Contacts of the helix formed by residues 2497 - 2501 (chain C) in PDB entry 1PXX
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 ASP2497 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2166C LYS* 4.1 19.1 - - - +
2167C GLY* 5.1 3.1 + - - +
2478C PHE* 3.2 12.7 - - - -
2495C TYR* 3.0 4.9 + - - +
2496C SER* 1.3 79.1 - - - +
2498C ILE* 1.3 75.4 + - - +
2499C ASP* 3.1 29.0 + - - +
2500C VAL* 3.3 31.5 + - + +
2501C MET 3.6 2.4 + - - -
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Residues in contact with ILE2498 (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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2463C LEU* 4.9 2.4 - - + +
2464C ASN* 4.0 9.1 + - - +
2475C TYR* 3.4 37.2 - - + +
2476C THR* 3.8 15.7 - - - +
2477C SER* 3.8 27.6 - - - +
2478C PHE* 3.6 36.8 - - + -
2481C LEU* 4.3 11.9 - - + -
2496C SER 4.1 0.4 + - - -
2497C ASP* 1.3 72.6 + - - +
2499C ASP* 1.3 69.3 + - - +
2500C VAL 3.0 9.4 + - - -
2501C MET* 3.1 27.8 + - + +
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Residues in contact with ASP2499 (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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2163C MET* 5.1 2.1 - - - +
2166C LYS* 3.4 40.0 + - + +
2462C SER* 3.6 19.4 + - - -
2464C ASN* 3.1 28.5 - - + +
2474C PRO* 5.2 2.4 - - - +
2475C TYR 4.3 1.6 - - - +
2497C ASP* 3.1 19.3 + - - +
2498C ILE* 1.3 84.7 - - - +
2500C VAL* 1.3 60.9 + - - +
2501C MET 3.5 0.2 - - - -
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Residues in contact with VAL2500 (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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2163C MET* 4.0 16.6 - - + +
2166C LYS* 3.8 11.2 - - + +
2167C GLY* 3.6 37.2 - - - +
2168C ASN 5.7 0.2 - - - +
2171C LEU* 3.8 24.2 - - + -
2172C PRO* 5.5 0.7 - - + -
2462C SER* 4.5 4.0 - - - -
2495C TYR* 3.9 23.3 - - + +
2497C ASP* 3.3 26.2 + - + +
2498C ILE 3.0 0.6 - - - -
2499C ASP* 1.3 81.1 - - - +
2501C MET* 1.3 69.1 + - - +
2502C GLU* 3.4 6.1 + - - +
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Residues in contact with MET2501 (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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2462C SER* 3.6 3.5 - - - -
2463C LEU* 2.9 47.5 + - + -
2478C PHE* 4.3 6.7 - - + -
2481C LEU* 3.7 19.3 - - + -
2491C LEU* 4.0 23.6 - - + -
2495C TYR* 3.5 29.8 - - - -
2497C ASP 3.6 3.0 + - - -
2498C ILE* 3.1 26.4 + - + +
2500C VAL* 1.3 81.1 - - - +
2502C GLU* 1.3 68.4 + - - +
2505C PRO* 4.4 6.5 - - + -
2506C ALA* 3.5 33.9 - - + +
2509C VAL* 4.8 1.3 - - + -
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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