Contacts of the helix formed by residues 346 - 353 (chain B) in PDB entry 2XFN
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 346 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170B ASN* 4.8 6.1 - - - +
174B THR 3.9 6.4 + - - -
175B ALA* 3.8 34.8 - - - +
176B GLU* 3.2 16.4 - - + +
293B SER* 2.8 28.4 + - - -
345B LEU* 1.3 74.8 - - + +
347B HIS* 1.3 65.7 + - - +
349B ALA* 2.9 17.5 + - - +
350B ARG* 3.5 13.6 + - - +
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Residues in contact with HIS 347 (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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409A GLN* 3.6 25.5 - - - +
170B ASN* 6.1 0.7 - - - -
176B GLU* 2.6 41.7 + - + +
320B GLU* 2.6 43.4 + - - -
345B LEU 3.3 1.0 + - - -
346B ALA* 1.3 71.9 - - - +
348B LYS* 1.3 77.7 + - + +
350B ARG* 3.2 20.2 + - - +
351B LYS* 2.8 35.9 + - + +
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Residues in contact with LYS 348 (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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317B ILE 5.6 0.2 + - - -
319B GLY 2.9 20.8 + - - -
320B GLU* 3.4 33.9 - - - +
322B ALA* 2.8 28.1 + - - +
323B PRO* 3.7 10.9 - - + +
325B ALA* 5.0 13.6 - - + +
344B ILE* 3.4 15.7 - - + +
345B LEU* 3.0 15.6 + - + +
347B HIS* 1.3 93.3 - - + +
349B ALA* 1.3 60.3 + - - +
351B LYS* 4.1 14.8 - - - +
352B LEU* 2.9 37.2 + - + +
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Residues in contact with ALA 349 (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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280A MET* 5.1 2.2 - - - -
293B SER* 4.0 5.4 - - - -
294B VAL* 3.9 20.4 - - - +
295B ILE* 3.8 17.4 - - + +
344B ILE* 3.6 28.7 - - - +
345B LEU 3.7 1.6 + - - -
346B ALA 2.9 11.6 + - - +
348B LYS* 1.3 76.6 - - - +
350B ARG* 1.3 63.9 + - - +
353B ALA* 3.1 27.0 + - - +
387B ASN* 4.5 1.0 + - - -
389B CYS* 4.3 4.7 - - - -
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Residues in contact with ARG 350 (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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280A MET* 4.6 4.7 - - - -
281A MET* 4.1 26.3 - - + +
284A GLN* 4.8 2.5 - - - +
288A ARG* 4.0 7.3 - - - +
409A GLN* 2.6 37.7 + - - +
410A TYR* 3.0 38.3 + - - +
174B THR 5.2 0.8 + - - -
176B GLU* 4.1 4.6 - - - +
179B GLU* 3.0 31.5 + - - -
293B SER* 2.9 40.4 + - - +
346B ALA* 3.9 7.5 - - - +
347B HIS* 3.2 29.9 + - - +
349B ALA* 1.3 80.5 - - - +
351B LYS* 1.3 62.4 + - - +
353B ALA* 3.7 9.5 + - - +
354B ARG* 4.4 8.3 + - - +
389B CYS* 5.1 2.7 - - - -
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Residues in contact with LYS 351 (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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320B GLU* 3.2 40.8 + - - +
321B GLU* 5.3 3.6 + - - +
347B HIS* 2.8 23.0 + - + +
348B LYS* 3.9 13.5 - - - +
350B ARG* 1.3 78.6 - - - +
352B LEU* 1.3 85.0 + - + +
353B ALA 3.5 0.2 + - - -
354B ARG* 3.2 41.0 + - - +
355B LEU* 5.3 1.6 - - - +
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Residues in contact with LEU 352 (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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295B ILE* 4.7 0.9 - - + -
323B PRO* 3.6 35.2 - - + +
344B ILE* 3.9 17.9 - - + -
348B LYS* 2.9 21.6 + - + +
349B ALA 4.0 0.4 - - - +
351B LYS* 1.3 100.3 - - + +
353B ALA* 1.3 61.1 + - - +
354B ARG 3.1 3.1 - - - -
355B LEU* 3.2 36.0 + - + +
360B ARG* 2.8 32.5 + - + -
363B LYS* 4.7 10.3 - - + -
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Residues in contact with ALA 353 (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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280A MET* 3.3 38.0 - - + +
295B ILE* 4.4 3.6 - - - +
349B ALA 3.1 19.8 + - - +
350B ARG 3.9 5.2 - - - +
351B LYS 3.3 1.0 - - - -
352B LEU* 1.3 77.0 - - - +
354B ARG* 1.3 61.1 + - - +
355B LEU 3.3 9.2 + - - +
360B ARG* 3.5 8.7 + - - +
387B ASN* 3.5 9.0 - - - +
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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