Contacts of the helix formed by residues 331 - 340 (chain A) in PDB entry 2XJF
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 SER 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A PHE* 3.4 30.3 - - - -
297A GLY 4.0 7.9 + - - -
298A GLU 4.0 7.7 + - - -
299A GLY* 3.9 13.0 - - - -
300A THR 5.2 0.2 - - - -
330A GLY* 1.3 75.9 - - - -
332A SER* 1.3 65.8 + - - +
333A ASP* 3.3 21.2 + - - +
334A THR* 3.1 25.4 + - - -
335A ILE 3.6 1.4 + - - -
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Residues in contact with SER 332 (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 PHE* 2.8 27.9 + - - -
296A PHE* 3.7 22.3 - - - -
297A GLY 5.2 0.9 + - - -
331A SER* 1.3 73.4 - - - +
333A ASP* 1.3 64.1 + - - +
335A ILE* 3.2 7.4 + - - +
336A CYS* 3.2 24.0 + - - -
364A GLN* 3.4 29.8 + - - +
366A TRP* 3.6 24.4 - - - -
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Residues in contact with ASP 333 (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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297A GLY 5.1 5.7 - - - +
331A SER* 3.1 11.5 + - - +
332A SER* 1.3 77.5 + - - +
334A THR* 1.3 55.1 + - - +
336A CYS* 3.2 10.4 + - - +
337A ASP* 2.8 50.5 + - - +
364A GLN* 4.0 20.2 + - - +
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Residues in contact with THR 334 (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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285A LEU* 5.0 1.8 - - + -
287A LEU* 4.4 12.1 - - + -
302A LEU* 4.1 27.8 - - + +
327A TYR* 5.5 1.3 - - + -
330A GLY* 4.0 5.7 - - - -
331A SER* 3.1 28.2 + - - -
333A ASP* 1.3 75.9 - - - +
335A ILE* 1.3 62.3 + - + +
337A ASP* 3.8 5.3 - - - +
338A LEU* 2.9 58.9 + - + +
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Residues in contact with ILE 335 (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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246A PHE* 3.6 56.8 - - + -
248A ALA* 3.9 10.5 - - + -
285A LEU* 4.0 24.5 - - + -
287A LEU* 4.5 7.4 - - + -
295A PHE* 3.6 32.1 - - + -
331A SER 4.4 0.7 - - - +
332A SER 3.2 9.7 + - - +
334A THR* 1.3 81.6 - - + +
336A CYS* 1.3 59.1 + - - +
339A LEU* 2.9 40.2 + - + +
341A ALA* 5.3 0.4 - - + +
346A ILE* 4.8 4.3 - - + -
366A TRP* 4.5 9.2 - - + -
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Residues in contact with CYS 336 (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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332A SER 3.2 15.1 + - - +
333A ASP* 3.7 13.7 - - - +
335A ILE* 1.3 72.4 - - - +
337A ASP* 1.3 64.0 + - - +
340A GLY* 2.9 25.1 + - - -
341A ALA* 3.0 32.5 + - - +
343A GLY 4.8 4.9 - - - -
346A ILE* 3.8 26.2 - - - -
364A GLN* 6.0 2.0 - - - -
366A TRP* 4.0 13.9 - - - -
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Residues in contact with ASP 337 (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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333A ASP* 2.8 32.7 + - - +
334A THR* 3.8 5.7 + - - +
336A CYS* 1.3 79.1 - - - +
338A LEU* 1.3 66.9 + - + +
340A GLY* 3.2 9.2 + - - -
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Residues in contact with LEU 338 (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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244A LYS* 4.6 3.1 + - - -
285A LEU* 4.0 19.3 - - + -
302A LEU* 5.0 4.7 - - + -
319A GLY 5.1 3.8 - - - +
320A PRO* 4.6 5.6 - - + -
321A LEU* 3.8 44.1 - - + +
327A TYR* 3.8 28.7 - - + +
334A THR* 2.9 45.1 + - + +
337A ASP* 1.3 77.8 - - + +
339A LEU* 1.3 62.1 + - - +
340A GLY 3.7 0.2 + - - -
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Residues in contact with LEU 339 (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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48A CYS* 4.1 23.8 - - - -
244A LYS* 3.1 37.8 + - + +
245A VAL 5.3 0.2 - - - +
246A PHE* 3.7 38.8 - - + -
284A ASP* 4.1 21.3 - - + -
285A LEU* 4.1 13.7 - - + -
321A LEU* 4.1 22.2 - - + -
335A ILE* 2.9 25.2 + - + +
338A LEU* 1.3 76.1 - - - +
340A GLY* 1.3 64.8 + - - +
341A ALA* 3.3 4.4 + - + +
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Residues in contact with GLY 340 (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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336A CYS 2.9 9.2 + - - -
337A ASP* 3.2 10.3 + - - -
338A LEU 3.4 0.8 + - - -
339A LEU* 1.3 78.7 - - - +
341A ALA* 1.3 59.5 + - - +
342A LYS* 4.4 9.4 + - - +
345A ASP* 4.7 1.7 - - - +
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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