Contacts of the helix formed by residues 306 - 320 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300I CYS* 5.0 3.1 - - - -
304I GLY 4.0 1.6 + - - -
305I ILE* 1.3 74.2 - - - +
307I LYS* 1.3 57.2 + - - -
308I ARG 3.2 3.4 - - - -
309I MET 3.1 1.6 + - - -
310I ALA* 2.7 36.1 + - - +
2L C 2.9 26.0 + - - -
3L C 4.4 9.2 - - - -
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Residues in contact with LYS 307 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296I TYR* 3.3 27.2 + - - +
300I CYS* 4.9 4.4 - - - -
306I GLY* 1.3 70.4 - - - -
308I ARG* 1.3 62.5 + - + +
310I ALA* 3.6 2.3 + - - -
311I GLU* 3.1 38.7 + - - +
2L C 4.0 1.0 + - - -
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Residues in contact with ARG 308 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306I GLY 3.2 0.8 - - - -
307I LYS* 1.3 78.4 - - + +
309I MET* 1.3 67.8 + - - +
311I GLU* 3.2 31.2 + - - +
312I LYS* 3.3 25.1 + - - +
1L G 3.0 39.6 + - - -
2L C 3.6 19.0 + - - +
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Residues in contact with MET 309 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260I LEU* 4.3 20.2 - - + -
278I GLY 4.2 2.7 - - - +
279I TYR* 3.8 43.1 - - + -
282I ALA* 3.6 32.5 - - + -
286I LEU* 5.5 0.2 - - + -
305I ILE* 4.2 9.6 - - + -
306I GLY 3.8 8.1 - - - +
308I ARG* 1.3 79.5 - - - +
310I ALA* 1.3 61.9 + - - +
312I LYS* 3.1 12.1 + - - +
313I ILE* 3.1 31.7 + - + +
1L G 3.6 27.6 + - + +
2L C 3.1 19.9 + - - +
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Residues in contact with ALA 310 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296I TYR* 3.8 13.2 - - + -
299I ALA* 3.8 17.9 - - + -
300I CYS* 3.6 27.4 - - - -
305I ILE* 3.9 7.9 - - + +
306I GLY 2.7 20.4 + - - +
307I LYS 4.0 0.7 - - - +
309I MET* 1.3 73.5 - - - +
311I GLU* 1.3 62.7 + - - +
313I ILE* 3.2 8.9 + - - +
314I ILE* 3.0 28.2 + - - +
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Residues in contact with GLU 311 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296I TYR* 4.0 10.0 + - + -
307I LYS* 3.1 28.3 + - - +
308I ARG* 3.2 22.1 + - - +
309I MET 3.2 0.2 - - - -
310I ALA* 1.3 78.0 - - - +
312I LYS* 1.3 62.6 + - + +
314I ILE* 3.6 15.0 - - + +
315I GLU* 3.5 18.7 + - - +
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Residues in contact with LYS 312 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260I LEU* 4.5 11.4 - - + -
263I LEU* 4.7 8.5 - - + -
279I TYR* 3.3 23.2 + - + +
308I ARG* 3.4 29.4 + - - +
309I MET* 3.1 17.5 + - - +
311I GLU* 1.3 77.4 - - + +
313I ILE* 1.3 66.2 + - - +
315I GLU* 3.3 5.2 + - - +
316I ILE* 3.1 29.1 + - - +
322I LEU* 3.8 22.7 - - + +
324I LYS* 6.3 4.0 - - + -
1L G 2.6 43.9 + - - -
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Residues in contact with ILE 313 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256I ILE* 3.9 23.5 - - + +
260I LEU* 4.5 5.6 - - + -
286I LEU* 3.8 31.4 - - + -
293I VAL* 3.6 26.7 - - + -
299I ALA* 4.1 22.9 - - + -
305I ILE* 4.3 12.1 - - + -
309I MET* 3.1 17.3 + - + +
310I ALA* 3.5 9.0 - - - +
312I LYS* 1.3 77.7 - - - +
314I ILE* 1.3 62.2 + - + +
316I ILE* 3.2 11.1 + - - +
317I LEU* 3.1 28.0 + - + +
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Residues in contact with ILE 314 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295I SER* 3.8 6.1 - - - +
296I TYR* 3.3 55.2 - - + +
310I ALA 3.0 17.1 + - - +
311I GLU* 3.6 15.7 - - + +
313I ILE* 1.3 76.0 - - + +
315I GLU* 1.3 83.0 + - + +
317I LEU* 3.3 14.5 + - + +
318I GLU* 3.1 47.6 + - + +
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Residues in contact with GLU 315 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311I GLU 3.5 11.2 + - - +
312I LYS* 3.3 10.9 + - - +
313I ILE 3.3 0.6 - - - -
314I ILE* 1.3 87.2 - - + +
316I ILE* 1.3 61.5 + - - +
318I GLU* 5.1 3.6 - - - -
319I SER* 2.9 42.3 + - - +
321I HIS* 3.3 20.1 - - - +
322I LEU* 3.5 16.2 - - - +
323I ARG* 3.5 42.1 + - - +
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Residues in contact with ILE 316 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255I HIS* 3.8 21.8 - - + +
256I ILE* 4.1 42.0 - - + +
259I LYS* 4.4 11.2 - - + -
260I LEU* 4.4 15.0 - - + -
312I LYS 3.1 17.9 + - - +
313I ILE* 3.2 5.1 + - - +
314I ILE 3.1 0.2 - - - -
315I GLU* 1.3 77.7 - - - +
317I LEU* 1.3 59.9 + - + +
320I GLY* 2.7 46.0 + - - +
321I HIS 3.5 16.8 - - - +
322I LEU* 4.1 13.0 - - + -
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Residues in contact with LEU 317 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256I ILE* 3.8 30.3 - - + -
293I VAL 3.8 14.8 - - - +
294I THR* 3.6 34.5 - - - +
295I SER 4.0 2.7 - - - +
313I ILE* 3.1 19.6 + - + +
314I ILE* 3.5 20.4 - - + +
316I ILE* 1.3 78.9 - - + +
318I GLU* 1.3 64.2 + - + +
320I GLY* 4.3 2.1 + - - -
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Residues in contact with GLU 318 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314I ILE* 3.1 34.1 + - + +
315I GLU* 4.5 3.1 - - - +
317I LEU* 1.3 81.1 - - + +
319I SER* 1.3 61.6 + - - +
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Residues in contact with SER 319 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315I GLU* 2.9 35.6 + - - +
318I GLU* 1.3 79.9 - - - +
320I GLY* 1.3 57.2 + - - +
321I HIS* 2.9 32.7 + - - +
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Residues in contact with GLY 320 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255I HIS* 5.8 0.5 + - - +
259I LYS* 2.3 31.1 + - - -
316I ILE* 2.7 31.8 + - - +
317I LEU 4.3 1.9 + - - -
318I GLU 3.6 1.2 - - - -
319I SER* 1.3 69.9 - - - +
321I HIS* 1.3 58.9 + - - +
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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