Contacts of the helix formed by residues 296 - 309 (chain A) in PDB entry 2KUL
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 PRO 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A LEU* 4.4 9.6 - - + -
286A MET* 3.9 14.3 - - - +
287A ASP* 3.7 43.5 + - - +
290A PHE* 4.5 7.9 - - + +
294A ASN* 3.4 25.1 - - - +
295A LYS* 1.3 86.9 - - + +
297A GLY* 1.3 58.8 + - - +
298A GLU 3.5 1.1 - - - -
299A ILE* 3.7 17.0 + - + +
300A ALA* 3.1 26.0 + - - +
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Residues in contact with GLY 297 (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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287A ASP* 5.2 3.6 - - - -
295A LYS* 3.3 22.8 - - - +
296A PRO* 1.3 78.4 - - - +
298A GLU* 1.3 63.7 + - - +
299A ILE 3.2 0.2 - - - -
300A ALA* 3.1 6.3 + - - +
301A LYS* 2.8 43.1 + - - +
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Residues in contact with GLU 298 (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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151A ARG* 3.4 23.3 - - - +
155A LEU* 5.1 7.9 - - + +
295A LYS* 3.2 34.4 + - - +
297A GLY* 1.3 84.9 + - - +
299A ILE* 1.3 64.5 + - + +
302A TYR* 3.0 29.8 + - - +
323A ILE* 3.2 17.9 - - + +
324A LEU* 3.6 22.6 - - + +
327A GLY* 3.6 38.1 - - - +
328A LEU* 4.2 3.3 + - - +
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Residues in contact with ILE 299 (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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151A ARG* 5.8 3.4 - - + -
154A VAL* 6.1 2.5 - - + -
155A LEU* 5.9 3.4 - - + -
248A GLY* 5.2 4.9 - - - +
251A MET* 4.0 31.4 - - + -
252A ILE* 5.0 14.6 - - + +
255A LEU* 3.9 28.9 - - + -
286A MET* 3.7 22.4 - - + -
295A LYS 4.9 0.2 - - - +
296A PRO* 4.0 15.9 - - + +
297A GLY 3.2 0.4 - - - -
298A GLU* 1.3 89.7 - - + +
300A ALA* 1.3 59.5 + - - +
302A TYR* 3.3 9.1 + - + +
303A MET* 2.8 39.2 + - + +
324A LEU* 4.9 0.9 - - - -
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Residues in contact with ALA 300 (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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282A ILE* 4.3 3.5 - - - +
283A ALA* 4.0 30.7 - - + +
286A MET* 4.0 15.5 - - + +
287A ASP* 4.7 4.5 - - + +
296A PRO 3.1 18.9 + - - +
297A GLY* 3.1 8.6 + - - +
299A ILE* 1.3 77.3 - - - +
301A LYS* 1.3 61.2 + - + +
303A MET* 3.8 1.7 - - - +
304A GLU* 3.0 29.8 + - - +
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Residues in contact with LYS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ALA* 5.8 3.6 - - - -
297A GLY* 2.8 23.8 + - - +
300A ALA* 1.3 71.6 - - + +
302A TYR* 1.3 57.6 + - - +
304A GLU* 2.6 37.1 + - - +
305A THR* 2.6 40.2 + - - +
323A ILE* 3.5 24.2 - - + -
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Residues in contact with TYR 302 (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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162A LEU* 5.4 2.0 - - + -
244A LEU* 3.0 36.2 + - - +
247A LEU* 3.6 23.1 - - + +
248A GLY* 4.0 11.7 - - - -
251A MET* 4.3 11.9 - - - -
298A GLU 3.0 20.2 + - - +
299A ILE* 3.4 6.7 - - + +
301A LYS* 1.3 75.7 - - - +
303A MET* 1.3 83.4 + - + +
305A THR* 3.2 7.5 + - - -
306A VAL* 2.9 40.7 + - + +
320A LEU* 3.6 45.8 - - + -
323A ILE* 4.0 6.6 - - + +
324A LEU* 3.9 26.0 - - + -
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Residues in contact with MET 303 (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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244A LEU 5.0 1.8 - - - +
245A GLU* 3.7 24.7 - - - +
248A GLY* 4.1 17.5 - - - -
249A TYR* 5.1 9.0 - - + -
279A ARG* 4.9 7.6 - - + -
282A ILE* 3.6 33.2 - - + +
286A MET* 4.0 22.7 - - + -
299A ILE* 2.8 28.3 + - + +
300A ALA 3.8 2.2 - - - +
302A TYR* 1.3 94.1 - - + +
304A GLU* 1.3 66.1 + - - +
306A VAL* 3.1 24.8 - - + +
307A LYS* 3.1 12.6 + - - +
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Residues in contact with GLU 304 (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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282A ILE* 3.4 24.1 - - + +
283A ALA* 4.1 17.1 - - + +
300A ALA 3.0 17.2 + - - +
301A LYS* 2.6 39.1 + - - +
303A MET* 1.3 76.5 - - - +
305A THR* 1.3 57.4 + - - +
307A LYS* 3.4 2.9 + - - +
308A LEU* 3.0 34.7 + - + +
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Residues in contact with THR 305 (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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301A LYS* 2.6 27.1 + - - +
302A TYR* 3.3 5.8 - - - -
304A GLU* 1.3 78.7 + - - +
306A VAL* 1.3 61.5 + - - +
308A LEU* 3.1 21.3 + - + +
309A LEU* 3.3 17.4 + - + +
319A ASN* 4.2 17.4 + - + +
320A LEU* 3.5 24.5 - - + -
323A ILE* 5.3 4.2 - - + +
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Residues in contact with VAL 306 (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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241A ARG* 2.9 38.4 - - - +
244A LEU* 3.8 35.4 - - + +
245A GLU* 4.7 0.4 - - - +
302A TYR* 2.9 40.2 + - + +
303A MET* 3.1 42.4 - - + +
305A THR* 1.3 75.3 - - - +
307A LYS* 1.3 59.1 + - + +
309A LEU* 3.0 19.8 + - - +
320A LEU* 3.9 8.1 - - + -
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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
----------------------------------------------------------
241A ARG* 4.6 14.1 - - - +
279A ARG* 2.9 31.1 + - + +
280A GLU* 3.0 21.6 + - - +
282A ILE* 3.9 20.1 - - + +
303A MET 3.1 17.3 + - - +
304A GLU 3.8 4.3 - - - +
306A VAL* 1.3 78.8 - - + +
308A LEU* 1.3 62.7 + - - +
309A LEU 3.2 0.6 + - - -
310A ASP* 3.3 13.3 + - - +
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Residues in contact with LEU 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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304A GLU* 3.0 22.4 + - + +
305A THR* 3.1 14.3 + - + +
307A LYS* 1.3 78.8 - - - +
309A LEU* 1.3 55.0 + - - +
310A ASP* 3.2 4.6 + - - +
313A GLU* 5.6 0.7 - - - +
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Residues in contact with LEU 309 (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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241A ARG* 3.5 22.0 - - + -
244A LEU* 4.0 15.0 - - + -
305A THR* 3.3 12.4 + - + +
306A VAL* 3.0 38.4 - - + +
308A LEU* 1.3 76.8 - - - +
310A ASP* 1.3 64.7 + - - +
311A TYR 2.9 16.8 + - - +
313A GLU* 3.1 20.8 + - - +
314A LYS* 3.3 35.4 - - + +
315A PRO* 3.9 22.0 - - + -
316A LEU 4.8 2.2 - - - +
320A LEU* 5.2 3.6 - - + -
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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