Contacts of the helix formed by residues 321 - 336 (chain B) in PDB entry 2Y4T
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 321 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B THR* 5.9 4.0 - - + -
316B PHE* 2.8 40.4 + - + +
317B SER* 5.5 0.4 - - - -
319B ASP* 3.4 35.8 + - + +
320B GLU* 1.3 77.5 + - - +
322B PRO* 1.3 62.1 - - + +
323B VAL 3.4 2.2 + - - -
324B GLU* 3.2 20.5 + - - +
325B ALA* 2.9 29.7 + - - +
352B ILE* 5.2 0.4 - - - +
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Residues in contact with PRO 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B GLU 3.2 13.0 - - - +
321B LYS* 1.3 84.5 - - + +
323B VAL* 1.3 66.6 + - + +
324B GLU* 4.5 2.0 - - - +
326B ILE* 3.2 32.5 + - - +
349B ALA* 3.5 20.7 - - + +
352B ILE* 4.1 22.0 - - + -
353B GLU* 3.4 37.0 - - + +
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Residues in contact with VAL 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B LYS 3.4 0.4 - - - -
322B PRO* 1.3 80.6 - - + +
324B GLU* 1.3 62.6 + - - +
326B ILE* 3.2 11.1 + - + +
327B ARG* 2.8 41.3 + - + +
353B GLU* 4.8 8.5 - - - +
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Residues in contact with GLU 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B PHE* 3.4 40.4 - - + -
321B LYS* 3.2 29.2 - - - +
322B PRO* 4.5 1.4 - - - +
323B VAL* 1.3 83.1 + - + +
325B ALA* 1.3 57.4 + - - +
327B ARG* 3.3 18.4 + - - +
328B VAL* 2.9 35.5 + - - +
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B CYS 4.5 0.2 - - - -
316B PHE* 3.6 9.1 - - - +
317B SER* 3.7 27.8 - - - +
321B LYS 2.9 17.6 + - - +
324B GLU* 1.3 75.8 - - - +
326B ILE* 1.3 55.6 + - - +
328B VAL* 5.1 0.2 - - - -
329B CYS* 2.7 45.8 + - - -
345B ASP 4.7 0.2 - - - +
346B ARG* 5.0 0.4 - - - -
349B ALA* 3.6 23.1 - - + -
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Residues in contact with ILE 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B PRO 3.2 22.7 + - - +
323B VAL* 3.6 7.2 - - + +
325B ALA* 1.3 77.0 - - - +
327B ARG* 1.3 59.6 + - - +
330B SER* 2.7 42.4 + - - +
346B ARG* 4.0 17.5 - - + -
349B ALA* 3.9 15.0 - - + +
350B TYR* 4.0 36.3 - - + +
353B GLU* 4.4 15.7 - - + -
355B MET* 5.2 3.6 - - + -
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Residues in contact with ARG 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B PHE* 4.4 12.3 - - - -
323B VAL* 2.8 26.7 + - + +
324B GLU* 3.5 15.7 + - - +
325B ALA 3.2 0.2 - - - -
326B ILE* 1.3 76.6 - - - +
328B VAL* 1.3 87.0 + - - +
330B SER* 4.1 2.8 - - - -
331B GLU* 3.6 20.7 + - - +
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B LYS* 3.4 40.8 - - + +
312B ILE* 4.1 8.5 - - + -
313B CYS* 3.7 15.0 - - - +
316B PHE* 3.7 15.5 - - + -
324B GLU 2.9 22.8 + - - +
327B ARG* 1.3 97.0 - - - +
329B CYS* 1.3 67.1 + - - +
331B GLU* 2.9 17.0 + - + +
332B VAL* 3.0 11.1 + - - +
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Residues in contact with CYS 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B CYS* 2.0 59.2 - - - +
325B ALA* 2.7 33.1 + - - +
328B VAL* 1.3 70.5 - - - +
330B SER* 1.3 60.0 + - - +
332B VAL* 3.2 5.5 + - - +
333B LEU* 3.0 30.3 + - + +
342B ALA* 4.0 4.0 - - - +
345B ASP* 4.1 2.2 - - - -
346B ARG* 3.7 35.7 - - + -
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Residues in contact with SER 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ILE* 2.7 31.2 + - - +
327B ARG* 4.1 4.5 - - - -
329B CYS* 1.3 76.0 - - - +
331B GLU* 1.3 56.7 + - - +
333B LEU* 3.3 3.6 + - - +
334B GLN* 2.9 33.3 + - - +
346B ARG* 3.1 31.3 + - - +
350B TYR* 5.1 0.7 + - - -
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Residues in contact with GLU 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B LYS* 2.6 38.3 + - + +
327B ARG* 3.6 13.6 + - - +
328B VAL* 2.9 10.8 + - - +
330B SER* 1.3 75.3 - - - +
332B VAL* 1.3 66.8 + - + +
334B GLN* 3.2 27.6 + - + +
335B MET* 3.3 20.0 + - + +
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B VAL* 4.6 10.5 - - + +
309B LYS* 3.6 20.0 - - + +
310B GLU* 3.6 35.2 - - + +
313B CYS* 4.2 1.3 - - + -
328B VAL 3.0 16.2 + - - +
329B CYS* 3.4 11.4 - - - +
331B GLU* 1.3 75.4 - - - +
333B LEU* 1.3 50.4 + - - +
335B MET* 3.0 15.7 + - - +
336B GLU* 2.7 30.5 + - - +
339B ASN* 3.8 26.2 - - - +
342B ALA* 3.9 12.8 - - + -
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B CYS 3.0 20.9 + - - +
330B SER* 3.7 4.0 - - - +
332B VAL* 1.3 72.0 - - - +
334B GLN* 1.3 64.8 + - - +
336B GLU 3.3 17.9 - - - +
337B PRO* 3.0 35.3 - - + +
339B ASN* 3.7 13.5 - - + +
342B ALA* 3.6 23.3 - - + -
343B LEU* 3.7 32.8 - - + +
346B ARG* 3.4 37.5 - - - +
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Residues in contact with GLN 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B SER* 2.9 22.8 + - - +
331B GLU* 3.2 20.6 - - + +
333B LEU* 1.3 76.8 - - - +
335B MET* 1.3 62.0 + - + +
337B PRO* 4.5 5.9 - - - +
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Residues in contact with MET 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B THR* 5.8 2.5 - - - -
306B VAL* 3.9 46.4 - - + -
309B LYS* 4.3 19.7 - - + -
331B GLU* 3.3 29.4 + - + +
332B VAL* 3.0 17.5 + - + +
334B GLN* 1.3 81.2 - - + +
336B GLU* 1.3 64.5 + - + +
337B PRO* 3.8 5.4 - - - +
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Residues in contact with GLU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLU* 4.6 4.7 - - - +
306B VAL* 3.4 16.8 - - + +
307B ARG* 2.8 36.3 + - - -
332B VAL 2.7 12.9 + - - +
333B LEU* 3.3 12.1 - - - +
335B MET* 1.3 80.0 - - - +
337B PRO* 1.4 68.1 - - - +
338B ASP* 3.2 12.8 - - - +
339B ASN* 2.8 46.2 + - + +
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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