Contacts of the helix formed by residues 349 - 364 (chain K) in PDB entry 5A31
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 349 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1267A ARG* 4.2 15.7 - - + +
1268A HIS* 3.5 14.4 + - + -
320K ARG* 4.1 1.6 + - - -
344K PHE* 3.0 26.2 + - + +
347K GLU* 3.0 38.5 - - + +
348K SER* 1.3 74.2 - - - +
350K HIS* 1.3 64.0 + - - +
351K ASP* 3.4 6.7 - - - +
352K GLN* 3.4 17.3 + - - +
353K ALA* 3.2 17.4 + - - +
150R LEU* 3.0 47.6 - - - +
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Residues in contact with HIS 350 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1267A ARG* 5.2 4.4 - - + +
1315A GLY* 4.5 17.9 + - - -
1318A ALA* 5.4 1.8 - - - +
345K ALA* 5.1 3.0 - - - -
348K SER* 3.2 35.9 + - - -
349K GLU* 1.3 69.1 - - - +
351K ASP* 1.3 60.2 + - - +
353K ALA* 3.2 2.6 + - - +
354K MET* 2.7 40.0 + - + +
377K GLU* 2.5 38.7 + - - +
380K LEU* 3.8 37.1 - - + +
381K THR* 3.6 32.8 - - + -
4W ARG* 5.9 0.4 - - - -
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Residues in contact with ASP 351 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1266A HIS* 3.9 24.8 + - - -
1267A ARG* 4.2 18.2 - - - +
1268A HIS* 5.3 3.0 - - - +
541C ASP* 3.7 15.5 - - - +
542C THR* 5.5 8.0 - - - +
547C LYS* 4.3 25.9 - - - +
349K GLU* 3.7 5.2 - - - +
350K HIS* 1.3 84.3 + - - +
352K GLN* 1.3 80.6 + - - +
354K MET* 3.3 6.1 - - - +
355K ALA* 3.2 16.5 + - - +
381K THR* 5.5 0.4 - - - +
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Residues in contact with GLN 352 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1268A HIS* 5.7 3.5 - - - +
542C THR* 4.9 7.4 + - - -
344K PHE* 3.8 25.8 - - + -
349K GLU* 3.4 35.9 + - - +
350K HIS 3.3 0.2 - - - -
351K ASP* 1.3 93.2 + - - +
353K ALA* 1.3 66.1 + - - +
355K ALA* 3.1 17.9 + - - +
356K ALA* 3.1 14.9 + - - +
147R PRO 4.2 6.2 - - - +
148R TYR* 3.8 26.0 - - - -
149R SER 3.8 6.7 - - - +
150R LEU* 3.6 26.9 - - - +
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Residues in contact with ALA 353 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341K GLY* 3.7 22.2 - - - +
344K PHE* 3.7 12.6 - - + +
345K ALA 4.0 6.1 - - - +
349K GLU 3.2 11.9 + - - +
350K HIS* 3.5 7.9 - - - +
352K GLN* 1.3 75.8 - - - +
354K MET* 1.3 56.0 + - - +
356K ALA* 3.2 1.4 + - - +
357K TYR* 2.7 53.9 + - + -
377K GLU* 4.1 12.3 - - - -
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Residues in contact with MET 354 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C ASP* 4.0 10.3 - - - +
547C LYS* 4.0 17.3 - - - +
350K HIS 2.7 17.6 + - - +
351K ASP* 3.3 12.3 - - - +
353K ALA* 1.3 70.6 - - - +
355K ALA* 1.3 54.8 + - - +
357K TYR* 3.1 6.8 + - - +
358K PHE* 2.8 61.8 + - + -
374K ILE* 4.3 13.0 - - + +
377K GLU* 3.4 38.4 - - + +
378K TYR* 3.9 34.8 - - + +
381K THR* 4.0 12.6 - - + +
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Residues in contact with ALA 355 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541C ASP* 3.2 30.9 + - + +
351K ASP 3.2 4.3 + - - +
352K GLN* 3.1 12.7 + - - +
354K MET* 1.3 79.8 - - - +
356K ALA* 1.3 58.4 + - - +
358K PHE* 3.3 4.5 + - - +
359K THR* 2.8 34.1 + - - +
147R PRO* 4.5 3.8 - - + +
148R TYR* 3.4 23.6 - - + -
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Residues in contact with ALA 356 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337K TRP* 4.1 22.9 - - + +
340K TYR* 4.2 6.3 - - + +
341K GLY* 3.6 31.4 - - - +
344K PHE* 4.7 4.5 - - + -
352K GLN 3.1 10.4 + - - +
353K ALA 3.9 0.2 - - - +
355K ALA* 1.3 76.7 - - - +
357K TYR* 1.3 62.7 + - - +
359K THR* 3.4 9.8 + - - +
360K ALA* 2.9 28.6 + - - +
148R TYR* 4.4 4.7 - - + -
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Residues in contact with TYR 357 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338K ILE* 3.6 24.9 - - + -
341K GLY* 3.3 9.7 + - - -
342K HIS* 2.8 47.2 + + - -
345K ALA* 3.8 0.9 - - - +
353K ALA* 2.7 45.5 + - + +
354K MET* 3.7 2.9 - - - +
356K ALA* 1.3 71.0 - - - +
358K PHE* 1.3 59.9 + - - +
360K ALA* 3.1 4.1 + - - +
361K ALA* 2.7 29.8 + - - +
370K PRO* 3.9 7.2 - - + +
373K TYR* 3.7 33.2 - + + -
374K ILE* 3.5 22.0 - - + -
377K GLU* 4.2 18.2 - - + -
4W ARG* 3.4 13.4 + - - -
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Residues in contact with PHE 358 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534C GLN* 6.1 5.8 - - + -
537C CYS* 6.1 5.2 - - + -
541C ASP* 4.4 9.0 - - - -
354K MET* 2.8 43.1 + - + +
355K ALA* 3.7 4.5 - - - +
357K TYR* 1.3 73.3 - - - +
359K THR* 1.3 57.9 + - - +
361K ALA* 2.9 8.4 + - + +
362K GLN* 2.8 51.2 + - + +
374K ILE* 3.6 34.1 - - + -
378K TYR* 3.6 28.5 - + - -
390K PHE* 4.0 16.2 - + - -
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Residues in contact with THR 359 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337K TRP* 3.3 29.1 + - + -
355K ALA 2.8 27.8 + - - +
356K ALA* 3.7 9.4 - - - +
358K PHE* 1.3 76.9 - - - +
360K ALA* 1.3 61.2 + - - +
362K GLN* 4.2 6.8 - - - +
363K LEU* 3.4 24.8 + - - +
148R TYR* 3.1 27.4 - - + +
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Residues in contact with ALA 360 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334K GLY 4.7 1.6 - - - +
337K TRP* 3.6 23.1 - - + +
338K ILE* 4.0 27.1 - - + +
356K ALA 2.9 14.7 + - - +
357K TYR* 3.4 10.1 - - - +
359K THR* 1.3 78.2 + - - +
361K ALA* 1.3 57.7 + - - +
363K LEU* 3.4 4.6 + - - +
364K MET* 2.9 36.2 + - - +
370K PRO* 4.3 4.5 - - + -
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Residues in contact with ALA 361 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357K TYR 2.7 17.2 + - - +
358K PHE* 2.9 11.9 + - + +
360K ALA* 1.3 72.0 - - - +
362K GLN* 1.3 68.6 + - + +
364K MET 3.1 20.6 + - - +
365K LYS* 3.5 6.6 + - - +
370K PRO* 3.5 23.3 - - + -
371K MET* 4.9 9.9 - - + +
374K ILE* 3.9 15.7 - - + -
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Residues in contact with GLN 362 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538C ALA* 5.5 9.4 - - - +
358K PHE* 2.8 37.5 + - + +
359K THR* 4.4 5.6 - - - +
360K ALA 3.3 0.2 - - - -
361K ALA* 1.3 80.8 - - + +
363K LEU* 1.3 59.8 + - - +
365K LYS* 3.3 30.3 - - - +
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Residues in contact with LEU 363 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146K ARG* 3.9 20.9 - - - +
173K HIS* 5.8 2.7 - - + +
175K MET* 3.1 37.9 - - + +
331K LYS 4.3 10.3 - - - +
332K THR 3.5 22.7 - - - +
333K TYR 4.3 1.6 - - - +
334K GLY* 4.0 20.0 - - - +
337K TRP* 3.6 30.3 - - + +
359K THR* 3.4 21.4 + - - +
360K ALA 3.9 5.2 - - - +
361K ALA 3.2 0.4 - - - -
362K GLN* 1.3 80.8 - - - +
364K MET* 1.3 59.5 + - + +
365K LYS* 3.6 2.4 + - - +
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Residues in contact with MET 364 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173K HIS* 3.5 26.7 - - + +
174K HIS* 3.4 9.6 - - + -
334K GLY* 3.4 19.5 - - - +
335K PRO* 3.2 43.5 - - + -
338K ILE* 3.9 24.9 - - + -
360K ALA* 2.9 21.3 + - - +
361K ALA 3.1 5.6 + - - +
363K LEU* 1.3 82.5 - - + +
365K LYS* 1.3 66.3 + - - +
366K GLY 3.1 4.4 + - - -
367K CYS* 3.3 26.6 + - + +
370K PRO* 4.5 6.4 - - + +
371K MET* 4.6 0.5 - - - +
1W MET* 4.7 9.0 - - + +
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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