Contacts of the helix formed by residues 337 - 350 (chain Q) in PDB entry 4UJ3
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 LYS 337 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396N ASP* 4.1 23.4 - - - +
397N SER* 5.1 4.8 - - - +
335Q PHE* 4.2 0.9 - - - +
336Q SER* 1.3 79.9 - - - +
338Q SER* 1.3 58.0 + - - +
339Q GLU* 3.2 3.5 + - + +
340Q LEU* 3.4 12.2 + - + +
341Q ALA* 2.9 28.2 + - - +
379Q CYS 5.5 0.7 - - - -
380Q ALA 3.1 20.6 - - - +
381Q LEU* 3.0 18.6 + - - +
383Q GLY* 4.0 30.9 - - - +
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Residues in contact with SER 338 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400N TYR* 4.4 20.4 + - - -
335Q PHE 4.3 6.5 - - - -
336Q SER 3.0 10.0 + - - -
337Q LYS* 1.3 70.6 - - - +
339Q GLU* 1.3 60.4 + - - +
341Q ALA* 3.6 8.2 - - - +
342Q SER* 2.8 38.5 + - - -
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Residues in contact with GLU 339 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136M THR* 6.6 0.4 - - - -
137M ASP* 4.3 14.7 - - - +
140M ARG* 4.3 23.8 + - - +
400N TYR* 5.9 2.2 - - - +
337Q LYS* 3.2 1.7 - - + -
338Q SER* 1.3 81.8 + - - +
340Q LEU* 1.3 62.4 + - - +
342Q SER* 3.6 3.7 + - - -
343Q ALA* 3.3 20.6 + - - +
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Residues in contact with LEU 340 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140M ARG* 5.0 3.8 - - - +
337Q LYS* 3.4 14.5 + - + +
339Q GLU* 1.3 76.6 - - - +
341Q ALA* 1.3 65.7 + - - +
343Q ALA* 3.2 7.2 + - + +
344Q VAL* 3.0 36.1 + - + +
372Q GLU* 4.3 4.5 - - + +
380Q ALA* 3.6 37.9 - - + +
381Q LEU* 3.5 23.6 - - + -
392Q ILE* 5.2 0.4 - - + -
394Q LEU* 4.6 7.2 - - + -
401Q TYR* 3.9 46.0 - - + -
403Q ILE* 5.1 0.2 - - + -
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Residues in contact with ALA 341 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333Q LEU* 3.6 26.3 - - - +
335Q PHE* 4.0 20.4 - - + +
337Q LYS 2.9 18.2 + - - +
338Q SER* 3.6 10.5 - - - +
339Q GLU 3.2 0.2 - - - -
340Q LEU* 1.3 76.9 - - - +
342Q SER* 1.3 62.8 + - - +
344Q VAL* 3.0 7.8 + - - +
345Q LEU* 3.0 22.3 + - - +
381Q LEU* 4.0 9.8 - - - +
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Residues in contact with SER 342 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338Q SER* 2.8 20.9 + - - -
339Q GLU* 4.1 4.3 - - - -
341Q ALA* 1.3 76.3 - - - +
343Q ALA* 1.3 61.4 + - - +
345Q LEU* 3.7 12.2 - - - +
346Q GLU* 3.3 21.8 + - - +
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Residues in contact with ALA 343 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140M ARG* 5.3 9.6 - - - +
339Q GLU 3.3 14.0 + - - +
340Q LEU* 3.2 14.3 + - + +
341Q ALA 3.1 0.4 - - - -
342Q SER* 1.3 76.2 - - - +
344Q VAL* 1.3 63.8 + - - +
346Q GLU* 3.4 6.3 + - - +
347Q ALA* 3.0 22.9 + - - +
394Q LEU* 3.6 24.3 - - + +
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Residues in contact with VAL 344 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333Q LEU* 5.0 6.5 - - + -
335Q PHE* 6.1 1.1 - - + -
340Q LEU* 3.2 20.2 - - + +
341Q ALA* 3.0 7.6 + - - +
343Q ALA* 1.3 74.7 - - - +
345Q LEU* 1.3 64.2 + - - +
347Q ALA* 3.1 8.3 + - - +
348Q VAL* 2.9 36.7 + - + +
353Q LEU* 4.1 12.8 - - + -
381Q LEU* 4.2 11.7 - - + -
392Q ILE* 3.6 25.6 - - + -
394Q LEU* 4.2 9.2 - - + -
411Q ILE* 3.7 28.3 - - + -
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Residues in contact with LEU 345 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316Q ARG* 6.0 0.9 - - - +
325Q TYR* 4.7 4.7 - - + -
329Q ILE* 4.2 15.9 - - + -
330Q PHE* 4.7 18.4 - - + -
333Q LEU* 3.4 36.1 - - + +
341Q ALA 3.0 11.9 + - - +
342Q SER* 3.7 15.0 - - - +
343Q ALA 3.3 0.2 - - - -
344Q VAL* 1.3 78.4 - - - +
346Q GLU* 1.3 66.8 + - + +
348Q VAL* 3.4 3.9 + - + +
349Q GLU* 3.3 47.3 + - + +
418Q PHE* 5.2 3.1 - - + -
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Residues in contact with GLU 346 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342Q SER 3.3 13.6 + - - +
343Q ALA* 3.9 6.0 - - - +
344Q VAL 3.2 0.4 - - - -
345Q LEU* 1.3 85.9 - - + +
347Q ALA* 1.3 66.1 + - - +
349Q GLU* 3.2 12.1 + - - +
350Q ASN* 3.1 40.4 + - - +
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Residues in contact with ALA 347 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343Q ALA 3.0 14.1 + - - +
344Q VAL 3.1 8.7 + - - +
346Q GLU* 1.3 76.8 - - - +
348Q VAL* 1.3 56.9 + - - +
350Q ASN* 3.4 1.2 + - - +
351Q ASN* 2.9 5.5 + - - -
352Q THR* 2.7 48.0 + - - +
353Q LEU* 3.1 19.6 + - + +
394Q LEU* 3.9 22.2 - - + -
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Residues in contact with VAL 348 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333Q LEU* 4.9 5.6 - - + -
344Q VAL* 2.9 26.5 + - + +
345Q LEU* 3.4 11.0 - - - +
347Q ALA* 1.3 75.2 - - - +
349Q GLU* 1.3 64.0 + - - +
351Q ASN* 3.1 14.5 + - - +
353Q LEU* 3.7 27.4 - - + -
411Q ILE* 4.6 3.1 - - + +
414Q VAL* 4.2 9.6 - - + -
415Q CYS* 3.9 20.0 - - - -
418Q PHE* 3.4 43.1 - - + +
422Q ARG* 4.6 4.2 + - - -
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Residues in contact with GLU 349 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314Q MET* 4.6 14.3 - - + +
316Q ARG* 3.6 26.4 + - - -
325Q TYR* 2.7 42.5 + - - +
345Q LEU* 3.3 31.4 + - + +
346Q GLU* 3.2 16.7 + - + +
348Q VAL* 1.3 78.0 - - - +
350Q ASN* 1.3 64.3 + - - +
351Q ASN 3.3 0.8 + - - -
418Q PHE* 3.9 19.3 - - + -
422Q ARG* 4.8 8.0 + - - -
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Residues in contact with ASN 350 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346Q GLU* 3.1 38.3 + - - +
347Q ALA* 4.1 0.4 - - - +
349Q GLU* 1.3 82.2 - - - +
351Q ASN* 1.3 70.8 + - - +
352Q THR* 3.1 26.9 + - + +
422Q ARG* 6.2 0.2 - - - -
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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