Contacts of the helix formed by residues 297 - 309 (chain E) in PDB entry 3KDO
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 297 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122E ARG* 3.6 31.7 + - - +
123E LEU 3.0 20.7 + - - -
124E GLU* 3.8 16.7 + - - -
289E THR* 4.3 0.4 - - - -
296E ILE* 1.3 76.5 - - - +
298E MET* 1.3 66.7 + - - +
299E PHE* 2.9 20.8 + - - +
300E VAL* 2.9 15.6 + - - +
301E LEU* 3.4 8.3 + - - +
333E PHE* 4.9 3.1 - - - -
351E HIS* 5.0 1.9 + - - -
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Residues in contact with MET 298 (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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122E ARG* 4.7 2.0 - - - +
282E ARG* 3.6 37.0 - - + +
285E HIS* 4.4 5.4 - - + -
289E THR* 3.9 18.0 - - - +
296E ILE 3.7 2.4 + - - -
297E SER* 1.3 72.8 + - - +
299E PHE* 1.3 55.7 + - - +
301E LEU* 3.2 27.1 + - + +
302E ALA* 2.9 32.9 + - + +
305E TYR* 5.2 0.9 - - + -
313E LEU* 4.0 24.0 - - + -
314E HIS 3.7 23.6 - - - +
315E VAL* 5.2 2.9 - - + -
333E PHE* 3.6 31.9 - - + -
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Residues in contact with PHE 299 (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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124E GLU 3.8 7.4 - - - +
125E ASP* 3.5 33.4 - - - -
297E SER* 3.0 15.1 + - - +
298E MET* 1.3 79.7 - - - +
300E VAL* 1.3 60.5 + - - +
302E ALA* 3.6 0.4 + - - -
303E LYS* 3.3 9.0 + - - +
332E GLY* 3.9 16.4 - - - -
333E PHE* 3.6 27.1 - + + -
336E LEU* 3.1 53.9 - - + +
342E TYR* 3.6 32.3 - + - -
351E HIS* 3.3 40.4 - + + +
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Residues in contact with VAL 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E LEU* 5.7 1.6 - - + -
123E LEU* 3.8 30.5 - - + +
124E GLU 3.8 1.1 - - - +
125E ASP* 3.7 39.9 - - - +
126E LEU* 4.2 11.7 - - + +
296E ILE* 4.0 15.5 - - + -
297E SER 2.9 9.0 + - - +
299E PHE* 1.3 76.0 - - - +
301E LEU* 1.3 66.1 + - + +
303E LYS* 3.3 7.1 + - - +
304E LEU* 3.0 44.0 + - + +
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Residues in contact with LEU 301 (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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257E VAL* 4.4 9.6 - - + -
261E TRP* 3.7 31.9 - - + -
285E HIS* 4.2 8.5 - - + -
288E PHE* 3.7 37.9 - - + -
289E THR* 3.8 14.1 - - + -
296E ILE* 4.7 9.2 - - + -
297E SER 3.4 8.5 + - - +
298E MET* 3.2 22.8 + - + +
300E VAL* 1.3 78.7 - - + +
302E ALA* 1.3 64.4 + - - +
304E LEU* 3.2 3.6 + - - +
305E TYR* 2.9 46.5 + - + +
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Residues in contact with ALA 302 (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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298E MET* 2.9 21.7 + - + +
299E PHE* 3.7 7.4 - - - +
300E VAL 3.3 0.2 - - - -
301E LEU* 1.3 76.5 - - - +
303E LYS* 1.3 61.3 + - - +
305E TYR* 4.0 1.2 - - - +
306E ARG* 3.2 17.8 + - - +
313E LEU* 3.7 16.8 - - + -
315E VAL* 5.7 0.4 - - + -
333E PHE* 4.7 13.5 - - + -
336E LEU* 4.0 10.8 - - + -
337E LEU* 3.4 31.6 - - + +
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Residues in contact with LYS 303 (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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125E ASP* 3.4 18.2 + - - +
126E LEU* 2.6 33.2 + - + +
127E TYR* 3.9 1.4 - - - +
128E PHE* 5.2 3.6 - - + -
299E PHE* 3.3 9.6 + - - +
300E VAL* 3.3 9.1 + - - +
301E LEU 3.2 0.6 - - - -
302E ALA* 1.3 78.9 - - - +
304E LEU* 1.3 70.0 - - + +
306E ARG* 3.2 7.1 + - - +
307E LEU* 3.0 41.5 + - + +
336E LEU* 3.8 27.7 - - + +
337E LEU* 5.5 0.2 - - - -
352E LEU* 5.3 1.0 + - - +
354E GLN* 2.8 43.1 - - - +
356E PHE* 4.2 12.1 - - + -
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Residues in contact with LEU 304 (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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101E LEU* 4.2 16.5 - - + +
105E LEU* 4.0 24.7 - - + -
126E LEU* 4.4 9.9 - - + -
128E PHE* 4.0 27.1 - - + -
136E PHE* 5.7 0.2 - - + -
261E TRP* 3.6 36.8 - - + -
300E VAL* 3.0 38.8 + - + +
301E LEU 3.8 2.2 - - - +
303E LYS* 1.3 81.4 - - + +
305E TYR* 1.3 58.3 + - - +
307E LEU* 3.3 8.3 + - + +
308E ILE* 2.9 34.6 + - - +
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Residues in contact with TYR 305 (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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256E VAL* 3.5 22.9 + - + -
257E VAL* 3.3 34.0 - - + +
261E TRP* 3.6 32.6 - + - -
264E LEU* 3.5 33.4 - - + -
282E ARG* 5.6 0.9 - - + -
298E MET* 5.2 1.6 - - + -
301E LEU* 2.9 44.9 + - + +
304E LEU* 1.3 76.9 - - - +
306E ARG* 1.3 58.6 + - - +
308E ILE* 3.9 2.2 - - + +
309E GLY 3.2 4.0 + - - -
310E ILE* 2.9 45.6 + - + +
313E LEU* 4.0 30.7 - - + -
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Residues in contact with ARG 306 (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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139E PRO* 3.2 22.1 - - + +
302E ALA 3.2 19.2 + - - +
303E LYS* 3.5 4.5 - - - +
305E TYR* 1.3 75.4 - - - +
307E LEU* 1.3 66.4 + - - +
309E GLY 3.1 9.4 + - - -
310E ILE 4.6 7.6 - - - -
336E LEU 2.8 35.1 + - - -
337E LEU* 3.2 30.6 + - + +
338E ARG 4.0 1.6 + - - -
339E GLU 2.9 32.9 + - - -
340E SER* 4.5 1.6 - - - +
356E PHE* 3.6 27.4 - - - +
359E ILE* 3.2 28.1 + - + +
360E LYS 3.0 22.3 + - - +
361E ALA* 3.6 9.3 - - - +
362E ALA* 4.2 10.3 - - + -
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Residues in contact with LEU 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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128E PHE* 3.6 35.0 - - + -
133E ILE* 3.7 28.3 - - + -
136E PHE* 3.2 36.2 - - + +
138E GLY* 2.8 28.8 + - - -
303E LYS* 3.0 31.7 + - + +
304E LEU* 3.6 9.6 - - + +
306E ARG* 1.3 77.2 - - - +
308E ILE* 1.3 56.9 + - - +
356E PHE* 4.1 11.9 - - + -
359E ILE* 3.9 24.2 - - + -
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Residues in contact with ILE 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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101E LEU* 4.1 25.1 - - + -
136E PHE* 4.2 11.4 - - + -
137E ASP* 4.9 2.1 + - - +
138E GLY 4.0 2.9 + - - +
261E TRP* 4.1 14.1 - - + +
264E LEU* 3.9 33.9 - - + +
265E ARG* 4.1 28.9 + - + +
268E ARG* 3.3 37.3 + - + +
304E LEU 2.9 21.4 + - - +
305E TYR* 3.9 6.1 - - + +
307E LEU* 1.3 77.8 - - - +
309E GLY* 1.3 58.5 + - - +
310E ILE* 4.7 6.1 - - + -
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Residues in contact with GLY 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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138E GLY 3.1 28.0 - - - -
139E PRO* 3.3 11.5 - - - +
140E ALA 4.5 0.9 + - - -
268E ARG* 3.9 11.2 + - - +
278E ILE* 3.8 14.9 - - - +
305E TYR 3.2 0.4 + - - -
306E ARG 3.1 5.3 + - - -
308E ILE* 1.3 79.2 - - - +
310E ILE* 1.3 66.8 + - - +
311E ASP* 3.3 6.8 + - - +
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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