Contacts of the helix formed by residues 306 - 320 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300E CYS* 4.7 4.5 - - - -
305E ILE* 1.3 74.7 - - - +
307E LYS* 1.3 67.9 + - - -
308E ARG 3.2 3.7 + - - -
309E MET 3.2 0.9 + - - -
310E ALA* 2.9 25.4 + - - +
2H C 3.1 29.1 + - - -
3H C 4.4 4.3 - - - -
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Residues in contact with LYS 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296E TYR* 3.4 22.6 + - - +
300E CYS* 4.7 4.6 - - - -
306E GLY* 1.3 70.4 - - - +
308E ARG* 1.3 70.8 + - + +
310E ALA* 3.4 5.4 + - - +
311E GLU* 2.9 48.0 + - - +
2H C 4.0 1.0 + - - -
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Residues in contact with ARG 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E ARG* 5.1 1.2 - - - +
306E GLY 3.2 1.0 - - - -
307E LYS* 1.3 86.0 - - + +
309E MET* 1.3 66.9 + - - +
311E GLU* 3.4 24.6 + - - +
312E LYS* 3.3 32.2 + - - +
1H G 2.7 54.8 + - - +
2H C 3.6 19.9 + - - +
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Residues in contact with MET 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E LEU* 4.3 12.8 - - + -
278E GLY 4.1 3.1 - - - +
279E TYR* 3.8 51.6 - - + -
282E ALA* 3.7 34.5 - - + -
305E ILE* 3.7 13.2 - - + -
306E GLY 4.2 1.1 - - - +
308E ARG* 1.3 75.4 - - - +
310E ALA* 1.3 65.0 + - - +
312E LYS* 3.0 15.2 + - - +
313E ILE* 2.9 38.7 + - + +
1H G 3.7 21.2 + - + +
2H C 3.0 19.8 + - - +
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Residues in contact with ALA 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296E TYR* 3.7 20.4 - - + -
299E ALA* 3.8 21.6 - - + +
300E CYS* 3.7 18.8 - - - -
305E ILE* 3.7 6.6 - - + +
306E GLY 2.9 17.3 + - - +
307E LYS 3.6 4.7 - - - +
309E MET* 1.3 76.9 - - - +
311E GLU* 1.3 62.2 + - - +
313E ILE* 3.2 3.3 + - - +
314E ILE* 2.9 26.7 + - - +
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Residues in contact with GLU 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296E TYR* 3.8 12.9 + - + +
307E LYS* 2.9 39.7 + - + +
308E ARG* 3.5 34.1 + - - +
309E MET 3.2 0.2 - - - -
310E ALA* 1.3 75.1 - - - +
312E LYS* 1.3 64.7 + - + +
314E ILE* 3.3 11.8 - - + +
315E GLU* 3.1 23.8 + - - +
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Residues in contact with LYS 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E LEU* 4.3 18.2 - - + -
263E LEU* 4.7 7.4 - - + +
279E TYR* 3.3 27.5 + - + +
308E ARG* 3.3 27.1 + - - +
309E MET* 3.0 23.1 + - - +
311E GLU* 1.3 78.7 - - + +
313E ILE* 1.3 63.6 + - - +
315E GLU* 3.4 5.9 + - - +
316E ILE* 3.0 28.6 + - - +
322E LEU* 4.0 22.9 - - + +
324E LYS* 5.9 3.8 - - - +
1H G 2.8 30.3 + - - -
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Residues in contact with ILE 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256E ILE* 3.8 36.5 - - + +
260E LEU* 4.5 6.5 - - + -
286E LEU* 4.0 21.8 - - + -
293E VAL* 4.3 19.3 - - + -
295E SER 5.5 0.7 - - - +
296E TYR* 6.5 0.2 - - - -
299E ALA* 4.3 7.9 - - + -
305E ILE* 4.1 22.9 - - + -
309E MET* 2.9 30.7 + - + +
310E ALA* 3.5 6.5 - - - +
312E LYS* 1.3 79.5 - - - +
314E ILE* 1.3 57.9 + - + +
316E ILE* 3.2 10.1 + - - +
317E LEU* 2.9 37.1 + - + +
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Residues in contact with ILE 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294E THR 4.8 1.3 - - - +
295E SER* 3.7 11.7 - - - -
296E TYR* 3.2 45.5 - - + +
310E ALA 2.9 15.1 + - - +
311E GLU* 3.3 18.8 - - + +
313E ILE* 1.3 73.0 - - + +
315E GLU* 1.3 65.0 + - - +
317E LEU* 3.5 14.6 - - + +
318E GLU* 2.9 58.6 + - + +
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Residues in contact with GLU 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311E GLU 3.1 18.7 + - - +
312E LYS* 3.6 5.6 - - - +
314E ILE* 1.3 79.3 - - + +
316E ILE* 1.3 61.1 + - - +
318E GLU* 3.8 4.6 - - - +
319E SER* 2.8 37.7 + - - +
321E HIS 3.6 9.0 - - - +
322E LEU* 3.4 17.0 - - - +
323E ARG* 2.9 46.0 + - - +
324E LYS* 5.9 0.2 - - - +
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Residues in contact with ILE 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255E HIS* 4.1 27.4 - - + +
256E ILE* 4.2 34.5 - - + +
259E LYS* 4.0 30.1 - - + +
260E LEU* 4.6 5.2 - - + -
312E LYS 3.0 26.2 + - - +
313E ILE* 3.2 5.1 + - - +
315E GLU* 1.3 73.7 - - - +
317E LEU* 1.3 59.6 + - - +
320E GLY* 2.7 34.7 + - - -
321E HIS 3.4 17.3 - - - +
322E LEU* 4.1 21.8 - - + -
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Residues in contact with LEU 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255E HIS* 3.7 26.2 - - - +
256E ILE* 4.3 5.6 - - + -
293E VAL* 3.6 29.4 - - + +
294E THR* 3.7 24.9 - - - +
295E SER* 4.1 1.8 - - - +
313E ILE* 2.9 27.8 + - + +
314E ILE* 3.5 23.6 - - + +
316E ILE* 1.3 78.7 - - - +
318E GLU* 1.3 64.5 + - + +
320E GLY 4.6 1.0 + - - -
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Residues in contact with GLU 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314E ILE* 2.9 44.5 + - + +
315E GLU* 4.1 4.0 + - - +
317E LEU* 1.3 79.2 - - + +
319E SER* 1.3 61.8 + - - +
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Residues in contact with SER 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315E GLU* 2.8 28.8 + - - +
318E GLU* 1.3 78.8 - - - +
320E GLY* 1.3 62.1 + - - +
321E HIS* 3.1 37.3 + - - +
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Residues in contact with GLY 320 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259E LYS* 3.4 21.9 + - - -
316E ILE* 2.7 25.3 + - - -
317E LEU 4.6 1.0 + - - -
318E GLU 3.8 0.6 - - - -
319E SER* 1.3 71.1 - - - +
321E HIS* 1.3 75.5 + - - +
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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