Contacts of the helix formed by residues 323 - 339 (chain A) in PDB entry 1JNK
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 GLU 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A SER* 1.3 74.6 + - - +
324A HIS* 1.3 63.8 + - - +
326A LYS* 3.2 34.0 + - - +
327A LEU* 3.3 22.9 + - - +
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Residues in contact with HIS 324 (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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163A HIS* 5.2 6.1 - - + -
164A GLU* 6.2 1.8 - - + -
322A SER* 2.9 10.8 + - - +
323A GLU* 1.3 80.5 - - - +
325A ASN* 1.3 70.1 + - - +
327A LEU* 3.6 5.1 + - - +
328A LYS* 3.1 64.5 + - + +
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Residues in contact with ASN 325 (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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163A HIS* 3.6 19.5 + - - +
319A PRO* 2.8 36.3 + - - +
320A ALA* 4.1 1.3 - - - -
321A ASP* 2.9 26.5 + - - +
322A SER* 3.5 14.6 + - - +
323A GLU 3.3 0.4 - - - -
324A HIS* 1.3 93.5 + - - +
326A LYS* 1.3 59.0 + - - +
328A LYS 3.9 0.9 - - - -
329A ALA* 3.0 30.1 + - - +
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Residues in contact with LYS 326 (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 ALA* 2.9 42.7 + - + +
321A ASP 3.5 13.1 + - - -
322A SER 3.1 15.6 + - - +
323A GLU* 3.2 34.1 - - - +
324A HIS 3.3 0.2 - - - -
325A ASN* 1.3 74.0 - - - +
327A LEU* 1.3 66.5 + - - +
329A ALA* 3.5 4.3 + - - +
330A SER* 3.4 19.6 + - - -
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Residues in contact with LEU 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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323A GLU 3.3 12.7 + - - +
324A HIS* 3.9 4.9 - - - +
326A LYS* 1.3 80.0 - - - +
328A LYS* 1.3 66.0 + - + +
330A SER* 2.9 32.4 + - - +
331A GLN* 3.0 31.7 + - + +
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Residues in contact with LYS 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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163A HIS* 3.6 29.6 - - + +
324A HIS* 3.1 50.7 + - + +
325A ASN 4.1 0.2 - - - +
327A LEU* 1.3 79.6 - - + +
329A ALA* 1.3 56.5 + - - +
331A GLN* 2.8 29.8 + - - +
332A ALA* 2.8 32.2 + - - +
357A PRO 3.4 17.4 + - - -
358A TYR* 3.7 18.8 + - + +
361A VAL* 3.9 17.2 - - - +
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Residues in contact with ALA 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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163A HIS* 3.9 9.4 + - - +
315A ASP* 5.2 7.6 - - - +
318A PHE* 3.6 32.9 - - + -
319A PRO 4.5 1.1 - - - +
320A ALA* 4.6 7.2 - - + -
325A ASN 3.0 21.1 + - - +
326A LYS* 3.7 7.6 - - - +
327A LEU 3.2 0.4 - - - -
328A LYS* 1.3 76.7 - - - +
330A SER* 1.3 60.3 + - - +
332A ALA* 4.1 1.5 - - - +
333A ARG* 3.4 29.1 + - - +
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Residues in contact with SER 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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326A LYS 3.4 8.9 + - - -
327A LEU* 2.9 22.3 + - - +
329A ALA* 1.3 75.3 - - - +
331A GLN* 1.3 62.4 + - - +
333A ARG* 3.3 16.3 + - - +
334A ASP* 2.8 35.4 + - - +
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Residues in contact with GLN 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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327A LEU* 3.2 34.5 - - + +
328A LYS* 2.8 43.8 + - - +
330A SER* 1.3 82.2 + - - +
332A ALA* 1.3 64.1 + - - +
334A ASP* 3.1 6.8 + - - +
335A LEU* 3.0 18.4 + - - +
356A HIS* 3.1 15.6 + - - +
357A PRO* 3.4 34.1 - - + +
358A TYR* 3.8 12.9 - - + +
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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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163A HIS* 4.7 0.4 - - + -
166A MET* 5.8 0.7 - - - -
253A MET* 3.7 18.6 - - + +
318A PHE* 3.6 26.0 - - + -
328A LYS 2.8 20.8 + - - +
329A ALA* 4.2 1.1 - - - +
331A GLN* 1.3 71.5 - - - +
333A ARG* 1.3 58.2 + - - +
335A LEU* 3.1 6.2 + - - +
336A LEU* 3.0 27.0 + - - +
358A TYR* 3.8 27.5 - - + +
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Residues in contact with ARG 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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309A PHE* 4.1 19.1 - - + +
310A PRO* 3.7 33.4 - - - +
313A PHE* 2.8 30.2 + - + +
314A PRO 3.3 2.6 + - - -
315A ASP* 3.1 49.5 + - - +
318A PHE* 3.8 16.6 - - + +
329A ALA* 3.4 24.4 + - - +
330A SER* 3.3 15.5 + - - +
332A ALA* 1.3 78.5 - - - +
334A ASP* 1.3 57.6 + - - +
336A LEU* 3.5 7.7 + - - +
337A SER* 3.0 27.4 + - - -
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Residues in contact with ASP 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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330A SER 2.8 13.4 + - - +
331A GLN* 3.1 13.4 + - - +
333A ARG* 1.3 75.0 - - - +
335A LEU* 1.3 61.7 + - - +
337A SER* 2.8 25.2 + - - -
338A LYS* 3.2 35.5 + - - +
356A HIS* 3.0 21.1 - - + -
357A PRO* 5.5 1.0 - - - +
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Residues in contact with LEU 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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170A LEU* 5.4 1.3 - - + -
253A MET* 3.8 23.3 - - + -
331A GLN 3.0 7.1 + - - +
332A ALA* 3.1 9.2 + - - +
334A ASP* 1.3 72.8 - - - +
336A LEU* 1.3 68.9 + - - +
338A LYS* 2.8 14.5 + - - +
339A MET* 3.0 46.1 + - + +
348A ILE* 4.7 6.3 - - + -
353A ALA* 4.2 13.0 - - + +
356A HIS* 3.6 38.5 + - + +
358A TYR* 4.3 4.3 - - + -
359A ILE* 3.7 32.3 - - + -
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Residues in contact with LEU 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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250A GLY* 3.5 26.7 - - - +
253A MET* 3.7 26.0 - - + -
254A GLY* 3.6 17.5 - - - +
257A VAL* 4.6 3.1 - - + -
309A PHE* 4.1 10.3 - - + -
313A PHE* 3.5 33.0 - - + -
318A PHE* 4.3 18.8 - - + -
332A ALA 3.0 10.5 + - - +
333A ARG* 3.6 10.1 - - - +
335A LEU* 1.3 75.1 - - - +
337A SER* 1.3 57.3 + - - +
339A MET* 2.8 22.2 + - - +
340A LEU* 2.9 29.9 + - + +
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Residues in contact with SER 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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309A PHE* 3.6 42.3 - - - -
333A ARG 3.0 15.1 + - - -
334A ASP* 2.8 28.2 + - - -
335A LEU 3.2 0.4 - - - -
336A LEU* 1.3 75.1 - - - +
338A LYS* 1.3 60.2 + - - +
340A LEU 4.5 0.2 - - - -
341A VAL* 3.3 18.4 - - - +
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Residues in contact with LYS 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 ASP* 3.2 41.5 + - - +
335A LEU* 2.8 10.5 + - - +
337A SER* 1.3 82.8 + - - +
339A MET* 1.3 57.5 + - - +
341A VAL* 3.7 10.8 - - - +
346A LYS 4.9 0.4 - - - +
347A ARG* 3.9 0.3 - - - +
348A ILE* 3.0 57.7 + - + +
356A HIS* 4.4 10.3 + - + +
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Residues in contact with MET 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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170A LEU* 5.2 0.2 - - + -
174A LEU* 4.1 9.0 - - + -
246A ILE* 3.5 34.5 - - + +
247A TRP* 3.9 8.7 - - - -
249A VAL* 3.5 34.1 - - + -
250A GLY* 3.9 15.7 - - - -
253A MET* 4.7 7.2 - - - +
335A LEU* 3.0 35.0 + - + +
336A LEU* 2.8 3.9 + - - +
338A LYS* 1.3 79.3 - - - +
340A LEU* 1.3 58.7 + - - +
341A VAL 3.0 10.5 + - - -
347A ARG* 3.4 20.6 + - - -
348A ILE* 3.8 7.2 - - + -
353A ALA* 3.9 26.2 - - + -
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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