Contacts of the strand formed by residues 1710 - 1719 (chain C) in PDB entry 3SE2
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 ALA1710 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1575C LEU* 5.4 4.3 - - - +
1579C TYR* 3.8 5.3 - - - +
1615C GLY* 4.9 2.1 - - - -
1616C PHE* 4.1 17.9 + - + -
1634C PHE* 3.7 32.1 - - + -
1660C VAL* 3.8 5.4 - - + -
1661C ARG 3.0 10.3 - - - +
1662C VAL* 4.1 5.8 - - + -
1704C ALA* 5.4 1.6 - - + -
1706C TYR 4.9 0.4 + - - +
1707C ASP 5.0 2.3 + - - +
1708C TYR* 3.2 6.8 + - - -
1709C GLN* 1.3 82.7 - - + +
1711C TYR* 1.3 61.7 + - - +
1712C PRO* 4.0 5.8 - - - +
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Residues in contact with TYR1711 (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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1570C ILE* 2.7 31.0 + - + +
1572C ASN* 3.0 25.8 + - + +
1575C LEU* 3.9 23.1 - - + -
1576C TRP* 3.6 46.9 - + + -
1579C TYR* 3.8 22.4 - - + -
1660C VAL* 3.2 4.1 - - - +
1661C ARG* 2.7 40.5 + - + +
1710C ALA* 1.3 73.6 - - - +
1712C PRO* 1.3 70.0 - - + +
1713C GLU* 2.9 29.2 + - + -
1721C GOL 3.1 20.7 + - - -
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Residues in contact with PRO1712 (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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1570C ILE* 3.4 22.4 - - + +
1575C LEU* 3.9 13.2 - - + -
1611C VAL* 3.7 35.2 - - + +
1612C ASN* 5.0 3.4 - - - -
1615C GLY* 4.4 5.6 - - - -
1616C PHE* 4.1 7.6 - - + -
1658C TYR* 3.5 25.8 - - + -
1659C TYR 4.5 0.2 - - - -
1660C VAL* 4.1 12.3 - - + -
1710C ALA 4.0 4.9 - - - +
1711C TYR* 1.3 93.9 - - + +
1713C GLU* 1.3 64.5 + - - +
1714C TYR 3.5 2.0 - - - -
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Residues in contact with GLU1713 (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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1547C GLU* 4.9 1.2 - - - +
1569C ARG* 3.5 7.8 - - + +
1570C ILE 3.0 25.7 + - - -
1576C TRP* 5.6 0.2 - - - -
1598C GLN* 3.9 3.8 + - - -
1659C TYR 3.6 8.2 + - - +
1661C ARG* 2.9 43.3 + - + +
1711C TYR* 2.9 26.6 + - + +
1712C PRO* 1.3 73.2 - - - +
1714C TYR* 1.3 97.8 + - + +
1721C GOL 3.2 32.4 + - - +
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Residues in contact with TYR1714 (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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1541C LEU* 4.0 21.5 - - + -
1547C GLU* 2.6 43.0 + - + +
1551C VAL* 3.6 31.9 - - + -
1567C ILE* 4.3 7.6 - - + -
1568C GLU 3.3 9.6 - - - +
1569C ARG* 4.2 7.6 - - + -
1570C ILE* 4.9 0.4 - - - -
1598C GLN* 4.6 8.1 - - - -
1658C TYR* 3.1 12.8 - - - -
1659C TYR* 2.9 49.7 + + + +
1661C ARG* 5.7 0.4 - - - -
1712C PRO 4.9 0.2 - - - -
1713C GLU* 1.3 120.9 + - + +
1715C LEU* 1.3 59.8 + - - +
1716C ILE* 5.3 0.2 - - + -
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Residues in contact with LEU1715 (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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1609A PRO* 6.1 2.0 - - + -
1566C LYS 3.6 2.1 - - - +
1567C ILE* 3.2 5.2 - - - -
1568C GLU* 2.9 60.8 + - - +
1570C ILE* 4.6 11.4 - - + +
1608C VAL* 3.9 29.6 - - + -
1612C ASN* 5.3 0.4 - - - +
1656C HIS* 4.2 13.9 - - + +
1657C VAL 3.9 15.5 - - - +
1658C TYR* 3.7 40.2 - - + +
1714C TYR* 1.3 72.8 - - - +
1716C ILE* 1.3 64.9 + - - +
1717C THR* 3.9 12.6 + - - +
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Residues in contact with ILE1716 (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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1551C VAL* 3.6 32.1 - - + +
1555C PHE* 3.6 31.6 - - + -
1564C ILE* 4.2 30.3 - - + -
1566C LYS 3.5 2.9 - - - +
1567C ILE* 4.4 8.1 - - + +
1600C PHE* 4.0 17.3 - - + -
1656C HIS* 3.6 3.6 - - - -
1657C VAL* 2.8 43.9 + - + +
1659C TYR* 4.6 4.9 - - + -
1715C LEU* 1.3 75.9 - - - +
1717C THR* 1.3 61.4 - - - +
1718C PHE* 3.6 19.6 - - + -
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Residues in contact with THR1717 (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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1564C ILE* 3.8 0.9 - - - -
1565C GLU* 2.8 33.9 + - + +
1566C LYS* 2.8 48.9 + - + +
1568C GLU* 4.3 0.5 + - - -
1654C ARG* 4.0 24.7 - - + -
1655C LYS 3.4 4.5 - - - +
1656C HIS* 3.8 31.4 + - + -
1715C LEU* 4.2 12.8 + - - +
1716C ILE* 1.3 71.8 - - - +
1718C PHE* 1.3 57.8 + - - +
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Residues in contact with PHE1718 (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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1555C PHE* 3.9 21.3 - + + -
1562C PHE* 3.5 36.3 - + + -
1563C ARG 3.3 16.8 - - - +
1564C ILE* 3.8 10.5 - - + -
1565C GLU* 4.1 3.6 - - - +
1642C ALA* 4.2 5.8 - - + -
1647C SER* 4.3 0.2 - - - -
1654C ARG* 3.5 4.7 - - - +
1655C LYS* 2.8 79.6 + - + -
1657C VAL* 3.5 37.0 - - + -
1716C ILE* 3.6 11.7 - - + -
1717C THR* 1.3 75.2 - - - +
1719C ARG* 1.3 66.3 + - - +
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Residues in contact with ARG1719 (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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1562C PHE* 3.6 8.4 - - - -
1563C ARG* 2.9 55.0 + - - +
1565C GLU* 3.1 26.9 + - - +
1652C ASN 2.5 32.1 + - - -
1653C GLY* 3.5 22.6 - - - +
1654C ARG* 4.0 11.3 - - - +
1655C LYS* 5.1 1.6 - - - -
1718C PHE* 1.3 82.9 - - - +
1720C LYS* 1.3 74.3 + - - +
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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