Contacts of the helix formed by residues 1607 - 1615 (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 SER1607 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1603C THR* 3.1 28.1 + - - -
1604C ASP* 3.0 19.0 + - - -
1606C GLY* 1.3 75.7 - - - +
1608C VAL* 1.3 60.0 + - - +
1609C PRO 3.4 1.6 - - - -
1610C HIS* 3.0 9.7 + - - +
1611C VAL* 2.9 30.5 + - - +
1620C TYR* 3.7 21.2 - - - -
1621C ALA* 5.1 6.4 - - - +
1622C GLY* 5.1 2.9 + - - -
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Residues in contact with VAL1608 (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* 3.7 22.7 - - + -
1603C THR* 4.9 0.2 - - + -
1604C ASP 4.3 4.7 - - - +
1605C ALA* 3.5 20.0 - - - +
1607C SER* 1.3 76.6 - - - +
1609C PRO* 1.3 69.0 - - + +
1612C ASN* 2.9 46.8 + - - +
1656C HIS* 4.4 17.7 - - + +
1658C TYR* 3.4 24.0 - - + +
1715C LEU* 3.9 26.0 - - + -
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Residues in contact with PRO1609 (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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1605A ALA* 3.5 24.7 - - + +
1608A VAL* 4.1 19.3 - - + -
1609A PRO* 4.1 6.5 - - + -
1656A HIS* 5.7 6.5 - - + +
2C CL 4.3 8.7 - - + -
1605C ALA 3.8 5.6 - - - +
1606C GLY 3.7 11.2 - - - +
1607C SER 3.7 2.2 - - - -
1608C VAL* 1.3 96.6 - - + +
1610C HIS* 1.3 63.0 + - - +
1612C ASN* 4.0 0.6 - - + +
1613C ARG* 2.6 47.8 + - - +
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Residues in contact with HIS1610 (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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1566A LYS* 6.1 0.2 - - - +
1652A ASN* 4.9 7.4 + - - +
1654A ARG* 5.4 8.1 + - - +
1606C GLY 4.9 2.2 + - - +
1607C SER* 3.0 14.9 + - - +
1609C PRO* 1.3 78.4 - - - +
1611C VAL* 1.3 56.9 + - - +
1613C ARG* 3.0 5.0 + - - +
1614C ASN* 2.8 62.5 + - + +
1615C GLY 3.8 11.4 - - - -
1617C ASN* 2.8 23.8 + - - -
1619C SER* 3.2 32.0 + - - -
1620C TYR* 3.5 24.2 + + + -
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Residues in contact with VAL1611 (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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1575C LEU* 4.1 0.2 - - - +
1603C THR* 5.2 0.4 - - + -
1607C SER* 2.9 21.9 + - - +
1610C HIS* 1.3 72.0 - - - +
1612C ASN* 1.3 63.5 + - - +
1615C GLY* 2.8 33.9 + - - +
1616C PHE* 3.7 22.4 - - + -
1620C TYR* 3.8 33.2 - - + -
1658C TYR* 3.4 35.9 - - + +
1712C PRO* 3.7 24.0 - - + +
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Residues in contact with ASN1612 (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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2C CL 3.6 16.8 - - - +
1536C PHE* 3.7 28.6 - - + -
1538C VAL* 4.0 4.0 - - - +
1570C ILE* 3.4 40.7 - - + +
1572C ASN* 3.1 24.1 + - - +
1575C LEU* 4.2 3.3 - - - +
1608C VAL* 2.9 36.0 + - - +
1609C PRO 4.0 1.6 - - - +
1611C VAL* 1.3 75.9 - - - +
1613C ARG* 1.3 58.9 + - - +
1658C TYR* 2.6 27.9 + - - -
1712C PRO* 5.0 1.1 - - - -
1715C LEU* 5.3 0.4 - - - +
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Residues in contact with ARG1613 (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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1538A VAL* 3.9 10.7 - - - +
1566A LYS* 2.8 26.5 - - - +
1568A GLU* 2.8 43.5 + - - +
1608A VAL* 5.2 3.6 - - - +
1612A ASN* 5.5 1.0 - - - +
1715A LEU* 4.0 12.9 - - - +
1534C GLN* 3.1 27.3 + - + +
1536C PHE* 3.4 29.1 - - + -
1572C ASN* 3.1 20.3 + - - +
1575C LEU* 4.1 2.1 - - - +
1609C PRO* 2.6 54.1 + - - +
1610C HIS* 3.0 7.7 + - - +
1612C ASN* 1.3 80.0 - - - +
1614C ASN* 1.3 73.6 + - - +
1615C GLY 3.7 0.4 - - - -
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Residues in contact with ASN1614 (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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1566A LYS* 5.3 2.0 - - - +
1654A ARG* 6.0 1.4 - - - +
1534C GLN* 3.9 13.7 + - - +
1575C LEU* 3.8 13.8 - - - +
1610C HIS* 2.8 48.0 + - - +
1613C ARG* 1.3 93.4 - - - +
1615C GLY* 1.3 63.5 + - - +
1616C PHE 3.9 0.2 + - - -
1617C ASN* 3.3 39.9 + - - +
1707C ASP 4.6 2.1 - - - +
1708C TYR* 5.1 2.1 - - - -
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Residues in contact with GLY1615 (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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1575C LEU* 3.5 16.9 - - - +
1610C HIS* 3.8 18.0 - - - -
1611C VAL* 2.8 23.9 + - - +
1614C ASN* 1.3 82.1 - - - +
1616C PHE* 1.3 63.1 + - - -
1617C ASN 3.0 6.6 + - - -
1707C ASP 5.4 1.1 - - - -
1710C ALA 4.9 2.9 - - - -
1712C PRO* 4.4 11.7 - - - -
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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