Contacts of the helix formed by residues 326 - 340 (chain A) in PDB entry 1XMK
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 LYS 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A GLU* 5.4 6.4 + - - -
299A ILE* 4.1 29.8 - - + +
302A LYS* 5.2 9.9 - - - +
322A ILE* 4.4 23.1 - - + +
323A GLY* 3.0 15.3 + - - +
325A THR* 1.4 89.5 + - - +
327A ALA* 1.3 65.1 + - - +
328A ARG 3.3 2.9 - - - -
329A ASP* 3.1 10.7 + - - +
330A ILE* 2.9 29.6 + - + +
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Residues in contact with ALA 327 (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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319A ALA* 4.2 20.6 - - + -
323A GLY 3.9 1.8 + - - -
324A LEU 3.4 15.1 + - - +
325A THR 3.5 1.4 - - - -
326A LYS* 1.3 76.4 - - - +
328A ARG* 1.3 63.2 + - - +
330A ILE* 3.3 3.4 + - - +
331A ASN* 3.0 36.3 + - - +
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Residues in contact with ARG 328 (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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288A GLY* 5.1 15.8 + - - -
325A THR 5.4 0.4 + - - -
326A LYS 3.3 1.2 - - - -
327A ALA* 1.3 78.1 - - - +
329A ASP* 1.4 61.4 + - - +
331A ASN* 3.4 10.7 + - + +
332A ALA* 3.0 27.0 + - - +
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Residues in contact with ASP 329 (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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288A GLY* 2.8 32.1 + - - -
290A HIS* 3.5 12.1 + - - -
296A MET* 3.5 17.6 - - - +
299A ILE* 3.3 25.8 - - + +
326A LYS* 3.1 10.7 + - - +
328A ARG* 1.4 78.5 - - - +
330A ILE* 1.4 64.0 + - - +
332A ALA* 3.2 2.1 + - - +
333A VAL* 2.9 28.1 + - - +
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Residues in contact with ILE 330 (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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299A ILE* 3.8 24.9 - - + -
303A ILE* 3.9 11.5 - - + +
315A ALA 4.5 5.4 - - - +
318A LEU* 4.2 16.6 - - + +
319A ALA* 3.6 34.8 - - + +
322A ILE* 4.0 24.9 - - + -
323A GLY 4.3 0.4 - - - +
326A LYS* 2.9 24.4 + - + +
327A ALA* 3.6 4.7 - - - +
329A ASP* 1.4 76.7 - - - +
331A ASN* 1.3 61.7 + - - +
333A VAL* 3.3 2.3 + - - +
334A LEU* 2.9 45.4 + - + +
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Residues in contact with ASN 331 (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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315A ALA* 3.4 27.7 - - - +
327A ALA* 3.0 29.4 + - - +
328A ARG* 3.7 8.8 - - + +
330A ILE* 1.3 75.5 - - - +
332A ALA* 1.3 61.1 + - - +
334A LEU* 3.4 6.6 + - - +
335A ILE* 3.1 32.7 + - + +
353A TRP* 6.5 0.2 - - - -
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Residues in contact with ALA 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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288A GLY* 3.8 29.6 - - - +
289A SER* 5.6 0.2 - - - -
291A MET* 4.4 4.2 - - - +
296A MET* 4.1 9.0 - - + -
328A ARG* 3.0 17.2 + - + +
329A ASP* 3.6 5.4 - - - +
331A ASN* 1.3 73.7 - - - +
333A VAL* 1.3 64.5 + - - +
335A ILE* 3.4 7.2 + - - +
336A ASP* 3.0 24.4 + - - +
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Residues in contact with VAL 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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291A MET* 3.8 19.7 - - + -
296A MET* 3.8 26.5 - - + +
299A ILE* 4.1 13.9 - - + -
300A LYS* 3.8 20.0 - - + -
303A ILE* 3.8 16.6 - - + -
329A ASP 2.9 20.5 + - - +
330A ILE 3.8 3.8 - - - +
332A ALA* 1.3 73.4 - - - +
334A LEU* 1.3 61.0 + - - +
336A ASP* 3.2 2.6 + - - +
337A MET* 2.8 50.4 + - + +
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Residues in contact with LEU 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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303A ILE* 3.9 29.8 - - + -
307A LEU* 4.6 3.1 - - + -
315A ALA* 3.9 17.5 - - + -
318A LEU* 4.0 12.8 - - + -
330A ILE* 2.9 24.9 + - + +
331A ASN* 3.8 6.5 - - - +
333A VAL* 1.3 76.4 - - - +
335A ILE* 1.3 55.9 + - - +
337A MET* 3.3 5.0 + - - -
338A GLU* 2.8 30.5 + - - +
343A VAL* 3.6 13.2 - - + +
353A TRP* 3.7 63.0 - - + +
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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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331A ASN* 3.1 20.6 + - + +
332A ALA* 3.8 5.8 - - - +
333A VAL 3.3 0.2 - - - -
334A LEU* 1.3 75.8 - - - +
336A ASP* 1.4 59.2 + - - +
338A GLU* 3.4 10.5 + - - +
339A ARG* 3.0 28.1 + - + +
345A ARG* 3.0 35.9 - - - +
353A TRP* 4.0 9.6 - - + -
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Residues in contact with ASP 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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291A MET* 4.1 35.4 - - + +
300A LYS* 5.4 2.3 + - - -
332A ALA 3.0 17.4 + - - +
333A VAL* 3.2 4.2 + - - +
335A ILE* 1.4 76.8 - - + +
337A MET* 1.3 65.2 + - - +
339A ARG* 2.8 37.2 + - - +
340A GLN* 3.2 38.8 + - - +
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Residues in contact with MET 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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291A MET* 6.3 0.2 - - + -
300A LYS* 3.9 24.9 - - + +
303A ILE* 4.4 17.0 - - + -
304A CYS* 5.3 2.0 - - + -
333A VAL* 2.8 38.1 + - + +
334A LEU* 3.7 2.2 - - - +
336A ASP* 1.3 77.1 - - + +
338A GLU* 1.3 60.7 + - - +
340A GLN* 3.3 9.2 + - - +
341A GLY 3.1 4.3 + - - -
342A ASP* 2.8 40.6 + - + +
343A VAL* 3.7 34.8 - - + -
355A LEU* 5.1 2.0 - - + -
359A LYS* 4.2 14.1 - - - -
399A CL 3.8 26.0 - - + -
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Residues in contact with GLU 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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334A LEU 2.8 18.1 + - - +
335A ILE* 3.5 11.7 - - - +
336A ASP 3.2 0.2 - - - -
337A MET* 1.3 74.9 - - - +
339A ARG* 1.4 66.0 + - - +
341A GLY* 3.0 14.4 + - - -
343A VAL* 3.5 20.0 - - - +
344A TYR* 4.7 2.2 - - - -
345A ARG* 2.7 58.8 + - - +
353A TRP* 3.8 12.4 - - + -
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Residues in contact with ARG 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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335A ILE* 3.0 15.8 + - + +
336A ASP* 2.8 35.4 + - - +
338A GLU* 1.4 76.4 - - - +
340A GLN* 1.3 92.3 + - - +
341A GLY 3.7 0.3 + - - -
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Residues in contact with GLN 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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300A LYS* 4.6 12.7 - - - +
336A ASP* 3.2 28.0 + - - +
337A MET* 3.8 7.4 - - - +
338A GLU 3.1 1.0 - - - -
339A ARG* 1.3 108.9 + - - +
341A GLY* 1.3 52.3 + - - +
342A ASP* 3.4 16.4 + - - +
358A LYS* 2.8 31.9 + - - +
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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