Contacts of the helix formed by residues 2108 - 2113 (chain A) in PDB entry 4YNP
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 CYS2108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2091A CYS* 3.5 7.4 - - - -
2093A CYS* 3.7 12.9 - - - -
2104A CYS* 3.6 13.2 - - + -
2105A VAL 3.3 17.5 + - - +
2106A ASP 3.4 0.2 - - - -
2107A ASP* 1.3 75.2 - - - +
2109A LEU* 1.3 68.0 + - - +
2110A ASN 3.9 9.4 - - - -
2111A ARG* 3.3 14.2 + - + +
2112A MET* 3.1 24.6 + - - +
2117A CYS* 4.1 7.4 - - - -
2130A ASN* 4.3 2.5 - - - -
2303A ZN 2.1 37.7 - - - -
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Residues in contact with LEU2109 (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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2090A THR 4.6 7.2 - - - +
2091A CYS 3.4 28.5 + - - +
2092A ASN* 5.1 5.4 - - + -
2093A CYS* 5.4 3.1 - - + +
2107A ASP 4.1 9.6 - - - +
2108A CYS* 1.3 73.2 - - - +
2110A ASN* 1.3 64.5 + - - +
2112A MET* 3.3 18.8 + - - +
2113A ILE* 3.5 13.3 + - - +
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Residues in contact with ASN2110 (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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2088A ALA 4.9 0.6 + - - -
2089A THR* 3.4 51.5 - - - +
2090A THR 3.8 14.2 + - - +
2091A CYS* 4.1 1.8 + - - -
2108A CYS* 3.3 3.7 - - - -
2109A LEU* 1.3 73.3 - - - +
2111A ARG* 1.3 60.8 + - - +
2112A MET 3.1 1.8 - - - -
2113A ILE* 3.2 18.3 + - - +
2115A ALA* 2.8 46.5 + - + +
2117A CYS* 3.7 20.4 - - - +
2130A ASN* 3.8 9.2 - - - +
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Residues in contact with ARG2111 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2104A CYS 3.4 16.3 + - - -
2105A VAL* 3.3 28.3 + - - -
2106A ASP* 4.3 9.7 + - - +
2108A CYS* 3.3 17.0 + - + +
2110A ASN* 1.3 79.0 - - - +
2112A MET* 1.3 71.4 + - + +
2114A PHE* 3.2 10.7 + - - +
2115A ALA 3.6 6.0 + - - -
2129A CYS* 2.8 36.4 + - - -
2130A ASN* 3.7 19.0 + - - +
2132A ARG* 3.1 35.4 - - - +
2163A GLY 5.8 0.2 + - - -
2229A TRP* 4.2 5.7 - - + -
2073B ARG* 3.2 38.9 + - - +
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Residues in contact with MET2112 (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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2106A ASP* 3.1 30.7 - - + +
2107A ASP 4.2 6.7 - - - +
2108A CYS 3.1 16.8 + - - +
2109A LEU* 3.5 11.4 - - - +
2110A ASN 3.1 0.8 - - - -
2111A ARG* 1.3 99.6 - - + +
2113A ILE* 1.3 59.2 + - + +
2114A PHE* 3.3 1.3 + - - -
2072B ILE* 3.3 5.7 - - - +
2073B ARG* 2.7 59.6 + - - +
2074B SER* 3.8 29.6 + - - +
2076B VAL* 6.3 0.7 - - + -
2136B HIS* 5.3 7.6 - - - -
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Residues in contact with ILE2113 (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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2086A TYR* 3.7 45.1 + - + -
2089A THR* 5.6 1.6 - - + -
2109A LEU 3.5 11.6 + - - +
2110A ASN* 3.4 20.6 - - - +
2112A MET* 1.3 77.8 - - + +
2114A PHE* 1.3 68.5 + - - +
2115A ALA* 3.8 8.7 - - + -
2070B LYS* 5.4 3.1 - - - +
2071B LYS 3.9 5.7 - - - +
2072B ILE* 3.7 14.1 - - + -
2076B VAL* 3.7 30.3 - - + -
2209B MET* 4.2 12.1 - - + -
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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