Contacts of the helix formed by residues 344 - 366 (chain B) in PDB entry 4MCA
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 344 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.9 24.7 - - + -
330B CYS* 3.8 5.4 - - - -
342B LYS* 4.1 11.4 - - - +
343B VAL* 1.3 77.1 - - - +
345B PRO* 1.3 76.5 - - + +
346B ALA* 3.6 8.6 + - - +
347B GLY* 3.0 24.1 + - - +
348B VAL* 3.1 14.2 + - - +
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Residues in contact with PRO 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B MET* 4.5 5.2 - - - -
326B ALA* 3.4 11.9 - - + +
327B GLN* 3.3 49.8 - - + +
330B CYS* 4.0 27.1 - - + -
344B THR* 1.3 87.6 - - - +
346B ALA* 1.3 64.3 + - - +
348B VAL 3.1 1.3 + - - +
349B GLN* 2.9 21.1 + - - +
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B MET* 4.8 10.9 - - + -
344B THR* 3.2 8.3 + - - +
345B PRO* 1.3 79.1 - - - +
347B GLY* 1.3 57.6 + - - +
349B GLN* 3.4 11.0 + - - +
350B ALA* 3.0 29.3 + - - +
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Residues in contact with GLY 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU* 3.6 14.4 - - - +
344B THR* 3.0 16.6 + - - -
346B ALA* 1.3 75.9 - - - +
348B VAL* 1.3 60.1 + - - +
350B ALA* 3.4 6.7 + - - +
351B ALA* 2.9 28.2 + - - +
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Residues in contact with VAL 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ILE* 3.9 17.5 - - + -
285B LEU* 4.3 9.4 - - + -
326B ALA* 3.9 9.4 - - + -
329B SER* 3.6 16.4 - - - +
330B CYS* 3.7 8.1 - - - -
336B ILE* 3.6 14.1 - - + -
343B VAL* 3.5 30.3 - - + -
344B THR 3.1 6.9 + - - +
345B PRO 3.8 4.9 - - - +
347B GLY* 1.3 72.8 - - - +
349B GLN* 1.3 68.9 + - - +
351B ALA* 3.2 2.5 + - - +
352B ILE* 3.0 41.7 + - + +
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Residues in contact with GLN 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B VAL* 3.0 41.2 + - - +
322B ILE* 4.0 19.5 - - + -
323B MET* 3.1 38.6 - - - +
326B ALA* 3.7 14.0 - - + +
345B PRO 2.9 16.5 + - - +
346B ALA* 3.8 6.8 - - - +
348B VAL* 1.3 77.3 - - - +
350B ALA* 1.3 62.4 + - - +
352B ILE* 3.3 1.0 + - - +
353B LEU* 3.0 37.9 + - + +
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Residues in contact with ALA 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B VAL* 5.1 0.4 - - - -
346B ALA 3.0 17.3 + - - +
347B GLY* 3.6 8.3 - - - +
349B GLN* 1.3 79.5 + - - +
351B ALA* 1.3 61.2 + - - +
353B LEU* 4.1 5.3 - - - +
354B THR* 2.8 34.3 + - - +
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Residues in contact with ALA 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ALA* 3.4 27.6 - - + +
284B VAL* 3.6 16.5 - - + +
285B LEU* 3.8 22.4 - - + +
347B GLY 2.9 17.3 + - - +
348B VAL* 3.6 6.1 - - + +
350B ALA* 1.3 75.4 - - - +
352B ILE* 1.3 59.7 + - - +
354B THR 3.8 0.2 - - - -
355B ALA* 2.9 30.7 + - - +
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Residues in contact with ILE 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B ILE* 3.9 12.8 - - + -
260B PHE* 4.1 10.5 - - + -
277B PHE* 3.9 17.4 - - + -
281B ALA* 3.9 21.3 - - + -
309B LEU* 4.3 3.8 - - + -
322B ILE* 3.3 34.5 - - + +
325B VAL* 3.7 29.4 - - + -
326B ALA 5.1 0.2 - - - +
348B VAL* 3.0 35.9 + - + +
349B GLN* 3.7 0.7 - - - +
351B ALA* 1.3 78.1 - - - +
353B LEU* 1.3 63.3 + - - +
355B ALA* 3.3 4.2 + - - +
356B ASP* 3.1 22.0 + - - +
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Residues in contact with LEU 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B LEU* 4.2 11.4 - - + -
318B ALA* 4.9 4.9 - - + -
319B VAL* 4.4 28.5 - - + -
322B ILE* 4.1 26.7 - - + -
349B GLN* 3.0 40.4 + - + +
350B ALA* 4.1 4.5 - - - +
352B ILE* 1.3 77.5 - - - +
354B THR* 1.4 62.0 + - - +
356B ASP* 3.5 8.1 + - + +
357B ARG* 3.2 28.3 + - - +
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Residues in contact with THR 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B VAL* 4.1 18.6 - - + +
350B ALA* 2.8 24.8 + - - +
351B ALA 3.9 2.5 - - - -
353B LEU* 1.4 75.7 - - - +
355B ALA* 1.3 66.4 + - - +
357B ARG* 3.1 10.9 + - + +
358B LEU* 2.9 34.2 + - + +
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Residues in contact with ALA 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B PHE* 4.2 8.3 - - + -
280B LEU* 3.7 34.1 - - + +
281B ALA* 4.0 15.9 - - - +
284B VAL* 4.1 10.9 - - + +
307B ILE 3.9 0.3 - - - +
351B ALA 2.9 18.1 + - - +
352B ILE 3.3 4.5 + - - +
354B THR* 1.3 76.6 - - - +
356B ASP* 1.3 59.1 + - - +
358B LEU* 3.3 7.4 + - - +
359B GLY* 2.9 24.9 + - - -
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Residues in contact with ASP 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B PHE* 4.1 8.0 - - + -
307B ILE 4.4 1.6 - - - -
308B THR* 3.4 9.2 - - - +
309B LEU* 2.9 52.7 + - + +
310B ALA 4.3 1.4 + - - -
352B ILE 3.1 13.8 + - - +
353B LEU* 3.6 11.9 - - - +
354B THR 3.1 0.2 - - - -
355B ALA* 1.3 77.0 - - - +
357B ARG* 1.3 63.7 + - - +
359B GLY* 3.3 0.9 + - - -
360B SER* 2.9 30.8 + - - -
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Residues in contact with ARG 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B LEU 3.2 14.9 + - - +
354B THR* 3.1 12.8 + - + +
356B ASP* 1.3 83.3 - - - +
358B LEU* 1.3 57.0 + - - +
360B SER* 3.3 8.1 + - - +
361B ALA* 3.0 30.5 + - - +
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Residues in contact with LEU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU* 5.6 2.2 - - + -
284B VAL* 3.8 26.7 - - + -
290B MET* 3.9 33.0 - - + -
293B ILE* 4.4 20.4 - - + -
297B LEU* 4.1 14.4 - - + +
354B THR* 2.9 26.7 + - + +
355B ALA* 3.6 7.4 - - - +
356B ASP 3.3 0.2 - - - -
357B ARG* 1.3 76.1 - - + +
359B GLY* 1.3 58.1 + - - +
361B ALA* 3.4 5.7 + - + +
362B TRP* 3.0 28.6 + - - +
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Residues in contact with GLY 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LEU* 3.9 17.9 - - - +
307B ILE* 3.2 24.6 - - - +
308B THR* 3.6 7.9 - - - -
355B ALA 2.9 11.7 + - - -
358B LEU* 1.3 76.7 - - - +
360B SER* 1.3 57.1 + - - +
362B TRP* 3.2 3.7 + - - +
363B LEU* 3.0 31.5 + - - +
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Residues in contact with SER 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B THR* 3.4 15.1 - - - +
356B ASP* 2.9 20.1 + - - -
357B ARG* 3.3 11.3 + - - +
359B GLY* 1.3 77.0 - - - +
361B ALA* 1.3 62.7 + - - +
363B LEU* 3.2 8.6 + - - +
364B GLN* 3.1 28.6 + - - +
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Residues in contact with ALA 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B ARG 3.0 14.7 + - - +
358B LEU* 3.8 7.0 - - + +
360B SER* 1.3 76.9 + - - +
362B TRP* 1.3 65.4 + - - +
364B GLN* 3.3 12.5 + - - +
365B GLN* 3.3 27.5 + - - +
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Residues in contact with TRP 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B GLU* 3.6 34.8 + - - -
297B LEU* 3.7 27.7 - - + +
298B ALA* 3.6 31.4 - - + +
301B HIS* 3.1 48.2 - + + -
307B ILE* 3.8 13.2 - - + -
358B LEU 3.0 15.3 + - - +
359B GLY* 3.2 8.9 + - - +
361B ALA* 1.3 77.9 - - - +
363B LEU* 1.3 66.6 + - + +
365B GLN* 3.1 12.8 + - - -
366B HIS* 2.8 70.5 + + + -
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Residues in contact with LEU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B HIS* 3.4 37.5 - - + +
307B ILE* 3.9 10.1 - - + -
308B THR* 3.9 25.1 - - + +
311B GLU* 3.9 21.3 - - + +
359B GLY 3.0 13.9 + - - +
360B SER* 3.2 8.3 + - - +
362B TRP* 1.3 78.5 - - + +
364B GLN* 1.3 69.5 + - - +
366B HIS* 2.8 23.6 + - + +
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Residues in contact with GLN 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B SER* 3.1 18.3 + - - +
361B ALA* 3.4 12.6 - - - +
362B TRP 3.2 0.4 - - - -
363B LEU* 1.3 81.2 - - - +
365B GLN* 1.3 59.1 + - + +
366B HIS 3.4 1.9 + - - -
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Residues in contact with GLN 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B GLU* 4.1 17.9 + - - +
361B ALA* 3.3 15.3 + - - +
362B TRP* 3.1 14.6 + - - +
364B GLN* 1.3 78.7 - - + +
366B HIS* 1.3 80.4 + - + +
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Residues in contact with HIS 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B GLU* 5.1 2.9 - - - -
301B HIS* 5.0 11.2 - - + -
362B TRP* 2.8 78.9 + + + +
363B LEU* 2.8 16.7 + - - +
364B GLN 3.2 2.2 - - - -
365B GLN* 1.3 100.6 + - + +
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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