Contacts of the helix formed by residues 308 - 324 (chain B) in PDB entry 3KXK
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 ASP 308 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B ILE* 4.6 2.9 - - - +
307B GLY* 1.3 74.8 - - - -
309B LEU* 1.3 74.2 + - - +
310B TYR* 3.6 15.7 + - - +
311B LYS* 3.0 39.9 + - + +
312B LYS* 3.6 29.0 + - - +
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU* 4.3 11.9 - - + -
302B ILE* 3.7 24.7 - - + -
305B ILE* 3.7 27.8 - - + -
307B GLY 4.2 0.6 + - - -
308B ASP* 1.3 76.8 + - - +
310B TYR* 1.3 75.9 + - + +
311B LYS 3.1 1.8 - - - -
312B LYS* 2.9 8.3 + - + +
313B LEU* 2.8 27.8 + - + +
332B PRO* 3.8 32.1 - - + -
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Residues in contact with TYR 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ASP* 3.6 12.4 + - - +
309B LEU* 1.3 90.8 - - + +
311B LYS* 1.3 54.5 + - - +
313B LEU* 3.9 21.5 - - + -
314B ASP* 2.7 48.3 + - - +
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Residues in contact with LYS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B GLU* 3.0 28.5 + - - +
308B ASP* 3.0 31.7 + - + +
309B LEU 3.1 0.2 - - - -
310B TYR* 1.3 76.9 - - - +
312B LYS* 1.3 63.0 + - + +
314B ASP* 4.2 5.2 - - - +
315B LEU* 3.2 22.3 + - - +
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Residues in contact with LYS 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B SER* 2.8 31.3 + - - +
268B THR* 4.1 5.7 + - - +
269B PHE 3.2 16.3 + - - -
270B SER* 5.2 4.2 - - - +
271B GLU* 5.7 9.0 - - + +
274B LEU* 3.8 21.8 - - + -
299B LEU* 4.2 10.8 - - + -
305B ILE* 4.1 24.4 - - + +
306B ASN 5.7 0.6 - - - +
307B GLY* 5.3 3.9 - - - +
308B ASP 3.6 21.5 - - - +
309B LEU* 2.9 7.2 + - - +
311B LYS* 1.3 78.6 - - + +
313B LEU* 1.3 57.0 + - - +
315B LEU* 3.3 5.9 + - - +
316B VAL* 2.8 40.7 + - - +
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Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU* 4.1 15.4 - - + +
309B LEU* 2.8 13.6 + - + +
310B TYR* 3.5 26.9 - - + +
312B LYS* 1.3 79.2 - - - +
314B ASP* 1.3 62.1 + - - +
316B VAL* 3.8 1.0 - - - +
317B GLU* 2.8 35.2 + - + +
330B VAL* 3.7 37.2 - - + +
331B ILE 4.4 0.9 - - - -
332B PRO* 3.7 39.5 - - + -
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Residues in contact with ASP 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B TYR* 2.7 31.3 + - - +
311B LYS* 4.2 5.0 - - - +
313B LEU* 1.3 76.0 - - - +
315B LEU* 1.3 60.4 + - - +
317B GLU* 3.8 16.2 - - - +
318B LYS* 2.9 32.9 + - - +
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B GLU* 5.2 17.0 - - + +
274B LEU* 4.6 13.5 - - + -
275B ILE* 4.2 30.5 - - + -
278B LEU* 4.5 8.7 - - + -
311B LYS 3.2 18.4 + - - +
312B LYS* 3.5 5.8 - - - +
313B LEU 3.3 0.2 - - - -
314B ASP* 1.3 79.0 - - - +
316B VAL* 1.3 70.6 + - + +
318B LYS* 4.0 5.0 - - + +
319B LEU* 2.9 40.5 + - + +
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Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ILE* 5.5 0.2 - - + -
274B LEU* 4.7 11.7 - - + -
278B LEU* 3.8 28.9 - - + -
297B VAL* 3.8 23.6 - - + -
299B LEU* 3.8 26.0 - - + -
312B LYS 2.8 24.5 + - - +
313B LEU* 3.9 4.0 - - - +
315B LEU* 1.3 75.4 - - + +
317B GLU* 1.3 59.8 + - - +
319B LEU* 4.1 0.3 - - - +
320B SER* 2.7 47.7 + - - +
330B VAL* 4.0 10.3 - - + -
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Residues in contact with GLU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 2.8 21.2 + - + +
314B ASP* 3.8 18.2 - - - +
316B VAL* 1.3 77.7 - - - +
318B LYS* 1.3 61.8 + - - +
320B SER* 3.8 1.4 - - - -
321B LYS* 3.2 56.0 + - + +
329B ASP* 5.6 2.4 - - - +
330B VAL* 3.9 32.2 - - + +
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Residues in contact with LYS 318 (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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314B ASP 2.9 18.4 + - - +
315B LEU* 4.0 5.8 - - + +
317B GLU* 1.3 75.8 - - - +
319B LEU* 1.3 65.3 + - - +
321B LYS* 3.3 7.1 + - - +
322B GLU* 3.1 51.8 + - + +
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Residues in contact with LEU 319 (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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275B ILE* 3.8 40.4 - - + +
278B LEU* 3.6 28.0 - - + -
279B GLN* 4.5 11.0 - - + +
315B LEU* 2.9 25.3 + - + +
316B VAL 4.1 2.0 - - - +
318B LYS* 1.3 77.2 - - - +
320B SER* 1.3 62.4 + - - +
322B GLU* 3.3 18.2 + - - +
323B LEU* 3.1 51.6 + - + +
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Residues in contact with SER 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LEU* 3.9 5.0 - - - +
282B PHE* 3.6 32.7 - - - -
297B VAL* 4.1 9.4 - - - +
316B VAL* 2.7 35.6 + - - +
317B GLU* 3.8 5.2 - - - -
319B LEU* 1.3 78.2 - - - +
321B LYS* 1.3 57.3 + - - +
323B LEU* 3.1 1.7 + - - +
324B TYR* 2.8 34.3 + - - +
327B ILE* 4.0 14.7 - - - +
330B VAL* 5.1 0.7 - - - -
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Residues in contact with LYS 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B GLU* 3.2 45.9 + - + +
318B LYS* 3.9 4.7 - - - +
320B SER* 1.3 76.2 - - - +
322B GLU* 1.3 60.1 + - + +
324B TYR 3.3 17.9 + - - +
325B SER* 5.2 2.3 - - - -
327B ILE* 3.9 35.8 + - + -
329B ASP* 6.1 2.0 - - - +
330B VAL* 5.5 0.7 - - - -
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Residues in contact with GLU 322 (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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318B LYS* 3.1 50.7 + - + +
319B LEU* 3.6 22.3 - - + +
320B SER 3.1 0.4 - - - -
321B LYS* 1.3 78.9 - - + +
323B LEU* 1.3 67.9 + - + +
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Residues in contact with LEU 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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278B LEU* 4.4 0.7 - - + -
279B GLN* 3.7 44.6 - - + +
282B PHE* 4.1 24.1 - - + +
286B ARG* 4.2 32.1 + - - +
319B LEU* 3.1 37.8 + - + +
320B SER 3.9 2.9 - - - +
322B GLU* 1.3 85.4 - - + +
324B TYR* 1.3 62.0 + - - +
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Residues in contact with TYR 324 (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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282B PHE* 3.5 27.6 - + + -
285B LEU* 5.8 4.0 - - + -
286B ARG* 6.0 6.7 - - + -
290B VAL* 3.6 34.3 - - + +
291B SER* 4.5 3.4 - - - -
292B GLY 3.5 2.3 + - - -
293B LYS* 2.6 45.9 + - - -
295B ILE* 3.4 22.2 - - + -
320B SER 2.8 13.6 + - - +
321B LYS* 3.3 17.7 - - - +
322B GLU 3.6 1.0 - - - -
323B LEU* 1.3 82.3 - - - +
325B SER* 1.3 94.1 + - - +
326B PRO 3.7 3.6 - - - -
327B ILE* 3.6 19.9 - - + +
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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