Contacts of the strand formed by residues 2229 - 2235 (chain C) in PDB entry 2C5L
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 GLY2229 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2192C GLU 3.1 10.8 - - - -
2193C VAL* 4.2 2.5 - - - -
2225C TRP* 3.4 34.0 - - - -
2227C GLY 3.6 2.6 + - - -
2228C ALA* 1.3 74.8 - - - +
2230C LYS* 1.3 63.7 + - - +
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Residues in contact with LYS2230 (chain C).
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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2140C GLN 5.5 0.2 - - - -
2142C HIS* 3.9 43.2 + - + +
2143C ASP* 5.7 2.8 + - - -
2190C LEU 3.6 0.7 - - - +
2191C GLU* 3.3 5.0 - - - +
2192C GLU* 2.9 64.7 + - + +
2225C TRP* 3.6 7.4 - - - -
2229C GLY* 1.3 74.8 - - - +
2231C PHE* 1.3 63.0 + - - +
2232C ILE* 4.0 22.6 - - + +
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Residues in contact with PHE2231 (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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2139C VAL* 3.5 21.5 - - + -
2140C GLN 4.0 12.8 + - - +
2141C VAL* 3.7 4.2 - - + -
2142C HIS* 2.9 29.6 + - - -
2189C LEU* 4.5 19.7 - - + -
2190C LEU 3.2 8.1 - - - +
2191C GLU* 3.8 31.2 - - + -
2212C LEU* 3.9 26.0 - - + -
2218C VAL* 3.7 34.8 - - + -
2221C ALA* 4.5 0.4 - - + -
2222C GLN* 3.9 23.3 - - + -
2225C TRP* 3.5 27.8 - + - -
2230C LYS* 1.3 73.0 - - - +
2232C ILE* 1.3 61.7 + - - +
2233C LEU 4.3 0.2 - - - -
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Residues in contact with ILE2232 (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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2142C HIS* 3.6 11.0 - - + -
2143C ASP* 3.6 28.3 - - + +
2188C VAL 3.7 0.5 - - - +
2189C LEU* 3.4 7.2 - - - -
2190C LEU* 2.7 47.1 + - + +
2192C GLU* 3.8 34.3 - - + +
2209C GLN* 4.0 11.0 - - - +
2230C LYS* 4.0 19.7 - - + +
2231C PHE* 1.3 76.3 - - - +
2233C LEU* 1.3 68.4 + - - +
2234C LYS* 3.7 27.7 + - + +
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Residues in contact with LEU2233 (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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2141C VAL* 3.8 16.6 - - + +
2142C HIS 3.0 11.0 + - - +
2143C ASP* 3.6 14.2 - - - +
2144C VAL* 4.0 26.7 - - + +
2165C ILE* 4.1 22.2 - - + -
2168C THR* 4.2 16.4 - - + -
2169C LEU* 4.0 17.9 - - + -
2178C ILE* 4.9 0.9 - - + -
2187C TYR* 3.7 37.2 - - + -
2188C VAL 3.7 14.6 - - - +
2189C LEU* 4.2 7.4 - - + -
2232C ILE* 1.3 74.6 - - - +
2234C LYS* 1.3 66.5 + - - +
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Residues in contact with LYS2234 (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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2143C ASP* 4.6 8.2 + - - -
2187C TYR* 3.3 9.2 - - - +
2188C VAL* 2.9 45.2 + - + +
2190C LEU* 4.0 22.5 - - + +
2209C GLN* 5.3 9.3 + - - +
2232C ILE* 3.7 25.3 + - + +
2233C LEU* 1.3 78.1 - - - +
2235C LEU* 1.3 67.8 + - - +
2238C GLN* 4.0 28.0 - - + +
2239C VAL* 5.5 3.1 - - + +
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Residues in contact with LEU2235 (chain C).
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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2181C ASN* 4.4 23.1 - - + +
2186C ASP* 3.5 22.0 - - + +
2187C TYR* 3.6 34.4 - - + +
2188C VAL* 4.8 0.2 - - - -
2234C LYS* 1.3 77.0 - - - +
2236C LYS* 1.3 65.5 + - - +
2237C GLU* 3.8 29.2 - - + +
2238C GLN* 2.9 43.8 + - + +
2239C VAL* 3.3 8.5 + - - +
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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