Contacts of the helix formed by residues 346 - 353 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A ASN* 5.0 5.2 - - - +
174A THR 3.8 7.0 + - - -
175A ALA* 3.8 34.5 - - - +
176A GLU* 3.2 16.4 - - + +
293A SER* 2.8 23.4 + - - -
345A LEU* 1.3 75.5 - - + +
347A HIS* 1.3 67.0 + - - +
349A ALA* 3.0 17.3 + - - +
350A ARG* 3.6 16.7 + - - +
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Residues in contact with HIS 347 (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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170A ASN* 6.1 0.7 - - - -
176A GLU* 2.6 43.1 + - + +
320A GLU* 2.7 42.3 + - - -
345A LEU 3.2 1.6 + - - -
346A ALA* 1.3 71.7 - - - +
348A LYS* 1.3 77.6 + - + +
350A ARG* 3.1 20.3 + - - +
351A LYS* 2.8 37.2 + - + +
409B GLN* 3.5 26.0 + - - +
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Residues in contact with LYS 348 (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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317A ILE 5.5 1.0 + - - -
319A GLY 3.1 19.0 + - - +
320A GLU* 3.5 30.2 - - - +
322A ALA* 2.8 30.3 + - - +
323A PRO* 3.7 11.2 - - + +
325A ALA* 5.0 13.4 - - + +
344A ILE* 3.5 15.4 - - + +
345A LEU* 3.0 15.0 + - + +
347A HIS* 1.3 95.5 - - + +
349A ALA* 1.3 60.0 + - - +
351A LYS* 4.1 15.3 - - - +
352A LEU* 2.8 39.2 + - + +
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Residues in contact with ALA 349 (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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293A SER* 3.9 7.0 - - - +
294A VAL* 3.8 23.1 - - - +
295A ILE* 3.8 14.8 - - + +
344A ILE* 3.6 27.6 - - - +
345A LEU 3.7 1.6 + - - -
346A ALA 3.0 11.6 + - - +
348A LYS* 1.3 77.0 - - - +
350A ARG* 1.3 62.6 + - - +
353A ALA* 3.2 26.3 + - - +
387A ASN* 4.3 1.4 + - - -
389A CYS* 4.2 4.9 - - - -
280B MET* 5.0 2.2 - - - -
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Residues in contact with ARG 350 (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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174A THR 5.0 1.4 + - - -
176A GLU* 4.3 3.2 - - - +
179A GLU* 2.9 30.3 + - - -
293A SER* 2.9 33.4 + - - +
346A ALA* 3.6 9.7 + - - +
347A HIS* 3.1 26.3 + - - +
349A ALA* 1.3 80.8 - - - +
351A LYS* 1.3 61.8 + - - +
352A LEU 3.5 0.2 + - - -
353A ALA* 3.6 10.9 + - - +
354A ARG* 4.4 8.3 + - - +
389A CYS* 5.2 0.9 - - - -
280B MET* 4.6 6.1 - - - -
281B MET* 3.6 37.8 - - + +
284B GLN* 4.4 2.9 - - - +
288B ARG* 3.9 8.3 - - - +
409B GLN* 3.0 39.3 + - - +
410B TYR* 3.2 28.8 + - + +
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Residues in contact with LYS 351 (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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320A GLU* 3.1 41.7 + - - +
321A GLU* 5.4 2.4 + - - +
347A HIS* 2.8 26.3 + - + +
348A LYS* 3.3 13.3 + - - +
350A ARG* 1.3 74.3 - - - +
352A LEU* 1.3 85.5 + - + +
353A ALA 3.6 0.3 + - - -
354A ARG* 3.1 47.7 + - - +
355A LEU* 5.3 1.2 - - - +
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Residues in contact with LEU 352 (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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295A ILE* 4.7 1.3 - - + -
323A PRO* 3.5 37.2 - - + -
344A ILE* 4.0 17.3 - - + -
348A LYS* 2.8 26.5 + - + +
349A ALA 4.8 0.4 - - - +
351A LYS* 1.3 99.0 - - + +
353A ALA* 1.3 61.3 + - - +
354A ARG 3.0 3.4 + - - -
355A LEU* 3.2 33.8 + - + +
360A ARG* 2.9 31.5 + - + -
363A LYS* 4.7 12.3 - - + -
364A LEU* 6.0 0.2 - - + -
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Residues in contact with ALA 353 (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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295A ILE* 4.5 2.4 - - - +
349A ALA 3.2 20.5 + - - +
350A ARG 3.8 6.1 - - - +
351A LYS 3.4 1.2 - - - -
352A LEU* 1.3 77.4 - - - +
354A ARG* 1.3 62.5 + - + +
355A LEU 3.4 8.5 - - - +
360A ARG* 3.5 9.3 + - - +
387A ASN* 3.6 8.3 - - - +
280B MET* 3.5 36.7 - - + +
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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