Contacts of the helix formed by residues 2138 - 2144 (chain B) in PDB entry 1DCX
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A GLN* 3.6 26.2 - - - -
334A LEU* 4.3 11.8 - - - +
544A TYR* 4.6 4.1 + - - -
2134B TYR* 3.2 29.6 - - - -
2136B TYR* 3.4 2.4 + - - -
2137B LYS* 1.3 77.1 - - - +
2139B TRP* 1.3 63.0 + - - +
2140B GLU 3.5 1.2 + - - -
2141B ALA* 3.0 23.5 + - - +
2142B PHE* 3.1 22.2 + - - +
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Residues in contact with TRP2139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A GLY* 5.6 7.4 - - - -
228A VAL 5.1 0.2 - - - -
229A ASP* 3.3 28.9 + - + +
330A GLN* 3.7 6.2 + - - +
333A ARG* 3.0 55.8 - - + +
334A LEU* 4.0 16.8 - - + +
337A ILE* 3.4 20.4 - - + -
537A ASN* 3.8 24.2 - - - -
538A PRO* 3.5 26.2 - - + -
539A ILE* 4.6 2.2 - - + -
544A TYR* 6.3 1.3 - + - -
2138B SER* 1.3 71.1 - - - +
2140B GLU* 1.3 55.8 + - - +
2142B PHE* 3.7 32.3 - + + -
2143B SER* 2.5 56.5 + - - -
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Residues in contact with GLU2140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A LEU* 4.0 25.1 - - - +
241A GLN* 4.8 6.3 + - - +
330A GLN* 3.7 15.8 + - - +
2134B TYR* 3.4 39.5 - - + +
2138B SER* 3.1 1.5 + - - +
2139B TRP* 1.3 78.0 - - - +
2141B ALA* 1.3 65.9 + - - +
2143B SER* 3.9 4.9 + - - -
2144B ASN* 2.8 61.9 + - - +
2147B TYR* 4.0 5.4 + - + +
2671F NAG 3.3 13.3 + - - +
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Residues in contact with ALA2141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2128B PRO* 5.8 1.0 - - - +
2129B THR 3.3 24.4 - - - +
2130B TYR 5.7 0.2 - - - +
2131B ASN* 3.5 28.6 - - - +
2134B TYR* 3.9 17.0 - - + -
2136B TYR 4.8 0.7 - - - +
2138B SER* 3.0 24.6 + - - +
2140B GLU* 1.3 77.7 - - - +
2142B PHE* 1.3 64.4 + - - +
2144B ASN 4.1 5.7 + - - +
2147B TYR* 5.6 1.0 - - - +
2376B ARG* 3.9 8.8 + - - -
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Residues in contact with PHE2142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A GLY 6.2 0.2 - - - -
373A TYR 6.0 1.8 - - - -
538A PRO* 3.5 40.2 - - + -
544A TYR* 3.6 23.3 - - + +
2127B PRO* 4.2 12.3 - - + -
2128B PRO* 4.3 10.3 - - + -
2129B THR 4.5 0.4 + - - -
2138B SER 3.1 14.2 + - - +
2139B TRP* 3.7 37.5 - + + +
2141B ALA* 1.3 78.4 - - - +
2143B SER* 1.3 66.7 + - - +
2145B LEU* 4.8 0.2 - - - +
2374B GLN* 5.2 2.7 - - - -
2376B ARG* 2.7 54.6 + - - +
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Residues in contact with SER2143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2139B TRP* 2.5 54.5 + - - -
2140B GLU* 3.7 6.6 + - - -
2142B PHE* 1.3 84.0 - - - +
2144B ASN* 1.3 60.6 + - - +
2145B LEU* 3.0 19.9 + - - +
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Residues in contact with ASN2144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2140B GLU* 2.8 34.0 + - - +
2141B ALA 4.3 2.9 - - - +
2142B PHE 3.5 0.8 - - - -
2143B SER* 1.3 74.7 + - - +
2145B LEU* 1.3 59.0 + - - +
2146B SER* 3.0 24.8 + - - -
2147B TYR* 3.5 27.1 + - + +
2376B ARG* 4.2 7.7 + - - -
2671F NAG 1.4 69.7 + - - +
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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