Contacts of the helix formed by residues 337 - 353 (chain A) in PDB entry 3VOC
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 LEU 337 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A HIS 3.1 8.5 + - - -
287A MET* 3.3 26.7 - - + +
288A ASN* 3.6 33.0 - - + +
328A ASP* 2.9 38.9 - - + +
329A SER 3.9 2.7 - - - +
330A GLY* 3.6 26.5 - - - +
335A TYR 3.9 0.2 + - - -
336A SER* 1.3 74.0 - - - +
338A PRO* 1.4 57.6 - - - +
340A THR* 4.1 9.0 - - + +
341A LEU 3.0 22.0 + - - -
511A PEG 4.6 12.6 - - - +
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Residues in contact with PRO 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A HIS* 3.6 26.0 - - + -
323A CYS* 4.0 10.2 - - + +
326A MET* 3.4 36.1 - - + -
327A SER 3.4 23.3 - - - +
336A SER* 3.2 20.6 - - - +
337A LEU* 1.4 89.6 - - - +
339A SER* 1.3 56.0 + - - +
341A LEU* 3.3 4.0 + - + +
342A VAL* 2.9 34.4 + - - +
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Residues in contact with SER 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A MET 3.6 19.5 + - - -
328A ASP* 2.9 24.4 + - - -
338A PRO* 1.3 78.4 - - - +
340A THR* 1.3 61.0 + - - +
342A VAL* 3.4 3.5 + - - +
343A ASP* 3.0 30.5 + - - +
371A LYS* 3.4 12.3 - - - -
375A LYS* 2.8 33.8 + - - +
509A TRS 3.1 11.5 + - - -
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Residues in contact with THR 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A MET* 4.4 11.4 - - + -
328A ASP* 2.5 28.0 + - - -
337A LEU* 3.6 17.4 - - + +
339A SER* 1.3 73.3 - - - +
341A LEU* 1.3 59.0 + - - +
343A ASP* 3.2 8.0 + - - +
344A THR* 2.8 41.2 + - - +
509A TRS 4.1 11.7 + - - -
511A PEG 4.6 14.8 - - - +
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Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLY* 4.0 2.2 - - - -
283A LEU 3.8 20.4 - - - +
284A HIS* 3.7 30.5 - - + +
287A MET* 3.8 13.2 - - + -
297A GLU* 3.6 9.9 - - - +
305A TYR* 3.6 33.7 - - + +
321A PHE* 3.6 20.4 - - + -
323A CYS* 5.4 1.3 - - - -
337A LEU 3.0 13.6 + - - +
338A PRO* 3.5 8.7 - - + +
340A THR* 1.3 75.1 - - - +
342A VAL* 1.3 66.2 + - - +
344A THR* 3.2 8.5 + - - -
345A VAL* 2.9 31.0 + - + +
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Residues in contact with VAL 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PHE* 3.8 11.0 - - + -
322A THR 3.5 25.1 - - - +
323A CYS* 3.8 17.7 - - + +
324A LEU* 4.0 14.8 - - + +
338A PRO 2.9 20.8 + - - +
339A SER* 3.6 8.1 - - - +
341A LEU* 1.3 75.5 - - - +
343A ASP* 1.3 56.7 + - - +
345A VAL* 4.2 0.3 - - - +
346A SER* 2.8 48.4 + - - +
375A LYS* 3.8 32.3 - - + -
379A PHE* 4.9 0.9 - - + -
381A TYR* 4.1 1.8 - - - +
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Residues in contact with ASP 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A SER 3.0 10.8 + - - -
340A THR* 3.5 8.7 - - - +
342A VAL* 1.3 74.3 - - - +
344A THR* 1.3 58.8 + - - +
346A SER* 4.0 0.2 - - - -
347A SER* 2.8 38.1 + - - +
375A LYS* 2.6 22.3 + - - -
378A LYS* 4.9 4.8 + - - +
379A PHE* 3.3 29.4 - - + -
509A TRS 2.5 32.7 + - - -
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Residues in contact with THR 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A MET* 5.9 0.3 - - - +
305A TYR* 4.5 18.4 - - + -
340A THR* 2.8 29.4 + - - +
341A LEU* 3.5 12.7 - - + -
343A ASP* 1.3 73.3 - - - +
345A VAL* 1.3 63.2 + - + +
347A SER* 3.7 4.0 - - - -
348A ILE* 3.1 45.2 + - + +
511A PEG 4.6 8.3 + - - +
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Residues in contact with VAL 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE* 5.2 2.9 - - + -
305A TYR* 4.3 25.1 - - + -
309A ILE* 3.7 11.8 - - + +
319A LEU* 3.8 26.2 - - + -
321A PHE* 3.9 45.1 - - + -
341A LEU* 2.9 31.0 + - + +
342A VAL 4.2 1.6 - - - +
344A THR* 1.3 74.1 - - - +
346A SER* 1.3 60.0 + - - +
348A ILE* 3.3 4.2 + - - +
349A ALA* 2.9 27.7 + - - +
356A LEU* 4.9 1.3 - - + -
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Residues in contact with SER 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PHE* 5.4 0.3 - - - -
342A VAL* 2.8 27.7 + - - +
343A ASP 4.0 0.4 - - - -
345A VAL* 1.3 78.4 - - - +
347A SER* 1.3 55.7 + - - +
349A ALA 3.4 0.9 + - - -
350A ASN* 2.9 33.6 + - - -
356A LEU* 3.6 14.1 - - - +
379A PHE* 3.4 33.9 - - - -
381A TYR* 2.7 28.8 + - - -
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Residues in contact with SER 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ASP* 2.8 27.2 + - - +
344A THR* 3.7 4.7 - - - -
346A SER* 1.3 72.4 - - - +
348A ILE* 1.3 59.6 + - - +
350A ASN* 3.5 3.9 + - - +
351A ALA* 2.9 30.3 + - - +
379A PHE* 3.5 18.9 - - - -
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Residues in contact with ILE 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A TYR* 3.8 25.8 - - + -
306A ASN* 3.4 41.1 - - - +
309A ILE* 3.7 18.4 - - + -
344A THR* 3.1 31.5 + - + +
345A VAL 3.7 3.4 - - - +
347A SER* 1.3 74.7 - - - +
349A ALA* 1.3 65.8 + - - +
351A ALA* 3.2 7.7 + - + +
352A LYS* 3.1 36.1 + - + +
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Residues in contact with ALA 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ILE* 3.8 12.5 - - + +
319A LEU* 4.1 10.5 - - + -
345A VAL 2.9 17.0 + - - +
346A SER 3.7 1.1 - - - +
348A ILE* 1.3 76.0 - - - +
350A ASN* 1.3 57.7 + - - +
352A LYS 3.1 2.6 + - - -
353A GLY 2.9 8.0 + - - -
354A VAL* 2.8 40.7 + - + +
356A LEU* 3.6 31.6 - - + -
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Residues in contact with ASN 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A SER 2.9 16.7 + - - +
347A SER* 4.0 4.9 - - - +
349A ALA* 1.3 73.5 - - - +
351A ALA* 1.3 66.0 - - - +
353A GLY* 3.1 13.6 + - - +
354A VAL 4.3 5.6 - - - +
356A LEU* 3.5 10.3 + - - +
378A LYS 4.9 0.4 + - - -
379A PHE* 2.8 53.6 + - - +
380A GLY 5.1 1.7 - - - +
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Residues in contact with ALA 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A SER 2.9 18.3 + - - +
348A ILE* 3.2 8.9 + - - +
350A ASN* 1.3 76.3 - - - +
352A LYS* 1.3 62.0 + - + +
353A GLY 3.8 0.2 + - - -
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Residues in contact with LYS 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ASN* 3.2 35.3 + - - +
309A ILE* 4.3 4.9 - - + +
310A GLN* 3.0 44.3 - - - +
313A LYS* 2.7 43.3 + - + +
348A ILE* 3.1 30.7 + - + +
349A ALA 3.8 3.6 - - - +
350A ASN 3.1 0.2 - - - -
351A ALA* 1.3 80.1 - - + +
353A GLY* 1.3 55.4 + - - +
354A VAL* 4.2 10.5 - - + -
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Residues in contact with GLY 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A LYS* 4.1 10.0 + - - +
349A ALA 2.9 3.9 + - - -
350A ASN* 3.1 12.9 + - - -
351A ALA 3.4 0.6 + - - -
352A LYS* 1.3 79.8 - - - +
354A VAL* 1.3 63.6 + - - +
355A ARG* 3.7 5.2 + - - +
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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
------------------------------------------------------------
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