Contacts of the helix formed by residues 306 - 320 (chain M) in PDB entry 4K4I
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 GLY 306 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300M CYS* 4.3 7.6 - - - -
305M ILE* 1.3 74.4 - - - +
307M LYS* 1.3 67.3 + - - -
310M ALA* 2.9 25.2 + - - +
2P C 3.0 24.0 + - - -
3P C 3.6 14.4 - - - -
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Residues in contact with LYS 307 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296M TYR* 3.6 24.9 - - - +
300M CYS* 4.4 4.4 - - - -
306M GLY* 1.3 70.1 - - - -
308M ARG* 1.3 76.5 + - + +
310M ALA* 3.1 4.1 + - - +
311M GLU* 2.9 45.9 + - - +
2P C 3.8 1.4 + - - -
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Residues in contact with ARG 308 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275M ARG* 5.1 2.0 - - - +
306M GLY 3.4 0.8 - - - -
307M LYS* 1.3 91.2 - - + +
309M MET* 1.3 64.3 + - - +
311M GLU* 3.1 27.9 + - - +
312M LYS* 3.3 24.3 + - - +
324M LYS* 5.1 5.3 - - - +
1P G 2.9 54.5 + - - +
2P C 3.0 22.9 - - - +
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Residues in contact with MET 309 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260M LEU* 4.0 26.6 - - + +
278M GLY 4.0 7.6 - - - +
279M TYR* 3.8 56.8 - - + -
282M ALA* 3.9 19.7 - - + -
286M LEU* 5.5 0.2 - - + -
305M ILE* 4.0 19.7 - - + -
306M GLY 4.1 1.1 - - - +
308M ARG* 1.3 77.6 - - - +
310M ALA* 1.3 63.6 + - - +
312M LYS* 3.3 9.8 + - - +
313M ILE* 3.1 22.2 + - + +
1P G 3.7 20.6 - - + +
2P C 2.9 19.5 + - - +
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Residues in contact with ALA 310 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296M TYR* 3.6 23.3 - - + -
299M ALA* 4.3 13.7 - - + -
300M CYS* 4.0 11.2 - - - -
305M ILE* 4.0 6.4 - - + +
306M GLY 2.9 19.4 + - - +
307M LYS 3.5 3.4 - - - +
309M MET* 1.3 76.6 - - - +
311M GLU* 1.3 64.7 + - - +
313M ILE* 2.9 10.5 + - - +
314M ILE* 2.9 26.3 + - - +
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Residues in contact with GLU 311 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296M TYR* 4.2 15.5 + - + -
307M LYS* 2.9 39.0 + - - +
308M ARG* 3.1 29.4 + - - +
310M ALA* 1.3 75.0 - - - +
312M LYS* 1.3 59.7 + - + +
314M ILE* 3.4 4.9 + - - +
315M GLU* 2.9 28.5 + - - +
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Residues in contact with LYS 312 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260M LEU* 4.4 18.8 - - + -
263M LEU* 4.1 17.9 - - + -
279M TYR* 3.4 23.1 + - + +
308M ARG* 3.3 26.3 + - - +
309M MET* 3.5 12.0 - - - +
310M ALA 3.1 0.4 - - - -
311M GLU* 1.3 75.5 + - + +
313M ILE* 1.3 67.3 + - - +
315M GLU* 3.2 6.5 + - - +
316M ILE* 3.0 29.6 + - - +
322M LEU* 3.8 21.5 - - + +
324M LYS* 4.3 13.7 - - - +
1P G 2.6 32.2 + - - -
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Residues in contact with ILE 313 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256M ILE* 3.7 40.6 - - + -
260M LEU* 5.1 3.8 - - + -
286M LEU* 3.9 32.3 - - + -
293M VAL* 4.3 11.9 - - + -
299M ALA* 4.1 18.6 - - + -
305M ILE* 4.4 10.8 - - + -
309M MET* 3.1 15.2 + - + +
310M ALA* 2.9 10.3 + - - +
312M LYS* 1.3 79.1 - - - +
314M ILE* 1.3 71.2 + - + +
316M ILE* 3.3 2.9 + - - +
317M LEU* 2.9 35.3 + - + +
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Residues in contact with ILE 314 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295M SER* 3.9 6.7 - - - +
296M TYR* 3.7 44.9 - - + +
299M ALA* 5.1 0.9 - - + -
310M ALA 2.9 17.5 + - - +
311M GLU* 4.0 6.3 - - - +
313M ILE* 1.3 88.6 - - + +
315M GLU* 1.3 67.5 + - - +
317M LEU* 3.7 14.6 - - + +
318M GLU* 2.9 45.6 + - + +
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Residues in contact with GLU 315 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311M GLU 2.9 18.4 + - - +
312M LYS* 3.7 8.1 - - - +
314M ILE* 1.3 79.6 - - - +
316M ILE* 1.3 53.9 + - - +
318M GLU* 3.5 11.7 - - - +
319M SER* 2.7 45.0 + - - +
321M HIS 3.4 12.6 - - - +
322M LEU* 3.6 11.5 - - + +
323M ARG* 3.0 64.8 + - - +
324M LYS 5.5 0.3 + - - -
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Residues in contact with ILE 316 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255M HIS* 3.8 25.4 - - + +
256M ILE* 4.0 43.3 - - + +
259M LYS* 4.2 16.8 - - + -
260M LEU* 4.9 4.0 - - + -
312M LYS 3.0 20.0 + - - +
313M ILE 3.6 5.2 - - - +
315M GLU* 1.3 73.0 - - - +
317M LEU* 1.3 65.1 + - - +
320M GLY* 2.7 37.9 + - - -
321M HIS 3.6 20.9 - - - +
322M LEU* 3.8 18.2 - - + -
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Residues in contact with LEU 317 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255M HIS* 3.8 30.3 - - + +
256M ILE* 3.9 16.2 - - + -
293M VAL 3.6 21.1 - - - +
294M THR* 4.3 15.5 - - - +
313M ILE* 2.9 26.3 + - + +
314M ILE* 3.7 19.7 - - + +
316M ILE* 1.3 78.3 - - - +
318M GLU* 1.3 61.0 + - + +
320M GLY 4.6 0.7 + - - -
606M CAC 4.4 4.0 + - - +
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Residues in contact with GLU 318 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314M ILE* 2.9 39.3 + - + +
315M GLU* 3.5 10.5 - - - +
317M LEU* 1.3 79.4 - - + +
319M SER* 1.3 57.6 + - - +
320M GLY 3.6 0.2 - - - -
606M CAC 2.3 51.6 + - - +
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Residues in contact with SER 319 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315M GLU* 2.7 33.3 + - - +
318M GLU* 1.3 76.7 - - - +
320M GLY* 1.3 58.2 + - - +
321M HIS* 2.8 29.7 + - - +
606M CAC 4.0 10.2 - - - +
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Residues in contact with GLY 320 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259M LYS* 3.9 17.7 + - - +
316M ILE* 2.7 32.1 + - - -
317M LEU 4.5 0.6 + - - -
318M GLU 3.6 1.0 - - - -
319M SER* 1.3 71.2 - - - +
321M HIS* 1.3 58.6 + - - +
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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