Contacts of the helix formed by residues 321 - 340 (chain l) in PDB entry 5M32
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 THR 321 (chain l).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220l ALA 5.6 0.5 + - - -
317l PRO 4.8 7.6 - - - +
318l ILE* 3.1 19.9 + - - -
319l ILE 4.2 0.2 - - - +
320l SER* 1.3 81.7 + - - +
322l HIS* 1.3 73.3 + - - +
323l LEU 3.5 0.3 + - - -
324l ALA* 3.8 13.9 + - - +
325l LYS* 4.3 3.8 + - - +
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Residues in contact with HIS 322 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219l ALA* 4.0 17.0 + - + -
220l ALA* 3.9 21.2 + - - -
225l TRP* 4.3 20.9 + + - -
256l LEU* 4.0 24.6 - - + +
260l MET* 4.5 15.4 - - + +
318l ILE* 3.6 20.3 + - + +
319l ILE* 2.8 11.1 + - + +
321l THR* 1.3 86.2 + - - +
323l LEU* 1.3 55.2 + - + +
324l ALA 3.2 2.7 - - - -
325l LYS* 3.1 8.6 + - + +
326l LEU* 2.7 37.8 + - + +
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Residues in contact with LEU 323 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313l LEU 5.6 0.2 - - - +
314l ARG* 4.8 20.2 - - + +
319l ILE* 3.0 27.8 + - + +
320l SER* 3.7 24.9 - - - +
321l THR 3.3 1.0 - - - -
322l HIS* 1.3 76.5 - - + +
324l ALA* 1.3 52.4 + - - +
326l LEU* 4.2 10.5 - - + +
327l TYR* 2.6 39.0 + - - +
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Residues in contact with ALA 324 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320l SER 4.0 4.4 + - - +
321l THR* 3.8 10.2 + - - +
322l HIS 3.2 0.4 - - - -
323l LEU* 1.3 79.7 - - - +
325l LYS* 1.3 57.4 + - - +
327l TYR* 3.6 4.2 - - - +
328l ASP* 2.9 32.1 + - - +
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Residues in contact with LYS 325 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260l MET* 4.5 18.8 - - + -
321l THR 4.3 3.0 + - - +
322l HIS* 3.1 12.6 + - + +
324l ALA* 1.3 75.7 - - - +
326l LEU* 1.3 61.2 + - - +
328l ASP* 3.9 3.2 - - - +
329l ASN* 2.9 31.4 + - - +
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Residues in contact with LEU 326 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259l ILE* 5.9 7.0 - - + -
260l MET* 4.9 10.9 - - + +
322l HIS* 2.7 22.8 + - + +
323l LEU* 4.2 13.2 - - + -
325l LYS* 1.3 72.5 - - - +
327l TYR* 1.3 58.1 + - - +
329l ASN* 3.5 6.1 - - - +
330l LEU* 2.9 31.0 + - - +
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Residues in contact with TYR 327 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323l LEU 2.6 23.6 + - - +
324l ALA* 3.6 5.8 - - - +
325l LYS 3.3 0.2 - - - -
326l LEU* 1.3 77.7 - - - +
328l ASP* 1.3 58.4 + - - +
330l LEU* 3.9 3.5 - - - +
331l LEU* 2.9 27.8 + - - +
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Residues in contact with ASP 328 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324l ALA 2.9 16.8 + - - +
325l LYS* 4.2 3.4 - - - +
327l TYR* 1.3 76.3 - - - +
329l ASN* 1.3 57.2 + - - +
331l LEU* 3.3 9.1 - - - +
332l GLU* 2.9 26.5 + - - +
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Residues in contact with ASN 329 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260l MET* 6.1 5.2 - - + -
262l ASN* 5.7 8.1 - - - +
325l LYS 2.9 21.6 + - - +
326l LEU* 3.5 8.1 - - - +
327l TYR 3.2 0.2 - - - -
328l ASP* 1.3 77.2 - - - +
330l LEU* 1.3 57.5 + - - +
332l GLU* 3.0 21.8 + - - +
333l GLN* 3.1 14.9 + - - +
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Residues in contact with LEU 330 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293l ALA* 5.3 8.3 - - + +
297l ARG* 5.8 1.1 - - - +
298l SER 5.0 15.4 + - - +
299l LEU* 5.0 4.9 + - + +
302l PHE* 6.2 2.7 - - + -
326l LEU 2.9 17.3 + - - +
327l TYR* 4.2 2.9 - - - +
329l ASN* 1.3 73.4 - - - +
331l LEU* 1.3 60.8 + - - +
333l GLN* 4.5 4.0 - - - +
334l ASN* 2.8 34.8 + - - +
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Residues in contact with LEU 331 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299l LEU* 6.1 3.3 - - - +
327l TYR 2.9 16.2 + - - +
328l ASP* 3.3 14.1 - - - +
329l ASN 3.1 0.2 - - - -
330l LEU* 1.3 76.8 - - - +
332l GLU* 1.3 56.2 + - - +
334l ASN* 4.5 2.5 - - - -
335l LEU* 3.0 33.6 + - - +
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Residues in contact with GLU 332 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328l ASP 2.9 14.3 + - - +
329l ASN* 3.0 12.3 + - - +
331l LEU* 1.3 75.7 - - - +
333l GLN* 1.3 59.7 + - + +
335l LEU* 3.2 4.6 + - - +
336l ILE* 2.9 25.9 + - - +
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Residues in contact with GLN 333 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297l ARG* 4.5 14.2 - - + +
329l ASN 3.1 9.5 + - - +
330l LEU* 4.9 2.5 - - - +
332l GLU* 1.3 76.7 - - + +
334l ASN* 1.3 61.0 + - - +
336l ILE* 3.4 11.2 - - + +
337l ARG* 3.0 26.0 + - - +
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Residues in contact with ASN 334 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297l ARG* 3.4 24.2 + - - +
298l SER* 4.0 12.3 - - - -
299l LEU* 4.3 7.2 - - + +
330l LEU* 2.8 23.1 + - - +
331l LEU* 4.1 3.6 - - - +
333l GLN* 1.3 74.1 - - - +
335l LEU* 1.3 58.4 + - - +
337l ARG* 3.1 4.3 + - - +
338l VAL* 2.9 27.6 + - - +
354l ILE* 6.2 4.3 - - + -
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Residues in contact with LEU 335 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331l LEU 3.0 20.7 + - - +
332l GLU* 3.5 5.2 - - - +
334l ASN* 1.3 71.8 - - - +
336l ILE* 1.3 65.0 + - - +
338l VAL* 3.4 9.1 + - - +
339l ILE* 3.0 24.3 + - - +
350l ILE* 6.1 0.5 - - - +
364l LYS* 6.1 5.4 - - + -
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Residues in contact with ILE 336 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332l GLU 2.9 13.7 + - - +
333l GLN* 3.4 15.3 - - + +
335l LEU* 1.3 75.0 - - - +
337l ARG* 1.3 57.0 + - - +
339l ILE* 2.8 23.0 + - - +
340l GLU* 2.8 16.8 + - - +
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Residues in contact with ARG 337 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394k SER* 6.1 0.7 - - - -
398k VAL* 5.4 10.7 - - + +
297l ARG* 4.4 17.3 - - + +
333l GLN 3.0 14.0 + - - +
334l ASN 3.1 8.5 + - - +
336l ILE* 1.3 75.5 - - - +
338l VAL* 1.3 63.5 + - - +
339l ILE 3.5 0.2 + - - -
340l GLU* 3.6 16.0 + - - +
341l PRO* 4.1 5.4 - - - +
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Residues in contact with VAL 338 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334l ASN 2.9 12.4 + - - +
335l LEU* 3.6 11.9 - - - +
337l ARG* 1.3 77.6 - - - +
339l ILE* 1.3 61.9 + - - +
341l PRO* 3.9 8.8 - - - +
342l PHE* 4.8 4.7 - - - +
349l HIS 5.3 2.5 - - - +
350l ILE* 4.9 24.2 - - + +
353l LEU* 5.4 11.4 - - + +
354l ILE* 6.1 2.5 - - + -
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Residues in contact with ILE 339 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335l LEU 3.0 14.9 + - - +
336l ILE* 2.8 8.4 + - - +
338l VAL* 1.3 79.2 - - + +
340l GLU* 1.3 52.0 + - - +
342l PHE* 2.9 39.9 + - - +
350l ILE* 6.3 3.1 - - + -
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Residues in contact with GLU 340 (chain l).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397k VAL* 6.3 1.1 - - + -
398k VAL* 5.7 9.6 - - + -
404k ALA 5.4 0.2 - - - +
336l ILE 2.8 14.0 + - - +
337l ARG* 3.9 10.8 - - - +
338l VAL 3.4 0.6 - - - -
339l ILE* 1.3 73.9 - - - +
341l PRO* 1.4 65.6 - - + +
342l PHE 4.5 1.9 - - - +
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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
------------------------------------------------------------
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