Contacts of the helix formed by residues 334 - 348 (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 GLY 334 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173K HIS* 5.0 3.0 - - - -
332K THR 4.0 0.2 + - - -
333K TYR* 1.3 70.1 - - - +
335K PRO* 1.3 65.7 - - - +
336K ALA 3.0 1.8 - - - -
337K TRP* 2.6 35.0 + - - +
338K ILE 3.2 3.6 + - - -
360K ALA 5.4 0.2 - - - -
363K LEU* 4.0 16.8 - - - +
364K MET* 3.4 29.7 - - - +
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Residues in contact with PRO 335 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173K HIS* 4.0 19.3 - - + +
269K PRO* 5.1 7.9 - - + -
303K PHE* 3.5 29.2 - - + -
333K TYR* 3.8 30.1 - - + +
334K GLY* 1.3 89.6 - - - +
336K ALA* 1.3 56.0 + - - +
338K ILE* 3.4 8.4 + - + +
339K ALA* 3.2 21.7 + - - +
364K MET* 3.2 20.3 - - + -
1W MET* 4.7 17.9 - - + +
2W LEU* 5.3 1.5 - - + +
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Residues in contact with ALA 336 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303K PHE* 4.0 12.8 - - + -
323K LEU* 3.9 11.6 - - + +
326K ALA* 4.0 20.9 - - + -
327K THR* 4.3 11.4 - - - +
333K TYR* 3.5 31.1 - - + +
334K GLY 2.8 0.4 + - - -
335K PRO* 1.3 77.9 - - - +
337K TRP* 1.3 60.7 + - - +
339K ALA* 3.7 3.7 - - - +
340K TYR* 3.1 25.1 + - - +
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Residues in contact with TRP 337 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327K THR* 2.7 34.0 + - + -
331K LYS* 3.8 17.3 + - + -
333K TYR 3.0 23.7 + - - -
334K GLY 2.6 12.7 + - - +
336K ALA* 1.3 71.2 - - - +
338K ILE* 1.3 65.9 + - - +
340K TYR* 2.8 41.7 + + + +
341K GLY* 2.8 11.8 + - - -
356K ALA* 4.1 12.9 - - + +
359K THR* 3.3 22.5 + - + -
360K ALA* 3.6 19.7 - - + +
363K LEU* 3.6 19.2 - - + +
148R TYR* 3.5 40.4 - + - -
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Residues in contact with ILE 338 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334K GLY 3.2 4.7 + - - +
335K PRO 3.8 7.2 - - - +
337K TRP* 1.3 76.6 - - - +
339K ALA* 1.3 65.9 + - - +
341K GLY* 3.0 4.7 + - - -
342K HIS* 2.9 49.9 + - + +
357K TYR* 3.6 15.4 - - + -
360K ALA* 4.0 14.1 - - + -
364K MET* 3.9 29.2 - - + -
367K CYS* 4.6 1.6 - - - -
369K LEU* 4.2 12.8 - - + -
370K PRO* 4.0 24.7 - - + -
373K TYR* 5.4 0.4 - - + -
1W MET 4.5 10.5 - - - +
2W LEU* 3.7 21.8 - - + +
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Residues in contact with ALA 339 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303K PHE* 3.9 6.3 - - + -
307K CYS* 5.1 0.4 - - + -
310K LEU* 4.0 6.2 - - + +
323K LEU* 3.5 33.0 - - + +
335K PRO 3.2 14.1 + - - +
336K ALA 3.7 1.3 - - - +
338K ILE* 1.3 81.7 - - - +
340K TYR* 1.3 63.4 + - - +
342K HIS* 3.0 15.0 + - - +
343K SER* 3.1 12.5 + - - -
2W LEU* 3.8 27.6 - - + -
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Residues in contact with TYR 340 (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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320K ARG* 3.6 30.9 + - + +
323K LEU* 3.6 14.6 - - + -
324K SER* 4.3 23.8 + - - -
327K THR* 4.6 8.1 - - + -
336K ALA 3.1 14.0 + - - +
337K TRP* 2.8 46.7 + + + +
339K ALA* 1.3 75.3 - - - +
341K GLY* 1.3 60.1 + - - +
343K SER* 2.6 23.1 + - - -
344K PHE* 3.4 32.2 - + - -
356K ALA* 4.2 2.7 - - + -
148R TYR* 4.0 25.6 - + - +
149R SER* 4.8 8.7 + - - -
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Residues in contact with GLY 341 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337K TRP 2.8 10.9 + - - -
338K ILE 3.0 4.4 + - - -
340K TYR* 1.3 76.5 - - - +
342K HIS* 1.3 60.7 + - - +
344K PHE* 3.0 11.2 + - - +
345K ALA 3.0 17.0 + - - -
353K ALA* 3.7 5.8 - - - +
356K ALA* 3.6 19.6 - - - +
357K TYR* 3.3 21.6 + - - -
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Residues in contact with HIS 342 (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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310K LEU* 4.4 10.3 - - + -
338K ILE* 2.9 35.1 + - + +
339K ALA* 3.2 8.5 - - - +
341K GLY* 1.3 75.4 - - - +
343K SER* 1.3 56.2 + - - +
345K ALA* 3.7 3.0 - - - +
346K VAL* 2.9 34.3 + - - +
357K TYR* 2.8 30.7 + + - -
373K TYR* 3.9 17.9 - + - -
2W LEU* 2.7 50.6 + - + -
3W ARG 4.0 6.7 - - - -
4W ARG* 3.9 20.7 - - + +
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Residues in contact with SER 343 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310K LEU* 4.0 18.7 - - - +
316K ASN* 3.9 5.1 - - - +
320K ARG* 3.4 47.7 + - - +
323K LEU* 3.9 5.0 - - - +
339K ALA 3.1 9.0 + - - -
340K TYR* 2.6 25.2 + - - -
342K HIS* 1.3 76.6 - - - +
344K PHE* 1.3 62.3 + - - +
346K VAL* 3.3 18.5 - - - +
347K GLU 3.3 4.7 + - - -
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Residues in contact with PHE 344 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320K ARG* 3.5 32.1 - - - -
340K TYR* 3.4 52.9 - + - -
341K GLY* 3.0 7.2 + - - +
343K SER* 1.3 74.7 - - - +
345K ALA* 1.3 55.8 + - - +
347K GLU* 3.2 5.2 + - - +
348K SER 2.7 29.8 + - - -
349K GLU* 3.0 41.7 + - - +
352K GLN* 3.8 30.3 - - + -
353K ALA* 3.7 5.6 - - - +
356K ALA* 4.8 2.2 - - + -
148R TYR* 4.1 7.4 - - + -
149R SER* 3.9 18.2 - - - -
150R LEU* 3.8 13.7 - - + -
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Residues in contact with ALA 345 (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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341K GLY 3.0 11.7 + - - +
342K HIS 3.2 6.3 + - - +
344K PHE* 1.3 77.3 - - - +
346K VAL* 1.3 58.7 + - - +
348K SER* 2.9 23.6 + - - +
349K GLU 4.8 0.4 - - - +
350K HIS* 5.1 2.9 - - - -
353K ALA* 4.0 4.9 - - + +
357K TYR* 3.8 6.5 - - - +
377K GLU* 3.3 26.4 - - - +
4W ARG* 3.6 31.2 + - - +
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Residues in contact with VAL 346 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310K LEU* 5.3 2.2 - - + -
316K ASN* 3.1 35.7 - - - +
342K HIS 2.9 14.8 + - - +
343K SER* 3.3 10.8 - - - +
345K ALA* 1.3 77.8 - - - +
347K GLU* 1.3 60.7 + - - +
348K SER* 3.2 4.0 + - - -
4W ARG* 4.8 5.8 - - - +
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Residues in contact with GLU 347 (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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1267A ARG* 4.1 6.1 + - - -
1271A GLU* 4.5 19.4 - - - +
316K ASN* 4.5 5.6 - - - +
320K ARG* 3.8 14.3 + - - +
343K SER 3.3 14.3 + - - +
344K PHE 3.2 3.9 + - - +
346K VAL* 1.3 78.9 - - - +
348K SER* 1.3 65.6 + - - +
349K GLU* 3.0 43.1 - - + +
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Residues in contact with SER 348 (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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1267A ARG* 3.1 27.6 + - - -
1318A ALA* 3.0 28.7 - - - +
344K PHE 2.7 9.9 + - - -
345K ALA 2.9 16.7 + - - -
346K VAL 4.3 2.9 - - - -
347K GLU* 1.3 78.4 - - - +
349K GLU* 1.3 56.2 + - - +
350K HIS* 3.2 32.1 + - - -
380K LEU* 5.9 0.3 - - - +
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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