Contacts of the helix formed by residues 306 - 320 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A CYS* 4.2 8.1 - - - -
305A ILE* 1.3 73.9 - - - +
307A LYS* 1.3 55.9 + - - -
310A ALA* 2.8 36.2 + - - +
2D C 3.1 31.1 + - - -
3D C 4.6 3.8 - - - -
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Residues in contact with LYS 307 (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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296A TYR* 3.5 22.5 + - - +
300A CYS* 4.4 4.3 - - - -
306A GLY* 1.3 69.2 - - - -
308A ARG* 1.3 77.9 + - + +
310A ALA* 3.0 7.0 + - - +
311A GLU* 2.7 62.3 + - - +
2D C 3.7 2.8 + - - +
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Residues in contact with ARG 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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275A ARG* 5.9 0.2 - - - +
306A GLY 3.6 0.2 - - - -
307A LYS* 1.3 93.4 - - + +
309A MET* 1.3 62.9 + - - +
311A GLU* 3.3 18.7 + - - +
312A LYS* 3.1 33.9 + - - +
324A LYS* 5.1 6.7 - - - +
1D G 3.0 52.9 + - - +
2D C 3.7 17.6 + - - +
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Residues in contact with MET 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU* 4.2 17.9 - - + -
279A TYR* 3.9 39.7 - - + +
282A ALA* 3.9 30.5 - - + -
305A ILE* 4.3 5.4 - - + -
306A GLY 3.8 7.2 - - - +
308A ARG* 1.3 74.0 - - - +
310A ALA* 1.3 51.8 + - - +
312A LYS* 3.3 6.0 + - - +
313A ILE* 2.8 54.3 + - + +
1D G 3.2 38.1 + - + +
2D C 2.8 20.2 + - - +
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A TYR* 3.6 22.0 - - + -
299A ALA* 4.2 13.7 - - + -
300A CYS* 3.6 18.4 - - - -
305A ILE* 4.2 1.8 - - + +
306A GLY 2.8 21.9 + - - +
307A LYS 3.2 4.9 - - - +
309A MET* 1.3 72.2 - - - +
311A GLU* 1.3 58.3 + - - +
313A ILE* 3.1 11.0 + - - +
314A ILE* 2.8 34.0 + - - +
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Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A TYR* 3.9 18.2 + - + -
307A LYS* 2.7 51.0 + - - +
308A ARG* 3.6 22.5 + - - +
309A MET 3.3 0.2 - - - -
310A ALA* 1.3 71.1 - - - +
312A LYS* 1.3 60.5 + - + +
314A ILE* 3.4 2.0 + - - +
315A GLU* 2.9 34.9 + - - +
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Residues in contact with LYS 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU* 4.5 15.5 - - + -
263A LEU* 5.5 2.7 - - + -
279A TYR* 3.5 26.1 + - + +
308A ARG* 3.1 26.9 + - - +
309A MET* 3.7 6.7 - - - +
310A ALA 3.2 0.2 - - - -
311A GLU* 1.3 74.3 + - + +
313A ILE* 1.3 67.0 + - - +
315A GLU* 3.7 8.6 - - - +
316A ILE* 3.0 29.5 + - - +
322A LEU* 4.2 23.7 - - + +
324A LYS* 4.6 19.5 - - + +
1D G 2.3 37.3 + - - -
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Residues in contact with ILE 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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256A ILE* 4.1 39.1 - - + +
260A LEU* 4.6 4.3 - - + -
286A LEU* 3.8 29.2 - - + -
293A VAL* 4.3 15.5 - - + -
299A ALA* 4.3 6.5 - - + -
305A ILE* 3.9 28.0 - - + -
309A MET* 2.8 33.6 + - + +
310A ALA* 3.5 4.7 - - - +
312A LYS* 1.3 74.3 - - - +
314A ILE* 1.3 75.5 + - + +
316A ILE* 3.3 3.1 + - - +
317A LEU* 3.0 20.9 + - + +
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Residues in contact with ILE 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A VAL* 4.4 2.2 - - + -
295A SER* 3.4 12.1 - - - +
296A TYR* 3.4 45.8 - - + +
299A ALA* 4.8 1.3 - - + -
310A ALA 2.8 24.2 + - - +
311A GLU* 4.0 3.1 - - - +
313A ILE* 1.3 80.1 - - + +
315A GLU* 1.3 61.4 + - - +
317A LEU* 2.7 22.7 + - + -
318A GLU* 2.6 55.8 + - + +
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Residues in contact with GLU 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 GLU* 2.9 20.4 + - - +
312A LYS* 3.7 5.3 - - - +
314A ILE* 1.3 76.5 - - - +
316A ILE* 1.3 57.2 - - - +
318A GLU* 4.8 3.4 - - - -
319A SER* 2.7 47.9 + - - +
321A HIS 4.3 3.3 - - - +
322A LEU* 3.7 18.9 - - + +
323A ARG* 2.8 60.9 + - - +
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Residues in contact with ILE 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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255A HIS* 4.0 24.5 - - + -
256A ILE* 3.9 37.9 - - + +
259A LYS* 4.0 30.5 - - + -
260A LEU* 4.8 4.7 - - + -
312A LYS 3.0 22.6 + - - +
313A ILE 3.7 5.4 - - - +
314A ILE 2.9 1.2 + - - -
315A GLU* 1.3 74.9 - - - +
317A LEU* 1.3 59.7 + - - +
320A GLY* 2.6 33.6 + - - +
321A HIS 3.5 9.2 - - - +
322A LEU* 3.6 32.3 - - + -
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Residues in contact with LEU 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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256A ILE* 4.6 14.4 - - + -
292A PRO* 6.0 2.7 - - + -
293A VAL* 3.5 25.6 - - + +
294A THR* 4.2 16.4 - - + +
313A ILE* 3.0 10.5 + - + +
314A ILE* 2.7 45.8 + - + +
316A ILE* 1.3 77.0 - - - +
318A GLU* 1.3 74.4 + - - +
320A GLY* 4.4 1.6 + - - -
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Residues in contact with GLU 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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294A THR 5.1 3.3 - - - +
314A ILE* 2.6 42.0 + - + +
315A GLU* 4.3 3.1 - - - +
317A LEU* 1.3 89.9 - - + +
319A SER* 1.3 60.2 + - - +
320A GLY* 3.8 0.5 + - - -
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Residues in contact with SER 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A GLU* 2.7 33.2 + - - +
318A GLU* 1.3 73.7 - - - +
320A GLY* 1.3 56.4 + - - +
321A HIS* 3.2 19.5 + - - +
323A ARG* 5.8 2.5 + - - -
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Residues in contact with GLY 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A HIS* 3.1 28.8 + - - -
316A ILE* 2.6 28.3 + - - -
317A LEU 4.9 1.8 - - - -
318A GLU 3.6 1.8 - - - -
319A SER* 1.3 69.7 + - - +
321A HIS* 1.3 73.2 + - - +
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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