Contacts of the helix formed by residues 255 - 259 (chain A) in PDB entry 3DLX
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 ALA 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A ALA 4.2 1.4 + - - -
254A PHE* 1.3 73.4 - - - +
256A PRO* 1.3 75.0 - - + +
257A GLU* 4.2 7.9 - - - +
258A ASP* 3.0 42.2 + - - +
259A ILE* 3.7 7.8 - - - +
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Residues in contact with PRO 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A PHE 3.4 4.2 - - - +
255A ALA* 1.3 84.8 - - + +
257A GLU* 1.3 72.8 + - - +
258A ASP 3.4 0.5 + - - -
259A ILE* 4.1 5.4 + - + -
373B ILE* 4.0 15.3 - - + -
377B ALA 3.4 28.9 - - - +
378B SER* 3.3 6.6 - - - -
379B PHE* 3.0 49.2 + - + +
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Residues in contact with GLU 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A ALA* 3.1 5.2 - - - +
256A PRO* 1.3 93.6 - - - +
258A ASP* 1.3 64.3 + - - +
259A ILE 3.6 2.6 + - - +
213B TRP* 4.5 11.1 - - + -
223B PHE 3.6 19.3 - - - +
224B ARG* 3.8 7.3 - - - +
225B LYS* 2.8 37.6 + - - +
228B ARG* 3.0 35.2 + - - +
260B HIS* 3.2 19.3 + - + -
379B PHE* 4.0 14.2 - - + +
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Residues in contact with ASP 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ILE* 3.5 18.5 - - - +
254A PHE* 4.9 2.2 - - + +
255A ALA* 3.0 34.9 + - + +
257A GLU* 1.3 87.8 - - - +
259A ILE* 1.3 60.5 - - - +
260A HIS* 3.6 12.0 + - - -
258B ASP* 3.5 40.2 - - - +
260B HIS* 3.4 15.3 + - - -
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Residues in contact with ILE 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ASP* 4.8 0.7 - - - +
220A ASN* 3.6 34.1 - - + +
221A VAL 4.3 3.1 - - - +
222A ILE* 4.4 1.3 - - - -
254A PHE* 3.7 33.7 - - + +
255A ALA 3.7 10.3 - - - +
256A PRO* 4.1 3.3 + - + +
257A GLU 3.6 3.5 - - - +
258A ASP* 1.3 76.2 - - - +
260A HIS* 1.3 62.7 + - - +
261A ILE 3.4 26.9 - - - +
262A PRO* 3.8 9.9 - - + +
376B GLY* 4.6 1.3 - - - +
377B ALA 3.2 27.1 - - - +
378B SER* 3.8 17.0 - - - -
379B PHE 4.9 7.8 - - - +
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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