Contacts of the helix formed by residues 307 - 326 (chain B) in PDB entry 3K6G
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 307 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308B GLN* 1.3 63.3 + - - +
309B PRO* 3.2 20.0 - - - +
310B GLU* 3.4 28.9 + - - +
311B VAL* 3.1 26.8 + - - +
287E THR* 5.4 3.7 + - - +
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Residues in contact with GLN 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B SER* 1.3 70.9 - - - +
309B PRO* 1.3 70.3 - - + +
311B VAL* 3.3 10.4 - - + +
312B GLY* 2.7 33.3 + - - -
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Residues in contact with PRO 309 (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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307B SER* 3.2 20.2 - - - +
308B GLN* 1.3 101.0 - - + +
310B GLU* 1.3 58.1 + - + +
312B GLY* 3.2 2.7 + - - -
313B ALA* 2.9 29.4 + - - +
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Residues in contact with GLU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B SER* 3.4 26.4 + - - +
308B GLN 3.3 0.2 - - - -
309B PRO* 1.3 80.8 - - + +
311B VAL* 1.3 57.7 + - - +
313B ALA* 3.3 7.7 + - - +
314B ALA* 2.8 29.8 + - - +
287E THR* 3.7 23.8 + - + +
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Residues in contact with VAL 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B SER 3.1 20.5 + - - +
308B GLN* 3.1 13.8 + - + +
310B GLU* 1.3 74.3 - - - +
312B GLY* 1.3 60.4 + - - +
314B ALA* 3.2 3.3 + - - +
315B ILE* 2.9 38.6 + - + +
287E THR* 4.0 17.3 - - + +
290E ALA* 3.9 23.8 - - + -
291E ALA* 4.1 23.5 - - - +
294E THR* 4.5 5.4 - - - +
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Residues in contact with GLY 312 (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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308B GLN 2.7 19.8 + - - -
309B PRO* 3.6 1.8 - - - -
311B VAL* 1.3 73.7 - - - +
313B ALA* 1.3 61.5 + - - +
315B ILE* 3.4 13.1 + - - +
316B LYS* 3.3 34.9 + - - +
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Residues in contact with ALA 313 (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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309B PRO 2.9 15.6 + - - +
310B GLU* 3.5 9.9 - - - +
312B GLY* 1.3 75.8 - - - +
314B ALA* 1.3 64.3 + - - +
316B LYS* 3.4 12.2 + - - +
317B ILE* 3.2 32.5 + - + +
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Residues in contact with ALA 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B GLU 2.8 17.4 + - - +
311B VAL 3.5 5.2 - - - +
313B ALA* 1.3 77.5 - - - +
315B ILE* 1.3 63.1 + - - +
317B ILE* 3.3 4.9 + - - +
318B ILE* 2.9 31.7 + - + +
283E ILE* 4.0 28.0 - - + -
287E THR* 4.0 17.3 - - + -
291E ALA* 4.1 12.3 - - + -
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Residues in contact with ILE 315 (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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311B VAL* 2.9 26.4 + - + +
312B GLY* 3.5 15.0 - - - +
313B ALA 3.2 0.2 - - - -
314B ALA* 1.3 77.2 - - - +
316B LYS* 1.3 63.5 + - + +
318B ILE* 3.4 5.9 + - - +
319B ARG* 2.9 49.3 + - - +
291E ALA* 3.8 16.4 - - + -
294E THR* 3.7 32.5 - - + -
295E LEU* 4.0 22.8 - - + +
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Residues in contact with LYS 316 (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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312B GLY* 3.3 21.6 + - - +
313B ALA* 3.8 10.8 - - - +
314B ALA 3.3 0.2 - - - -
315B ILE* 1.3 80.6 - - + +
317B ILE* 1.3 59.9 + - + +
319B ARG* 3.2 9.8 + - - +
320B GLN* 2.9 30.7 + - - +
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Residues in contact with ILE 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ALA* 3.2 21.9 + - + +
314B ALA* 3.6 7.0 - - - +
316B LYS* 1.3 78.9 - - + +
318B ILE* 1.3 62.4 + - - +
320B GLN* 3.3 7.3 + - - +
321B LEU* 3.0 25.2 + - + +
336B PHE* 3.8 17.0 - - + -
343B LEU* 3.7 45.5 - - + -
281E THR* 5.0 7.9 - - + -
283E ILE* 4.4 17.3 - - + -
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Residues in contact with ILE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ALA* 2.9 23.4 + - + +
315B ILE* 3.7 5.8 - - - +
317B ILE* 1.3 75.0 - - - +
319B ARG* 1.3 56.8 + - - +
321B LEU* 3.2 3.7 + - - +
322B MSE 2.9 54.4 + - + +
329B LEU* 3.8 19.3 - - + -
332B VAL* 4.1 18.1 - - + +
333B THR* 4.6 9.6 - - - +
336B PHE* 4.1 20.4 - - + -
283E ILE* 5.1 2.0 - - + -
288E LEU* 4.1 21.1 - - + +
291E ALA* 3.9 24.2 - - + -
292E PHE 5.1 1.6 - - - +
295E LEU* 4.4 3.4 - - + -
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Residues in contact with ARG 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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315B ILE* 2.9 44.7 + - + +
316B LYS* 3.2 9.2 + - - +
318B ILE* 1.3 75.8 - - - +
320B GLN* 1.3 64.2 + - - +
322B MSE 3.0 25.0 + - + +
323B GLU* 3.1 28.8 + - - +
295E LEU* 4.5 14.7 - - + +
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Residues in contact with GLN 320 (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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316B LYS 2.9 16.3 + - - +
317B ILE* 3.6 7.9 - - - +
318B ILE 3.3 0.2 - - - -
319B ARG* 1.3 78.1 - - - +
321B LEU* 1.3 60.4 + - + +
323B GLU* 2.8 32.4 + - - +
324B LYS* 2.9 46.9 + - + +
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Residues in contact with LEU 321 (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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317B ILE* 3.0 20.1 + - + +
318B ILE 3.8 3.4 - - - +
320B GLN* 1.3 77.2 - - + +
322B MSE 1.3 64.9 + - - +
324B LYS* 4.3 7.6 - - + -
325B PHE* 3.1 52.0 + - + +
332B VAL* 4.0 14.6 - - + +
336B PHE* 3.5 37.9 - - + -
343B LEU* 4.4 10.3 - - + -
346B THR* 4.3 5.6 - - + -
347B SER* 3.9 18.6 - - - +
350B LEU* 4.2 17.7 - - + -
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Residues in contact with MSE 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 ILE* 2.9 30.6 + - + +
319B ARG* 3.0 58.8 + - + +
321B LEU* 1.3 77.2 - - - +
323B GLU* 1.3 57.4 + - - +
326B ASN* 2.8 24.4 + - - -
327B LEU 2.8 24.8 + - - +
328B ASP* 4.1 2.5 - - - +
329B LEU* 3.7 28.9 - - - -
332B VAL* 3.7 21.1 - - + -
295E LEU* 4.1 10.8 - - + -
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Residues in contact with GLU 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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319B ARG* 3.1 18.8 + - - +
320B GLN* 2.8 43.7 + - - +
322B MSE 1.3 77.2 - - - +
324B LYS* 1.3 63.7 + - - +
325B PHE 3.3 0.5 + - - -
326B ASN* 3.4 21.7 + - - +
310D GLN* 4.5 0.2 + - - -
311D LYS* 4.7 4.0 + - - -
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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
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320B GLN* 2.9 31.6 + - + +
321B LEU* 3.9 9.9 - - + +
323B GLU* 1.3 77.5 - - - +
325B PHE* 1.3 91.1 + - + +
347B SER* 4.0 15.6 + - - -
351B ALA* 5.9 1.5 - - - +
310D GLN* 3.1 15.9 + - - +
311D LYS* 5.3 0.7 + - - -
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Residues in contact with PHE 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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364A ARG* 3.0 21.8 + - - +
321B LEU* 3.1 46.8 + - + +
324B LYS* 1.3 106.6 - - + +
326B ASN* 1.3 70.2 + - - +
327B LEU* 3.8 17.0 - - + -
347B SER* 3.6 22.2 - - - -
350B LEU* 3.8 33.0 - - + -
351B ALA* 3.5 28.3 - - + -
310D GLN* 3.2 19.2 - - - +
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Residues in contact with ASN 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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364A ARG* 2.9 35.8 + - + +
368A ILE* 3.8 4.3 - - - +
322B MSE 2.8 13.3 + - - -
323B GLU* 3.4 12.2 + - - +
325B PHE* 1.3 78.4 - - - +
327B LEU* 1.3 57.5 + - - +
310D GLN* 2.6 32.2 + - + +
311D LYS* 2.8 29.7 + - - +
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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
------------------------------------------------------------
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