Contacts of the helix formed by residues 334 - 353 (chain I) in PDB entry 3J5M
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 SER 334 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333I VAL* 1.3 72.2 - - - +
335I LYS* 1.3 59.9 + - - +
336I ALA* 3.8 10.2 + - - +
337I THR* 2.9 43.3 + - - -
338I TRP* 3.5 5.2 - - - -
412I ASP 4.2 7.3 + - - -
413I SER* 3.6 13.8 - - - -
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Residues in contact with LYS 335 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333I VAL 3.0 3.0 + - - -
334I SER* 1.3 71.4 + - - +
336I ALA* 1.3 60.9 + - - +
338I TRP* 3.3 2.2 - - - +
339I ASN* 3.1 22.2 + - - +
412I ASP* 4.3 7.2 - - + +
413I SER* 2.8 17.8 + - - +
414I ILE* 1.3 217.8 - - + +
415I THR* 2.6 9.4 + - - +
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Residues in contact with ALA 336 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334I SER* 3.2 9.3 + - - +
335I LYS* 1.3 77.5 - - - +
337I THR* 1.3 64.7 + - - +
338I TRP 3.4 0.2 - - - -
339I ASN* 3.4 11.7 + - - +
340I GLU* 3.0 22.9 + - - +
412I ASP* 4.3 11.2 + - - +
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Residues in contact with THR 337 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291I PRO 5.0 3.1 - - - +
292I VAL* 3.7 30.5 - - + -
293I GLN 5.3 1.3 - - - +
333I VAL* 4.8 2.9 - - + -
334I SER* 2.9 32.1 + - - -
336I ALA* 1.3 82.5 - - - +
338I TRP* 1.3 58.5 - - - +
340I GLU* 3.4 25.4 - - - +
341I THR* 3.8 8.0 + - - +
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Residues in contact with TRP 338 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288I PHE* 5.9 1.6 - - + -
292I VAL* 4.1 14.1 - - + -
294I ILE* 5.3 1.3 - - + -
333I VAL* 3.6 33.6 + - + +
334I SER 3.5 10.0 + - - -
335I LYS* 3.3 13.2 - - - +
337I THR* 1.3 74.6 - - - +
339I ASN* 1.3 69.1 + - + +
340I GLU 3.3 0.2 - - - -
341I THR* 2.6 30.6 + - - +
342I LEU* 3.0 44.2 + - + +
389I GLY 4.1 4.3 - - - -
390I LEU* 3.5 45.6 - - + +
414I ILE* 1.1 82.7 - - + +
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Residues in contact with ASN 339 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335I LYS 3.1 20.9 + - - +
336I ALA* 3.4 13.1 + - - +
338I TRP* 1.3 86.2 - - + +
340I GLU* 1.3 63.5 + - - +
342I LEU* 3.4 6.3 + - - +
343I GLY* 3.1 18.5 + - - -
395I TRP* 3.7 25.0 + - - +
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Residues in contact with GLU 340 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290I THR* 5.3 3.2 - - - +
336I ALA 3.0 11.7 + - - +
337I THR* 3.4 17.3 - - - +
339I ASN* 1.3 77.1 - - - +
341I THR* 1.3 64.9 + - - +
343I GLY* 3.0 12.9 + - - -
344I LYS* 3.0 38.8 + - + +
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Residues in contact with THR 341 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270I VAL* 6.2 0.2 - - - -
288I PHE* 3.8 29.2 - - + -
290I THR* 3.7 30.3 - - + -
292I VAL* 3.8 16.6 - - + -
337I THR 3.8 13.7 - - - +
338I TRP* 2.6 27.6 + - - +
340I GLU* 1.3 77.4 - - + +
342I LEU* 1.3 58.6 + - - +
344I LYS* 3.1 13.9 + - - +
345I VAL* 2.9 33.1 + - - +
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Residues in contact with LEU 342 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338I TRP* 3.0 42.6 + - + +
339I ASN* 3.6 6.5 - - - +
340I GLU 3.2 0.2 - - - -
341I THR* 1.3 76.2 + - - +
343I GLY* 1.3 63.7 + - - +
345I VAL* 3.2 7.3 + - + +
346I VAL* 3.0 31.9 + - - +
361I PHE* 3.7 22.7 - - + -
390I LEU 3.4 24.5 - - - +
391I PHE* 5.9 2.2 - - + -
395I TRP* 3.7 31.2 - - + -
452I LEU* 4.2 25.8 - - + -
454I LEU* 6.1 0.4 - - + -
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Residues in contact with GLY 343 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339I ASN 3.1 10.7 + - - -
340I GLU* 3.0 9.3 + - - -
342I LEU* 1.3 76.9 - - - +
344I LYS* 1.3 60.1 + - - +
346I VAL* 3.1 23.1 - - - +
347I LYS* 3.1 25.1 - - - +
395I TRP* 4.2 10.9 - - - +
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Residues in contact with LYS 344 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270I VAL* 3.8 18.4 - - + -
289I ASN* 2.9 35.9 + - - +
290I THR* 3.7 19.5 - - + +
340I GLU* 3.0 35.3 + - + +
341I THR* 3.1 18.8 + - - +
343I GLY* 1.3 75.0 - - - +
345I VAL* 1.3 63.6 + - - +
347I LYS* 3.3 13.4 + - + +
348I GLN* 3.1 29.7 + - + +
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Residues in contact with VAL 345 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270I VAL* 4.4 5.6 - - + -
272I ILE* 4.5 2.9 - - + -
286I VAL* 3.6 36.6 - - + -
288I PHE* 3.7 16.2 - - + -
341I THR 2.9 20.3 + - - +
342I LEU* 3.2 14.3 + - + +
344I LYS* 1.3 75.8 - - - +
346I VAL* 1.3 58.1 + - - +
348I GLN* 3.0 9.2 + - - +
349I LEU* 2.8 48.3 + - + +
361I PHE* 3.9 13.0 - - + -
452I LEU* 5.4 2.0 - - + -
454I LEU* 4.9 4.7 - - + -
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Residues in contact with VAL 346 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342I LEU 3.0 13.9 + - - +
343I GLY* 3.1 20.9 - - - +
345I VAL* 1.3 75.5 - - - +
347I LYS* 1.3 59.6 + - + +
349I LEU* 4.1 7.9 - - - -
350I ARG* 3.0 39.1 + - - +
359I ILE* 3.6 22.0 - - + +
361I PHE* 3.5 29.2 - - + -
395I TRP* 3.6 39.7 - - + -
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Residues in contact with LYS 347 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343I GLY* 3.1 24.5 + - - +
344I LYS* 3.4 14.4 - - + +
345I VAL 3.2 0.2 - - - -
346I VAL* 1.3 78.1 - - + +
348I GLN* 1.3 66.4 + - + +
350I ARG* 3.5 34.4 - - - +
351I LYS* 3.2 38.1 + - - +
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Residues in contact with GLN 348 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269I GLU* 2.8 37.2 + - - +
270I VAL* 3.6 34.0 - - + +
272I ILE* 3.5 16.2 - - + -
344I LYS* 3.1 15.6 + - - +
345I VAL 3.0 8.0 + - - +
347I LYS* 1.3 78.9 - - - +
349I LEU* 1.3 61.5 + - - +
351I LYS* 3.4 15.0 + - - +
352I HIS* 3.0 47.5 + - + -
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Residues in contact with LEU 349 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272I ILE* 3.6 27.1 - - + -
284I ILE* 5.0 2.9 - - + -
286I VAL* 5.8 0.7 - - + -
345I VAL* 2.8 38.6 + - + +
346I VAL 3.9 2.5 - - - +
347I LYS 3.3 0.2 - - - -
348I GLN* 1.3 73.6 - - - +
350I ARG* 1.3 55.9 + - - +
352I HIS* 2.8 22.4 + - - +
353I PHE* 2.9 33.6 + - + -
359I ILE* 3.7 36.1 - - + -
361I PHE* 3.8 9.0 - - + -
454I LEU* 5.2 2.0 - - + -
468I PHE* 3.7 36.1 - - + -
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Residues in contact with ARG 350 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346I VAL* 3.0 26.1 + - - +
347I LYS* 3.5 35.9 + - - +
349I LEU* 1.3 77.1 - - - +
351I LYS* 1.3 65.8 + - + +
353I PHE 3.7 7.0 + - - +
355I ASN* 2.6 37.9 + - - -
356I ASN* 3.2 6.7 + - - +
357I THR 3.1 27.4 - - - +
359I ILE* 3.9 6.9 - - + +
395I TRP* 6.3 0.4 - - - +
396I ILE 4.3 4.0 + - - -
397I SER* 3.4 47.2 + - - +
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Residues in contact with LYS 351 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269I GLU* 5.3 9.9 + - - -
347I LYS* 3.2 26.8 + - - +
348I GLN* 3.6 16.7 - - - +
349I LEU 3.1 0.6 - - - -
350I ARG* 1.3 90.1 - - + +
352I HIS* 1.3 66.6 + - + +
353I PHE 3.5 0.2 - - - -
355I ASN* 2.9 29.7 - - - +
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Residues in contact with HIS 352 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270I VAL 5.7 0.2 - - - -
272I ILE* 4.0 40.3 - - + +
277I ILE* 4.7 15.6 - - + +
348I GLN* 3.0 40.1 + - + -
349I LEU* 2.8 10.0 + - - +
351I LYS* 1.3 88.7 - - + +
353I PHE* 1.3 80.3 + - + +
354I GLY 3.8 2.7 + - - -
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Residues in contact with PHE 353 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272I ILE* 6.3 1.1 - - + -
277I ILE* 3.8 46.0 - - + -
278I THR* 5.2 4.0 - - + -
284I ILE* 5.9 2.9 - - + -
349I LEU* 2.9 50.7 + - + +
350I ARG* 3.7 3.1 - - - +
352I HIS* 1.3 89.4 - - + +
354I GLY* 1.3 50.2 + - - +
355I ASN 3.4 3.4 + - - -
357I THR* 2.7 34.2 + - - +
359I ILE* 5.3 3.6 - - + -
456I ARG* 3.8 32.5 - - - -
466I GLU* 4.9 14.8 - - + -
468I PHE* 4.1 15.0 - + - -
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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
------------------------------------------------------------
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