C TYR* 3.9 18.8 - - + -
1519C VAL 3.9 6.5 - - - +
1520C MET* 3.7 19.5 - - + -
1553C LEU* 3.6 25.1 - - + +
1554C LYS 3.2 25.1 - - - +
1555C VAL* 3.6 4.0 - - - +
1556C ASN* 2.5 33.2 + - - +
1557C ASP 2.8 10.7 + - - +
1559C TYR* 3.2 26.8 - - + +
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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