Contacts of the helix formed by residues 1688 - 1696 (chain A) in PDB entry 5LYH
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 SER1688 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1684A THR* 3.2 17.5 - - - -
1685A ASP* 2.6 21.1 + - - -
1686A ALA 3.2 0.8 - - - -
1687A GLY* 1.3 76.5 - - - +
1689A VAL* 1.3 65.0 + - - +
1690A PRO 3.3 0.2 - - - -
1691A HIS* 2.9 13.5 + - - +
1692A VAL* 2.8 24.4 + - - +
1901A 7B8 3.1 27.9 + - - -
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Residues in contact with VAL1689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1684A THR* 4.6 1.3 - - + +
1685A ASP 3.6 13.7 + - - +
1686A ALA* 3.6 8.5 - - - +
1688A SER* 1.3 76.2 - - - +
1690A PRO* 1.3 65.6 - - + +
1693A ASN* 2.9 44.3 + - - +
1737A HIS* 4.2 31.0 - - + +
1739A TYR* 3.0 28.7 + - + +
1796A LEU* 4.0 17.5 - - + -
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Residues in contact with PRO1690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1617A PHE* 4.2 11.1 - - + -
1686A ALA 3.6 6.1 - - - +
1687A GLY 3.1 27.6 - - - +
1689A VAL* 1.3 84.6 - - + +
1691A HIS* 1.3 62.5 + - - +
1693A ASN* 3.8 9.0 - - + +
1694A ARG* 3.2 22.5 + - - +
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Residues in contact with HIS1691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1687A GLY 4.6 1.8 + - - +
1688A SER* 2.9 15.5 + - - +
1690A PRO* 1.3 77.5 - - - +
1692A VAL* 1.3 62.8 + - + +
1694A ARG* 2.9 3.0 + - - -
1695A ASN* 2.8 57.0 + - + +
1696A GLY 4.6 7.6 - - - -
1698A ASN* 4.2 12.0 - - - +
1700A SER* 4.1 16.3 + - - -
1901A 7B8 3.6 35.0 + + - -
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Residues in contact with VAL1692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1684A THR* 5.0 2.0 - - + -
1688A SER* 2.8 18.1 + - - +
1691A HIS* 1.3 76.7 - - + +
1693A ASN* 1.3 59.4 + - - +
1696A GLY* 2.8 36.4 + - - +
1697A PHE* 3.8 31.4 - - + -
1739A TYR* 3.3 43.5 - - + +
1793A PRO* 3.6 18.1 - - + +
1901A 7B8 4.2 18.6 - - + +
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Residues in contact with ASN1693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1617A PHE* 3.5 45.2 - - + +
1619A VAL* 4.3 3.1 - - - +
1651A ILE* 3.9 30.2 - - + +
1653A ASN* 3.0 23.0 + - - +
1656A LEU* 4.4 2.3 - - - +
1689A VAL* 2.9 28.0 + - - +
1690A PRO* 3.8 1.8 - - - +
1691A HIS 3.1 0.2 - - - -
1692A VAL* 1.3 79.9 - - - +
1694A ARG* 1.3 58.7 + - - +
1739A TYR* 2.6 41.2 + - - -
1793A PRO* 4.9 0.2 - - - -
1796A LEU* 5.7 0.4 - - - +
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Residues in contact with ARG1694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1614A GLN* 2.8 38.6 + - - +
1615A GLN* 3.2 33.0 + - + +
1616A ASN* 3.0 26.8 + - - +
1617A PHE* 4.0 21.8 - - + +
1653A ASN* 2.7 21.3 + - - -
1656A LEU* 4.2 1.6 - - - +
1690A PRO 3.2 13.0 + - - +
1691A HIS* 2.9 2.4 + - - -
1693A ASN* 1.3 75.9 - - - +
1695A ASN* 1.3 82.5 + - - +
1696A GLY 4.0 0.3 + - - -
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Residues in contact with ASN1695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1615A GLN* 4.0 15.3 + - - +
1656A LEU* 3.9 11.7 - - - +
1691A HIS* 2.8 37.7 + - - +
1694A ARG* 1.3 99.2 - - - +
1696A GLY* 1.3 62.5 + - - +
1697A PHE 3.4 1.6 + - - -
1698A ASN* 3.5 38.4 + - + +
1789A TYR* 5.5 2.4 - - - -
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Residues in contact with GLY1696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1656A LEU* 3.9 17.2 - - - +
1691A HIS* 4.6 6.1 - - - -
1692A VAL* 2.8 42.9 + - - +
1694A ARG 3.7 1.2 - - - -
1695A ASN* 1.3 75.8 - - - +
1697A PHE* 1.3 70.6 + - - -
1698A ASN 3.7 1.6 + - - -
1791A ALA 4.7 3.1 - - - -
1793A PRO* 4.5 4.9 - - - -
1901A 7B8 5.3 0.7 + - - -
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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