Contacts of the helix formed by residues 2347 - 2354 (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 ASP2347 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2343B ILE* 2.9 21.1 + - + +
2346B GLU* 1.3 85.6 - - - +
2348B TYR* 1.3 59.3 + - - +
2349B VAL 3.6 0.2 - - - -
2350B GLN* 3.6 1.2 - - - +
2351B HIS* 3.0 31.4 + - - +
2562B ALA 4.5 0.5 - - - +
2563B SER* 3.1 17.5 - - - -
2564B ILE* 2.8 37.6 + - + +
2580B PHE* 3.7 19.8 - - + -
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Residues in contact with TYR2348 (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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2701 ACD 5.2 4.7 - - + -
2198B PHE* 3.4 32.9 - + - -
2201B PHE* 3.6 33.2 - + + -
2202B ALA* 3.0 32.4 - - + +
2205B PHE* 5.1 5.4 - + - -
2343B ILE 3.0 5.2 + - - -
2344B VAL* 3.2 34.5 - - + +
2347B ASP* 1.3 78.7 - - - +
2349B VAL* 1.3 70.6 + - + +
2351B HIS* 3.4 3.3 - - - +
2352B LEU* 3.1 36.8 + - + +
2385B TYR* 2.5 31.5 + - - -
2387B TRP* 3.7 3.0 - + - -
2580B PHE* 3.4 16.4 - + + -
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Residues in contact with VAL2349 (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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2701 ACD 4.0 29.2 - - + -
2344B VAL* 2.7 38.9 + - + +
2345B ILE* 3.7 10.3 - - + +
2348B TYR* 1.3 78.2 - - + +
2350B GLN* 1.3 68.1 + - - +
2352B LEU* 3.1 9.6 + - + +
2353B SER* 2.7 23.4 + - - -
2359B LEU* 3.5 19.7 - - + -
2530B SER* 4.6 13.2 - - - +
2534B LEU* 5.0 2.0 - - + -
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Residues in contact with GLN2350 (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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2345B ILE 3.2 5.3 + - - +
2346B GLU 3.0 31.9 - - - +
2347B ASP* 3.6 2.9 - - - +
2349B VAL* 1.3 76.8 - - - +
2351B HIS* 1.3 63.7 + - - +
2353B SER* 2.7 24.4 + - - -
2354B GLY* 3.3 3.8 + - - -
2355B TYR* 3.3 19.8 + - - +
2356B HIS 5.0 0.6 - - - -
2357B PHE 3.1 19.1 + - - -
2358B LYS* 3.5 9.5 - - + +
2359B LEU* 2.6 45.0 + - - +
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Residues in contact with HIS2351 (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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2190B ASP* 4.6 0.2 + - - -
2192B GLN* 3.2 46.1 + - + +
2194B SER* 2.8 32.2 + - - -
2198B PHE* 3.8 24.7 - + - -
2347B ASP 3.0 19.0 + - - +
2348B TYR 3.4 3.4 - - - +
2350B GLN* 1.3 79.2 - - - +
2352B LEU* 1.3 69.8 + - + +
2353B SER 3.2 0.9 + - - -
2354B GLY* 3.3 5.4 + - - -
2580B PHE* 3.6 16.8 + - + -
2581B ASN* 3.5 33.5 + - + +
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Residues in contact with LEU2352 (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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2701 ACD 5.0 15.4 - - + +
2192B GLN* 3.2 19.3 + - - +
2194B SER* 4.8 2.9 - - - +
2198B PHE* 3.2 45.1 - - + -
2348B TYR* 3.1 27.5 + - + +
2349B VAL* 3.5 11.4 - - + +
2351B HIS* 1.3 85.9 - - + +
2353B SER* 1.3 63.7 + - - +
2387B TRP* 3.9 15.0 - - + -
2517B ILE* 4.3 15.7 - - + +
2518B PHE* 3.8 29.5 - - + -
2523B VAL* 6.1 0.3 - - - +
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Residues in contact with SER2353 (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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2701 ACD 4.3 18.4 - - - +
2090B HIS* 4.0 14.7 - - - -
2192B GLN* 4.7 1.9 + - - +
2349B VAL 2.7 18.8 + - - -
2350B GLN* 2.7 21.5 + - - -
2351B HIS 3.2 0.2 - - - -
2352B LEU* 1.3 75.7 - - - +
2354B GLY* 1.3 60.3 + - - +
2355B TYR* 2.9 57.3 + - - +
2359B LEU* 4.4 2.8 - - - +
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Residues in contact with GLY2354 (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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2094B THR* 3.3 20.5 - - - +
2192B GLN* 4.1 10.8 - - - -
2350B GLN 3.3 2.5 + - - -
2351B HIS 3.3 14.2 + - - -
2353B SER* 1.3 78.8 + - - +
2355B TYR* 1.3 64.7 + - - +
2356B HIS* 3.8 6.4 + - - -
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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