Contacts of the helix formed by residues 307 - 325 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A VAL* 1.3 72.6 - - - +
308A GLN* 1.3 65.2 + - - +
309A PRO* 3.5 12.4 - - - +
310A GLU* 2.9 42.8 + - - +
311A VAL* 3.2 23.7 + - - +
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Residues in contact with GLN 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A VAL 4.6 3.3 - - - +
307A SER* 1.3 74.1 - - - +
309A PRO* 1.3 65.9 - - + +
311A VAL* 3.3 14.8 + - - +
312A GLY* 2.9 27.5 + - - -
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Residues in contact with PRO 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A SER* 3.4 16.6 - - - +
308A GLN* 1.3 95.2 - - + +
310A GLU* 1.3 57.6 + - + +
312A GLY* 3.4 1.6 + - - -
313A ALA* 3.0 30.1 + - - +
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Residues in contact with GLU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A VAL* 4.0 7.8 - - + +
307A SER* 2.9 41.4 + - - +
309A PRO* 1.3 77.8 - - + +
311A VAL* 1.3 63.2 + - + +
313A ALA* 3.4 6.1 + - - +
314A ALA* 3.0 17.8 + - - +
287D THR* 3.4 29.9 + - + +
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Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A VAL* 3.9 25.8 - - + -
307A SER 3.2 17.6 + - - +
308A GLN* 3.8 16.8 - - - +
310A GLU* 1.3 73.4 - - - +
312A GLY* 1.3 61.3 + - - +
314A ALA* 3.3 2.1 + - - +
315A ILE* 2.8 49.3 + - + +
287D THR* 4.0 8.7 - - + -
290D ALA* 3.9 13.7 - - + +
291D ALA* 3.9 23.6 - - - +
294D THR* 4.3 4.7 - - - +
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Residues in contact with GLY 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLN 2.9 16.4 + - - -
309A PRO* 3.8 1.8 - - - -
311A VAL* 1.3 76.6 - - - +
313A ALA* 1.3 61.4 + - - +
315A ILE* 3.3 10.6 + - - +
316A LYS* 3.0 32.4 + - - +
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A PRO 3.0 16.8 + - - +
310A GLU* 3.8 5.8 - - - +
312A GLY* 1.3 73.9 - - - +
314A ALA* 1.3 64.0 + - - +
316A LYS* 3.3 9.4 + - - +
317A ILE* 3.1 34.4 + - + +
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Residues in contact with ALA 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A GLU 3.0 17.7 + - - +
311A VAL 3.6 4.0 - - - +
313A ALA* 1.3 77.4 - - - +
315A ILE* 1.3 56.4 + - - +
317A ILE* 3.3 3.8 + - - +
318A ILE* 2.9 37.1 + - + +
283D ILE* 3.9 28.7 - - + -
287D THR* 3.8 18.4 - - + -
291D ALA* 4.0 11.9 - - + -
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Residues in contact with ILE 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A VAL* 2.8 34.2 + - + +
312A GLY* 3.3 8.0 + - - +
314A ALA* 1.3 75.4 - - - +
316A LYS* 1.3 69.9 + - - +
318A ILE* 3.7 5.6 - - - +
319A ARG* 2.9 55.3 + - - +
291D ALA* 3.8 17.5 - - + +
294D THR* 3.8 31.0 - - + -
295D LEU* 3.7 20.6 - - + -
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Residues in contact with LYS 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A GLY* 3.0 23.5 + - - +
313A ALA* 3.5 9.4 - - - +
314A ALA 3.2 0.2 - - - -
315A ILE* 1.3 89.4 - - - +
317A ILE* 1.3 64.0 + - + +
319A ARG* 3.1 37.3 + - - +
320A GLN* 3.0 35.2 + - + +
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Residues in contact with ILE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A ALA* 3.1 21.7 + - + +
314A ALA 3.6 5.2 - - - +
316A LYS* 1.3 77.9 - - + +
318A ILE* 1.3 61.9 + - - +
320A GLN* 3.2 16.5 + - - +
321A LEU* 3.0 25.5 + - + +
336A PHE* 3.8 18.2 - - + -
343A LEU* 3.6 43.1 - - + -
283D ILE* 4.3 18.6 - - + -
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Residues in contact with ILE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A ALA* 2.9 22.8 + - + +
315A ILE* 3.7 4.0 - - - +
317A ILE* 1.3 75.5 - - - +
319A ARG* 1.3 61.7 + - - +
321A LEU* 3.4 2.3 + - - +
322A MSE 2.8 38.4 + - + +
329A LEU* 3.9 15.5 - - + -
332A VAL* 4.1 14.0 - - + +
333A THR* 4.6 10.1 - - - +
336A PHE* 4.2 20.4 - - + -
283D ILE* 4.8 1.6 - - + -
288D LEU* 4.0 19.7 - - + +
291D ALA* 3.7 26.2 - - + -
292D PHE 4.9 3.4 - - - +
295D LEU* 3.8 21.5 - - + -
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Residues in contact with ARG 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A ILE* 2.9 42.9 + - + +
316A LYS* 3.1 30.5 - - - +
318A ILE* 1.3 74.2 - - - +
320A GLN* 1.3 64.8 + - + +
322A MSE 3.1 27.3 + - + +
323A GLU* 3.1 23.6 + - - +
295D LEU* 4.2 13.4 - - + +
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Residues in contact with GLN 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A LYS* 3.0 32.7 + - + +
317A ILE* 3.6 18.6 - - - +
319A ARG* 1.3 76.2 - - + +
321A LEU* 1.3 60.3 + - + +
323A GLU* 3.1 13.5 - - + +
324A LYS* 2.8 32.9 + - + +
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A ILE* 3.0 23.8 + - + +
318A ILE 3.8 4.3 - - - +
320A GLN* 1.3 78.6 - - + +
322A MSE 1.3 62.1 - - - +
324A LYS* 4.4 7.4 - - + -
325A PHE* 3.1 53.7 + - + +
332A VAL* 3.9 16.1 - - + +
336A PHE* 3.4 39.7 - - + -
343A LEU* 4.3 10.3 - - + -
346A THR* 4.5 3.8 - - + -
347A SER* 4.2 15.5 - - - +
350A LEU* 4.4 13.9 - - + -
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Residues in contact with MSE 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ILE* 2.8 30.4 + - + +
319A ARG* 3.1 47.8 - - + +
321A LEU* 1.3 76.0 - - - +
323A GLU* 1.3 57.1 + - - +
326A ASN* 2.9 8.7 + - - -
327A LEU 2.9 38.7 + - - +
328A ASP 4.4 0.2 - - - -
329A LEU* 3.7 33.4 - - - -
332A VAL* 3.7 19.5 - - + -
295D LEU* 4.3 7.4 - - + -
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Residues in contact with GLU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A ARG 3.1 11.5 + - - +
320A GLN* 3.1 20.7 - - - +
322A MSE 1.3 76.2 - - - +
324A LYS* 1.3 72.2 + - + +
325A PHE 3.2 0.7 + - - -
326A ASN* 3.4 10.9 + - - +
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Residues in contact with LYS 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A GLN* 2.8 22.9 + - + +
321A LEU* 4.1 9.4 - - + +
323A GLU* 1.3 79.4 - - + +
325A PHE* 1.3 95.0 + - + +
326A ASN 4.0 0.2 + - - -
347A SER* 6.1 1.6 - - - -
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Residues in contact with PHE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A LEU* 3.1 45.5 + - + +
324A LYS* 1.3 108.8 - - + +
326A ASN* 1.3 73.6 + - - +
327A LEU* 3.4 23.0 - - + +
347A SER* 3.6 23.1 - - - -
350A LEU* 3.9 33.4 - - + +
351A ALA* 3.5 25.6 - - + -
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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