Contacts of the helix formed by residues 2217 - 2224 (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 CYS2217 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2157C ARG 3.3 27.4 - - - -
2158C VAL* 4.4 9.2 - - - +
2159C SER 3.6 8.5 - - - -
2160C THR* 4.5 1.8 - - + +
2215C GLN 3.8 1.8 + - - -
2216C GLU* 1.3 75.8 - - - +
2218C VAL* 1.3 68.5 + - - +
2219C PHE* 4.0 2.5 - - - -
2220C GLN* 3.2 38.7 + - + +
2221C ALA* 3.2 19.6 + - - +
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Residues in contact with VAL2218 (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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2137C PHE* 3.9 15.7 - - + -
2139C VAL* 4.5 6.5 - - + -
2159C SER 3.2 9.1 + - - +
2160C THR 3.7 1.1 - - - +
2161C ALA* 3.6 33.4 - - - +
2164C VAL* 3.7 22.2 - - + -
2189C LEU* 4.0 11.0 - - + -
2212C LEU* 4.0 12.1 - - + -
2217C CYS* 1.3 71.2 - - - +
2219C PHE* 1.3 57.5 + - - +
2221C ALA* 3.0 4.5 + - - +
2222C GLN* 2.9 26.3 + - - +
2231C PHE* 3.7 32.5 - - + -
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Residues in contact with PHE2219 (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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2137C PHE* 3.7 43.3 - + + -
2157C ARG* 3.4 72.0 - - + +
2159C SER 4.7 0.4 + - - -
2217C CYS* 3.4 2.8 - - - -
2218C VAL* 1.3 77.7 - - - +
2220C GLN* 1.3 71.3 + - - +
2222C GLN* 3.9 9.6 - - - +
2223C SER* 2.8 48.7 + - - -
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Residues in contact with GLN2220 (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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2217C CYS* 3.2 34.2 + - + +
2219C PHE* 1.3 82.9 - - + +
2221C ALA* 1.3 63.1 + - - +
2223C SER* 3.4 8.1 + - - -
2224C LYS* 3.3 44.6 + - - +
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Residues in contact with ALA2221 (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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2191C GLU* 3.7 19.6 - - - +
2210C ARG* 3.8 19.5 - - - +
2212C LEU* 4.4 6.5 - - + -
2216C GLU* 3.8 10.5 - - - +
2217C CYS 3.2 7.2 + - - +
2218C VAL 3.0 10.1 + - - +
2220C GLN* 1.3 75.6 - - - +
2222C GLN* 1.3 62.5 + - - +
2224C LYS* 3.2 21.6 + - - +
2225C TRP* 3.4 14.0 - - - -
2231C PHE* 4.4 7.2 - - + -
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Residues in contact with GLN2222 (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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2137C PHE* 3.4 27.6 - - - +
2138C PHE 3.7 19.4 + - - +
2139C VAL* 4.2 6.1 - - - +
2140C GLN 5.5 0.2 - - - +
2218C VAL 2.9 14.9 + - - +
2219C PHE* 3.9 14.0 - - - +
2221C ALA* 1.3 75.6 - - - +
2223C SER* 1.3 62.5 + - - +
2225C TRP* 3.3 56.0 + - + +
2231C PHE* 3.9 18.8 - - + -
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Residues in contact with SER2223 (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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2219C PHE* 2.8 48.3 + - - -
2220C GLN* 3.7 9.9 - - - -
2221C ALA 3.3 0.2 - - - -
2222C GLN* 1.3 75.5 + - - +
2224C LYS* 1.3 59.7 + - - +
2225C TRP 3.4 3.9 + - - +
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Residues in contact with LYS2224 (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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2220C GLN* 3.3 33.3 + - - +
2221C ALA* 3.2 13.2 + - - +
2223C SER* 1.3 77.2 - - - +
2225C TRP* 1.3 64.0 + - - +
2226C LYS* 3.5 16.1 + - - +
3240C GOL 5.4 8.7 + - - -
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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