Contacts of the strand formed by residues 2143 - 2147 (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 GLU2143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2141A CYS 4.0 1.3 - - - +
2142A LEU* 1.3 76.0 - - - +
2144A ARG* 1.3 72.8 + - - +
2145A PHE* 3.7 3.1 + - - -
2154A ILE* 3.4 7.4 - - - +
2155A ARG* 3.0 69.6 + - + +
2157A LYS* 3.5 41.7 + - + +
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Residues in contact with ARG2144 (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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2068A SER 5.9 2.0 - - - +
2069A TYR* 3.6 13.5 + - - -
2143A GLU* 1.3 81.0 - - - +
2145A PHE* 1.3 63.0 + - - +
2152A TRP* 4.5 25.1 - - + -
2153A GLY 3.4 10.8 - - - +
2154A ILE* 3.9 3.5 - - + +
2212A GLU* 3.0 42.5 + - - +
2215A PHE* 3.4 40.1 - - + -
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Residues in contact with PHE2145 (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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2143A GLU* 3.7 7.2 - - - -
2144A ARG* 1.3 76.4 - - - +
2146A ARG* 1.3 68.1 + - - +
2147A ALA* 3.0 21.7 + - + -
2148A GLU* 5.3 0.9 - - + -
2152A TRP* 3.3 14.4 - - - -
2153A GLY 2.8 49.1 + - - -
2154A ILE 3.5 30.1 - - - -
2155A ARG* 3.5 56.1 - - + +
2248A GLY 5.8 0.4 - - - -
2250A GLU* 3.8 30.5 - - + -
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Residues in contact with ARG2146 (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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2145A PHE* 1.3 79.3 - - - +
2147A ALA* 1.3 63.8 + - - +
2148A GLU* 3.8 1.2 + - - -
2151A GLY 3.8 6.7 - - - +
2152A TRP* 3.6 34.3 - - + -
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Residues in contact with ALA2147 (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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2145A PHE* 3.0 20.6 + - + -
2146A ARG* 1.3 72.7 - - - +
2148A GLU* 1.3 64.1 + - - +
2149A GLU 3.2 4.0 + - - -
2150A LYS* 4.2 11.9 - - + -
2151A GLY* 2.9 28.1 + - - +
2153A GLY* 3.7 20.9 - - - +
2217A ASN* 4.1 14.4 - - - +
2250A GLU* 4.4 5.6 - - - +
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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