Contacts of the helix formed by residues 2138 - 2144 (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 SER2138 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2134C TYR* 3.3 20.3 - - - -
2136C TYR* 3.4 21.2 + - - -
2137C LYS* 1.3 76.4 - - - +
2139C TRP* 1.3 64.5 + - - +
2140C GLU 3.7 0.9 + - - -
2141C ALA* 3.1 22.9 + - - +
2142C PHE* 3.0 22.5 + - - +
3330D GLN* 3.5 18.6 - - - -
3334D LEU* 4.2 11.9 - - - -
3544D TYR* 4.5 3.0 + - - -
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Residues in contact with TRP2139 (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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2138C SER* 1.3 71.7 - - - +
2140C GLU* 1.3 56.0 + - - +
2142C PHE* 3.6 31.9 - + + +
2143C SER* 2.5 62.0 + - - -
3225D GLY* 5.7 6.5 - - - -
3228D VAL 5.1 0.2 - - - -
3229D ASP* 3.4 32.1 + - + +
3330D GLN* 3.7 5.4 + - - +
3333D ARG* 3.7 42.8 - - + +
3334D LEU* 4.1 19.2 - - + +
3337D ILE* 3.6 22.2 - - + -
3537D ASN* 3.5 27.6 - - - -
3538D PRO* 3.5 21.8 - - + -
3539D ILE* 4.6 2.9 - - + -
3544D TYR* 6.5 0.9 - + - -
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Residues in contact with GLU2140 (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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2134C TYR* 3.5 29.6 - - + +
2138C SER* 3.2 4.0 - - - +
2139C TRP* 1.3 81.4 - - - +
2141C ALA* 1.3 56.3 - - - +
2143C SER* 3.9 5.4 + - - -
2144C ASN* 2.8 70.5 + - - +
2147C TYR* 3.9 5.8 + - + +
3238D LEU* 4.4 25.4 - - + +
3241D GLN* 4.7 4.7 - - - +
3330D GLN* 3.7 24.4 + - - +
3333D ARG* 5.8 0.4 - - - +
1G NAG 3.7 7.7 + - - +
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Residues in contact with ALA2141 (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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2128C PRO* 5.9 0.5 - - - +
2129C THR 3.4 22.7 - - - +
2130C TYR* 4.8 0.7 - - - -
2131C ASN* 3.6 28.2 - - - +
2134C TYR* 4.0 15.0 - - + -
2136C TYR 5.0 0.2 - - - +
2138C SER* 3.1 23.4 + - - +
2140C GLU* 1.3 82.8 - - - +
2142C PHE* 1.3 63.6 + - - +
2143C SER 3.4 0.2 + - - -
2144C ASN 3.8 12.0 + - - +
2147C TYR* 5.2 0.9 - - - +
2376C ARG* 4.1 3.6 + - - -
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Residues in contact with PHE2142 (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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2127C PRO* 4.0 19.3 - - + -
2128C PRO* 4.3 13.0 - - + -
2129C THR 4.4 1.5 + - - -
2138C SER 3.0 11.4 + - - +
2139C TRP* 3.6 44.9 - + + +
2141C ALA* 1.3 80.1 - - - +
2143C SER* 1.3 63.4 + - - +
2374C GLN* 5.3 3.4 - - - -
2376C ARG* 2.3 38.3 + - - +
3373D TYR 6.0 0.7 - - - -
3538D PRO* 3.6 33.9 - - + -
3544D TYR* 3.3 23.6 - - + +
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Residues in contact with SER2143 (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 TRP* 2.5 59.5 + - - -
2140C GLU* 3.7 6.6 + - - -
2142C PHE* 1.3 79.9 - - - +
2144C ASN* 1.3 61.8 + - - +
2145C LEU* 3.1 19.6 + - - +
2376C ARG* 4.3 0.7 - - - -
1G NAG 6.1 0.2 - - - +
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Residues in contact with ASN2144 (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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2140C GLU* 2.8 34.0 + - - +
2141C ALA 3.9 7.1 - - - +
2142C PHE 3.7 0.2 - - - -
2143C SER* 1.3 74.6 + - - +
2145C LEU* 1.3 63.1 + - - +
2146C SER* 2.9 19.9 + - - -
2147C TYR* 3.6 27.0 + - + +
2376C ARG* 4.4 4.7 + - - -
1G NAG 1.4 69.8 + - - +
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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