Contacts of the helix formed by residues 316 - 336 (chain A) in PDB entry 5JJA
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 316 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A SER* 3.8 29.3 - - - +
282A THR* 5.6 0.6 + - - -
314A VAL 3.8 5.0 + - - +
315A ILE* 1.3 78.4 - - - +
317A PRO* 1.3 80.7 - - + +
318A SER* 4.4 7.0 - - - +
319A GLU* 2.9 20.5 + - + +
320A PHE* 2.9 21.5 + - - +
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Residues in contact with PRO 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A GLU* 1.3 93.4 - - + +
318A SER* 1.3 61.1 + - - +
320A PHE* 3.2 19.1 + - + +
321A VAL* 3.2 20.0 + - + +
354A TYR* 3.7 17.9 - - + +
358A LEU* 4.1 18.6 - - + -
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Residues in contact with SER 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A GLU* 4.4 8.3 - - - +
317A PRO* 1.3 79.5 - - - +
319A GLU* 1.3 67.4 + - - +
321A VAL* 3.2 26.6 - - - +
322A LYS* 3.8 14.1 - - - +
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Residues in contact with GLU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A SER* 3.4 30.5 + - - +
280A THR* 3.7 19.0 - - - +
282A THR* 3.9 24.8 - - + +
283A GLU* 4.4 7.1 + - - +
315A ILE* 4.2 5.6 - - + -
316A GLU* 2.9 23.8 + - + +
318A SER* 1.3 80.4 + - - +
320A PHE* 1.3 67.4 + - - +
322A LYS* 3.3 45.4 + - - +
323A ILE* 3.6 11.3 + - - +
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Residues in contact with PHE 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A LEU* 4.0 28.5 - - + -
315A ILE* 3.7 15.4 - - + +
316A GLU 2.9 11.3 + - - +
317A PRO* 3.2 15.5 + - + +
319A GLU* 1.3 76.5 - - - +
321A VAL* 1.3 59.8 + - + +
323A ILE* 3.2 7.6 + - + +
324A MET* 2.9 50.3 + - + +
328A PHE* 3.6 36.1 - + - -
355A ILE* 5.4 2.7 - - + -
358A LEU* 3.6 51.4 - - + -
359A ILE 4.3 0.7 - - - -
362A ASN* 3.7 15.0 - - - -
366A ILE* 4.0 7.4 - - + -
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Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A PRO 3.2 10.9 + - - +
318A SER* 3.2 24.5 - - - +
320A PHE* 1.3 76.4 - - + +
322A LYS* 1.3 65.5 + - + +
323A ILE 3.4 0.3 + - - -
324A MET* 3.6 29.9 + - + +
325A GLU* 5.1 1.2 + - - +
362A ASN* 3.8 31.2 - - - +
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Residues in contact with LYS 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLU* 3.7 30.8 + - + +
318A SER 3.8 14.4 - - - +
319A GLU* 3.3 36.9 + - - +
320A PHE 3.2 0.8 - - - -
321A VAL* 1.3 82.1 - - + +
323A ILE* 1.3 66.0 + - + +
325A GLU 5.2 0.2 + - - -
326A PRO* 4.8 7.3 - - - +
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Residues in contact with ILE 323 (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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282A THR* 4.7 2.9 - - + -
283A GLU* 4.0 34.3 - - + +
286A VAL* 4.0 26.2 - - + +
287A MET* 4.1 20.6 - - - -
315A ILE* 4.2 18.6 - - + -
319A GLU 3.6 11.7 - - - +
320A PHE* 3.2 12.0 + - + +
322A LYS* 1.3 81.6 - - + +
324A MET* 1.3 69.4 + - - +
325A GLU 3.3 3.0 + - - -
326A PRO* 3.5 9.1 - - - +
327A LEU* 3.1 48.0 + - + +
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Residues in contact with MET 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PHE* 2.9 37.1 + - + +
321A VAL* 3.6 30.3 - - + +
322A LYS 3.6 0.4 - - - -
323A ILE* 1.3 83.2 - - - +
325A GLU* 1.3 69.5 + - + +
327A LEU* 4.3 0.9 - - - -
328A PHE* 2.9 44.2 + - + +
362A ASN* 3.8 42.0 - - + +
365A LYS* 4.3 28.5 - - + +
366A ILE* 3.9 9.6 - - + -
369A ILE* 5.1 0.2 - - - +
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Residues in contact with GLU 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A VAL 5.1 1.5 + - - +
322A LYS 5.2 0.2 + - - -
324A MET* 1.3 91.5 - - + +
326A PRO* 1.3 73.3 - - + +
328A PHE 3.9 0.2 - - - -
329A ARG* 3.1 52.8 + - - +
365A LYS* 3.5 35.3 + - + +
366A ILE* 6.2 0.2 - - + -
369A ILE* 4.0 20.6 - - + +
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Residues in contact with PRO 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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287A MET* 4.1 26.2 - - + -
290A LEU* 3.7 20.9 - - + +
322A LYS 4.8 4.9 - - - +
323A ILE* 3.5 15.3 - - - +
325A GLU* 1.3 95.4 - - + +
327A LEU* 1.3 60.9 + - - +
329A ARG* 3.4 20.4 + - + +
330A GLN* 3.2 20.3 + - - +
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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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286A VAL* 4.6 4.7 - - + -
290A LEU* 3.9 15.1 - - + +
308A LEU* 3.9 39.7 - - + +
312A LEU* 3.8 28.9 - - + -
323A ILE* 3.1 39.8 + - + +
324A MET 3.8 4.0 - - - +
326A PRO* 1.3 75.7 - - - +
328A PHE* 1.3 86.6 + - + +
330A GLN* 3.1 7.3 + - - +
331A LEU* 2.9 27.7 + - + -
349A TYR* 4.8 2.9 - - + -
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Residues in contact with PHE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A LEU* 5.2 2.5 - - + -
320A PHE* 3.6 32.8 - + - -
324A MET* 2.9 34.0 + - + +
325A GLU 4.4 0.4 - - - +
327A LEU* 1.3 89.7 - - + +
329A ARG* 1.3 60.6 + - - +
330A GLN 3.3 0.2 - - - -
331A LEU* 3.6 31.4 - - + -
332A ALA* 2.9 30.1 + - - +
355A ILE* 4.5 9.6 - - + -
359A ILE* 3.5 37.7 - - + -
366A ILE* 4.0 20.4 - - + -
369A ILE* 3.4 17.2 - - + +
370A MET* 3.7 16.5 - - + +
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Residues in contact with ARG 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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325A GLU* 3.1 45.0 + - - +
326A PRO* 3.6 35.2 - - + +
328A PHE* 1.3 77.3 - - - +
330A GLN* 1.3 60.9 + - - +
332A ALA* 3.6 4.4 + - - +
333A LYS* 3.4 35.3 + - - +
369A ILE* 3.5 24.8 - - + +
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Residues in contact with GLN 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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290A LEU* 3.9 23.6 + - + +
293A TRP* 3.5 63.7 + - + +
294A PRO 5.1 1.6 + - - -
301A GLU* 4.0 2.9 - - - +
308A LEU* 6.0 1.1 - - + -
326A PRO 3.2 4.6 + - - +
327A LEU 3.1 9.4 + - - +
329A ARG* 1.3 75.9 - - - +
331A LEU* 1.3 66.5 + - - +
333A LYS* 3.0 31.7 + - - +
334A CYS* 3.0 17.0 + - - -
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Residues in contact with LEU 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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305A LEU* 3.8 19.3 - - + -
308A LEU* 5.5 1.8 - - + +
327A LEU* 2.9 19.5 + - + +
328A PHE* 3.4 38.3 + - + +
330A GLN* 1.3 77.4 - - - +
332A ALA* 1.3 57.0 + - - +
334A CYS* 3.1 6.4 + - - +
335A VAL* 2.9 27.8 + - + +
346A ALA* 3.8 28.9 - - + +
349A TYR* 3.7 40.4 - - + -
350A TRP* 5.7 2.5 - - + +
359A ILE* 5.8 0.2 - - + -
370A MET* 3.9 14.6 - - + -
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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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328A PHE 2.9 17.9 + - - +
329A ARG* 3.8 6.5 - - - +
331A LEU* 1.3 75.5 - - - +
333A LYS* 1.3 63.3 + - + +
335A VAL* 3.4 4.7 + - - +
336A SER* 3.3 23.7 + - - -
369A ILE* 3.6 24.0 - - + +
370A MET* 3.9 21.0 - - - +
372A PRO* 6.0 1.1 - - + -
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Residues in contact with LYS 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 HIS* 4.2 16.0 + - + +
301A GLU* 6.0 0.2 - - - +
329A ARG* 3.4 23.6 + - - +
330A GLN* 3.0 29.0 + - - +
332A ALA* 1.3 76.6 - - + +
334A CYS* 1.3 63.2 + - - +
336A SER* 3.2 8.9 + - - -
337A SER* 3.2 18.7 + - - -
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Residues in contact with CYS 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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293A TRP* 3.7 20.6 - - - -
297A HIS* 5.8 0.7 - - - -
301A GLU* 3.3 26.5 - - - -
305A LEU* 4.2 11.4 - - + -
330A GLN* 3.0 26.6 + - - -
331A LEU* 3.1 8.3 + - - +
333A LYS* 1.3 74.3 - - - +
335A VAL* 1.3 65.2 + - - +
337A SER* 3.0 20.6 + - - -
342A VAL* 4.0 11.0 - - + -
343A ALA* 3.3 10.7 + - - -
346A ALA* 3.7 17.9 - - + -
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Residues in contact with VAL 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LEU* 2.9 17.9 + - + +
332A ALA* 3.8 8.7 - - - +
333A LYS 3.4 0.2 - - - -
334A CYS* 1.3 74.5 - - - +
336A SER* 1.3 61.6 + - - +
337A SER 3.3 0.4 - - - +
343A ALA* 3.4 22.7 - - - +
346A ALA* 3.8 22.7 - - + +
347A LEU* 3.9 33.8 - - + +
350A TRP* 5.1 2.0 - - - +
370A MET* 4.0 20.4 - - + -
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Residues in contact with SER 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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297A HIS* 5.1 1.8 + - - -
332A ALA 3.3 13.5 + - - -
333A LYS* 3.2 9.6 + - - -
334A CYS 3.2 1.2 - - - -
335A VAL* 1.3 78.1 - - - +
337A SER* 1.3 65.4 + - - +
338A PRO* 3.6 2.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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