Contacts of the helix formed by residues 294 - 305 (chain A) in PDB entry 3KXG
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 294 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ASP* 5.5 0.3 - - - -
134A ARG* 3.3 26.6 + - - -
290A GLN 5.3 0.2 + - - -
292A LEU 3.7 3.5 + - - -
293A VAL* 1.3 78.7 - - - +
295A PRO* 1.4 76.6 - - - +
296A GLU* 3.1 7.4 + - - +
297A ALA* 3.1 16.8 + - - +
298A ILE* 3.1 19.5 + - - +
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Residues in contact with PRO 295 (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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293A VAL 4.7 0.7 - - - +
294A SER* 1.4 85.5 - - - +
296A GLU* 1.3 58.1 + - + +
298A ILE* 3.8 7.0 - - + +
299A ASP* 2.8 30.7 + - - +
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Residues in contact with GLU 296 (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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134A ARG* 4.5 6.1 - - - +
294A SER* 3.1 7.9 + - - +
295A PRO* 1.3 76.6 - - + +
297A ALA* 1.3 65.8 + - - +
299A ASP* 3.5 4.2 + - - +
300A PHE* 3.1 25.3 + - - +
321A HIS* 3.3 27.2 - - - -
322A PRO* 3.8 25.1 - - - +
323A TYR* 3.9 22.1 - - + +
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Residues in contact with ALA 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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222A PHE* 3.5 12.8 - - + -
226A ILE* 4.1 16.6 - - + -
292A LEU 4.0 11.2 - - - +
293A VAL 4.1 1.3 - - - -
294A SER* 3.1 28.5 + - - +
296A GLU* 1.3 76.9 - - - +
298A ILE* 1.3 58.2 + - - +
300A PHE* 3.3 2.1 + - - +
301A LEU* 2.8 31.0 + - - +
323A TYR* 3.6 23.0 - - + -
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Residues in contact with ILE 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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226A ILE* 4.2 5.6 - - + -
227A PHE* 3.5 32.8 - - + -
281A TRP* 3.7 36.5 - - + +
282A LEU* 4.6 13.7 - - + +
293A VAL* 3.5 22.2 - - + +
294A SER 3.1 13.0 + - - +
295A PRO* 3.9 9.9 - - + +
297A ALA* 1.3 73.0 - - - +
299A ASP* 1.3 67.2 + - - +
301A LEU* 3.9 3.5 - - + +
302A ASP* 2.8 24.5 + - + +
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Residues in contact with ASP 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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295A PRO 2.8 21.8 + - - +
296A GLU* 3.9 8.4 - - - +
298A ILE* 1.3 74.8 - - - +
300A PHE* 1.3 62.2 + - - +
302A ASP* 3.4 6.8 + - - +
303A LYS* 3.1 55.7 + - - +
321A HIS* 2.7 26.7 + - + +
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Residues in contact with PHE 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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137A ILE* 4.4 9.2 - - + -
141A LEU* 4.4 4.0 - - + -
218A LEU* 5.0 2.0 - - + -
222A PHE* 3.4 32.8 - + - -
296A GLU 3.1 18.2 + - - +
297A ALA 3.5 1.8 - - - +
299A ASP* 1.3 74.4 - - - +
301A LEU* 1.3 64.1 + - - +
303A LYS* 3.0 15.1 + - - +
304A LEU* 3.3 35.1 + - + +
313A LEU* 3.8 17.3 - - + -
318A ALA* 3.5 31.0 - - + -
321A HIS* 3.7 27.5 + + + +
323A TYR* 3.9 11.9 - + + -
324A PHE* 3.5 29.8 - + - -
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Residues in contact with LEU 301 (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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219A GLY* 3.4 28.7 - - - +
222A PHE* 3.8 20.4 - - + -
223A ALA* 3.8 11.2 - - + -
226A ILE* 4.2 4.7 - - + -
227A PHE* 3.5 33.4 - - + -
281A TRP* 3.7 24.0 - - + -
297A ALA 2.8 21.4 + - - +
298A ILE* 3.9 6.1 - - + +
300A PHE* 1.3 71.7 - - - +
302A ASP* 1.3 63.9 + - - +
304A LEU* 2.9 14.4 + - - +
305A LEU* 3.0 29.5 + - + +
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Residues in contact with ASP 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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249A LEU* 5.9 0.2 - - - +
278A ARG* 3.0 24.9 + - - -
281A TRP* 2.8 36.7 + - + +
298A ILE* 2.8 22.6 + - + +
299A ASP* 3.7 8.2 - - - +
301A LEU* 1.3 74.5 - - - +
303A LYS* 1.3 59.3 + - - +
304A LEU 3.2 1.1 + - - -
305A LEU 3.9 6.9 + - - +
306A ARG* 3.0 49.3 + - - +
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Residues in contact with LYS 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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299A ASP* 3.1 42.6 + - - +
300A PHE 3.0 11.2 + - - +
302A ASP* 1.3 75.7 - - - +
304A LEU* 1.3 59.5 + - - +
306A ARG* 3.9 24.8 - - - +
311A GLU 4.4 1.4 - - - +
312A ARG* 3.4 8.7 - - - -
313A LEU* 3.1 47.7 + - + -
321A HIS* 4.3 15.3 + - + -
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Residues in contact with LEU 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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215A MET* 3.9 42.4 - - + +
216A TRP* 4.2 2.4 - - - -
218A LEU* 4.3 9.2 - - + -
219A GLY* 3.6 34.5 - - - +
222A PHE* 4.6 8.1 - - + -
300A PHE* 3.6 46.0 - - + +
301A LEU* 2.9 6.1 + - - +
303A LYS* 1.3 79.5 - - - +
305A LEU* 1.3 62.1 + - - +
306A ARG 3.0 8.8 + - - -
312A ARG* 3.4 25.3 + - - +
313A LEU* 4.1 17.3 - - + +
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Residues in contact with LEU 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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216A TRP* 3.7 56.5 - - + +
219A GLY* 3.8 16.2 - - - +
220A CYS* 3.8 3.8 - - - +
223A ALA* 4.3 6.1 - - + -
232A PHE* 4.7 0.2 - - + -
233A PHE* 3.9 18.6 - - + -
249A LEU* 3.5 19.6 - - + +
281A TRP* 3.5 34.0 - - + -
301A LEU* 3.0 34.7 + - + +
302A ASP* 3.9 8.4 - - - +
304A LEU* 1.3 74.3 - - - +
306A ARG* 1.3 60.7 + - - +
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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