Contacts of the helix formed by residues 322 - 336 (chain B) in PDB entry 1TVK
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 322 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ARG* 4.0 19.4 - - - +
222A PRO* 3.5 15.7 + - - +
223A THR* 5.1 2.5 - - - +
321B MET* 1.3 73.7 - - - +
323B MET* 1.3 62.8 + - - +
324B LYS* 3.1 27.2 + - - +
325B GLU* 2.9 51.5 + - - +
326B VAL* 3.0 13.5 - - - +
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Residues in contact with MET 323 (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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210A TYR* 2.7 20.9 - - - +
222A PRO 4.0 4.9 - - - +
223A THR* 4.5 0.4 - - - -
224A TYR* 3.5 61.9 - - + +
245B GLN* 3.8 31.4 - - + +
246B LEU* 5.0 2.0 - - + -
321B MET 3.5 15.5 - - - +
322B SER* 1.3 72.9 + - - +
324B LYS* 1.3 50.0 + - - +
326B VAL* 2.8 27.3 + - - +
327B ASP* 2.7 28.2 + - - +
353B VAL* 3.9 24.7 - - + -
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Residues in contact with LYS 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A VAL* 5.7 1.5 - - + +
207A GLU* 6.2 1.1 - - - -
210A TYR* 3.2 57.8 + - + -
211A ASP* 5.2 2.0 - - - -
214A ARG* 3.7 26.6 - - + +
220A GLU* 3.8 18.6 + - - +
222A PRO* 3.5 26.2 - - + +
322B SER* 3.1 14.4 - - - +
323B MET* 1.3 79.5 - - - +
325B GLU* 1.3 56.0 + - + +
327B ASP* 3.8 2.5 - - + +
328B GLU* 3.2 49.0 + - - +
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Residues in contact with GLU 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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220A GLU 3.1 17.3 - - - +
221A ARG* 4.7 0.7 - - - +
285B THR* 4.6 10.8 - - - +
286B VAL* 3.2 31.9 - - + +
287B PRO* 5.9 0.7 - - + -
321B MET* 4.9 0.9 - - - +
322B SER* 2.9 42.4 + - - +
324B LYS* 1.3 76.8 - - - +
326B VAL* 1.3 57.8 + - - +
327B ASP 3.2 0.2 - - - -
328B GLU* 3.7 12.6 - - - +
329B GLN* 2.3 52.9 + - - +
363B MET* 5.6 0.9 - - - +
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B VAL* 4.2 8.5 - - + -
317B PHE* 3.6 18.8 - - + -
321B MET* 3.8 26.9 - - + -
322B SER 3.0 24.4 + - - +
323B MET* 2.8 12.2 + - - +
325B GLU* 1.3 76.5 - - - +
327B ASP* 1.3 56.9 + - - +
329B GLN 3.5 0.2 - - - -
330B MET* 2.5 43.4 + - + +
351B THR* 3.2 35.9 - - + +
353B VAL* 4.5 11.2 - - + -
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Residues in contact with ASP 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A VAL* 3.3 34.9 - - + +
178A SER 3.8 15.8 - - - +
179A THR* 5.1 1.0 + - - -
210A TYR* 2.8 32.7 + - + -
224A TYR* 5.4 3.3 + - - -
323B MET* 2.7 17.8 + - - +
324B LYS* 3.7 2.4 + - - +
326B VAL* 1.3 80.2 - - - +
328B GLU* 1.3 54.6 + - - +
330B MET* 3.0 4.7 + - - -
331B LEU* 2.5 42.3 + - - +
351B THR* 5.0 4.9 + - - +
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Residues in contact with GLU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A VAL* 4.4 2.5 - - - +
214A ARG* 3.9 12.5 + - - -
220A GLU* 5.4 2.6 - - - +
324B LYS* 3.2 38.5 + - - +
325B GLU* 2.9 10.5 + - - +
327B ASP* 1.3 78.1 - - - +
329B GLN* 1.3 66.4 + - - +
331B LEU* 2.9 11.2 + - + +
332B ASN* 2.7 58.6 + - - +
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Residues in contact with GLN 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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286B VAL* 3.8 15.7 - - + +
287B PRO* 2.8 54.1 - - + +
290B THR* 4.0 11.7 - - + +
325B GLU* 2.3 41.8 + - - +
326B VAL 3.6 2.0 - - - +
328B GLU* 1.3 89.1 + - - +
330B MET* 1.3 51.6 + - - +
331B LEU 3.1 0.2 - - - -
332B ASN* 4.0 6.5 - - - +
333B VAL* 2.6 42.3 + - + +
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Residues in contact with MET 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B THR* 3.9 6.3 - - - +
293B MET* 4.1 4.0 - - - -
294B PHE* 4.3 11.2 - - + -
315B ALA* 3.1 40.8 - - + +
317B PHE* 3.4 34.5 - - + -
326B VAL* 2.5 28.7 + - + +
327B ASP* 3.3 3.8 - - - +
329B GLN* 1.3 71.6 - - - +
331B LEU* 1.3 55.6 + - - +
333B VAL* 4.1 7.4 - - - +
334B GLN* 3.2 22.9 + - - +
349B VAL* 3.3 48.3 - - + +
351B THR* 3.7 15.5 - - - +
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Residues in contact with LEU 331 (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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176A GLN* 4.2 39.3 - - + +
177A VAL* 3.9 23.1 - - + -
207A GLU* 4.7 3.1 - - - +
327B ASP 2.5 20.9 + - - +
328B GLU* 3.2 7.0 - - - +
330B MET* 1.3 73.7 - - - +
332B ASN* 1.3 63.8 + - - +
333B VAL 3.1 0.9 - - - -
334B GLN* 2.8 15.7 + - - +
335B ASN* 2.6 64.6 + - - +
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Residues in contact with ASN 332 (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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328B GLU* 2.7 42.8 + - - +
329B GLN* 4.2 9.3 + - - +
331B LEU* 1.3 86.5 - - - +
333B VAL* 1.3 57.0 + - + +
334B GLN 3.2 0.2 - - - -
335B ASN* 3.7 9.1 - - - +
336B LYS* 2.8 38.2 + - + +
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Residues in contact with VAL 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B THR* 3.2 26.0 - - + +
294B PHE* 3.8 41.5 - - + -
329B GLN* 2.6 26.9 + - + +
330B MET* 4.5 5.4 - - - +
331B LEU 3.1 0.6 - - - -
332B ASN* 1.3 78.1 - - + +
334B GLN* 1.3 59.4 + - - +
336B LYS* 5.3 0.2 - - - -
337B ASN* 2.9 38.5 - - + +
341B PHE* 4.2 4.2 - - + -
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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 MET 3.2 13.9 + - - +
331B LEU* 2.8 23.9 + - + +
333B VAL* 1.3 81.1 - - - +
335B ASN* 1.3 59.5 + - - +
337B ASN 3.7 0.2 - - - -
338B SER* 3.0 27.5 + - - -
341B PHE* 4.0 22.7 - - + -
346B PRO 4.5 4.8 - - - +
347B ASN* 3.2 22.7 - - - +
348B ASN* 3.3 38.1 - - - +
349B VAL* 3.3 26.6 - - - +
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Residues in contact with ASN 335 (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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176A GLN* 4.9 5.5 + - - -
331B LEU* 2.6 50.6 + - - +
332B ASN* 4.3 7.2 - - - +
334B GLN* 1.3 75.9 - - - +
336B LYS* 1.3 55.8 + - - +
337B ASN 2.4 17.6 + - - -
338B SER* 2.6 25.8 + - - -
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Residues in contact with LYS 336 (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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332B ASN* 2.8 24.2 + - + +
333B VAL* 5.3 0.2 - - - -
335B ASN* 1.3 73.9 - - - +
337B ASN* 1.3 56.9 + - + +
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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