Contacts of the helix formed by residues 292 - 308 (chain A) in PDB entry 5UFL
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 ASP 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A GLY 4.5 4.6 - - - +
248A THR* 4.5 8.1 - - - -
290A GLY 3.4 2.2 - - - -
291A LYS* 1.3 75.4 - - - +
293A PRO* 1.4 71.5 - - - +
294A ASP* 3.0 30.1 - - - +
295A SER* 3.2 20.1 - - - -
296A SER* 2.8 29.2 + - - +
347A TRP* 3.7 1.1 - - - -
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Residues in contact with PRO 293 (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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291A LYS 3.4 8.9 - - - +
292A ASP* 1.4 93.6 - - - +
294A ASP* 1.3 57.1 + - - +
296A SER 3.3 1.2 + - - -
297A SER* 3.0 32.2 + - - -
347A TRP* 3.9 20.2 - - + -
350A GLN* 5.6 6.3 - - - +
358A CYS* 3.3 9.4 - - - -
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Residues in contact with ASP 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A THR* 4.5 9.2 + - - -
292A ASP* 3.0 23.8 - - - +
293A PRO* 1.3 78.2 - - - +
295A SER* 1.3 77.3 + - - +
297A SER* 3.6 18.6 - - - -
298A LYS* 3.7 14.0 - - - +
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Residues in contact with SER 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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247A GLY 3.1 15.2 + - - -
248A THR* 4.9 5.6 - - - -
251A ARG* 2.8 40.0 + - - +
292A ASP* 3.2 28.0 + - - -
293A PRO 3.3 0.6 - - - -
294A ASP* 1.3 81.9 + - - +
296A SER* 1.3 62.2 + - - +
298A LYS* 3.3 19.1 + - - +
299A VAL* 3.3 14.2 + - - +
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Residues in contact with SER 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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251A ARG* 5.8 1.0 + - - +
287A LEU 4.1 9.2 + - - -
288A LEU* 4.3 5.6 + - - +
290A GLY 3.5 10.6 + - - -
292A ASP* 2.8 23.1 + - - +
293A PRO 3.3 1.5 + - - -
295A SER* 1.3 75.3 - - - +
297A SER* 1.3 59.5 + - - +
299A VAL* 3.3 9.9 + - - +
300A LEU* 2.9 34.8 + - - +
347A TRP* 3.2 36.5 - - - -
358A CYS* 4.5 0.7 - - - -
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Residues in contact with SER 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PRO 3.0 16.1 + - - -
294A ASP* 3.6 13.9 - - - -
295A SER 3.3 0.4 - - - -
296A SER* 1.3 75.5 - - - +
298A LYS* 1.3 52.8 + - - +
300A LEU* 3.3 1.6 + - - -
301A GLU* 2.8 45.9 + - - +
357A ASN* 4.1 12.1 + - - +
358A CYS* 3.2 22.5 + - - -
361A LEU* 3.6 19.2 - - - +
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Residues in contact with LYS 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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129A TYR* 3.6 11.5 + - - -
130A ASN* 5.3 2.2 - - - +
251A ARG* 4.5 5.6 - - + +
252A LYS* 4.0 31.0 - - + +
255A VAL* 3.3 37.5 - - + +
256A ASP* 2.8 28.7 + - - -
259A MET* 5.6 0.2 - - - -
294A ASP 3.7 15.2 + - - +
295A SER* 3.3 10.0 + - - +
296A SER 3.3 0.4 - - - -
297A SER* 1.3 74.2 - - - +
299A VAL* 1.3 65.5 + - + +
301A GLU* 3.6 28.9 + - - +
302A LEU* 3.0 19.2 + - - +
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Residues in contact with VAL 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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242A LEU* 4.9 4.0 - - + -
251A ARG* 4.4 12.6 - - - +
255A VAL* 4.9 2.7 - - + -
284A VAL* 3.6 35.0 - - + +
287A LEU* 3.8 31.2 - - + +
288A LEU* 3.6 22.9 - - + -
295A SER 3.3 13.2 + - - +
296A SER* 3.3 11.1 + - - +
298A LYS* 1.3 78.5 - - + +
300A LEU* 1.3 59.9 - - - +
302A LEU* 3.4 7.7 + - - +
303A LEU* 3.1 26.8 + - + +
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Residues in contact with LEU 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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288A LEU* 3.6 15.9 - - + -
296A SER 2.9 21.0 + - - +
297A SER* 3.6 4.5 - - - +
299A VAL* 1.3 74.0 - - - +
301A GLU* 1.3 63.5 + - - +
303A LEU* 3.4 5.7 + - + +
304A LEU* 3.1 28.6 + - - +
344A LEU* 3.4 33.7 - - + -
347A TRP* 4.3 12.1 - - + +
358A CYS* 3.7 44.9 - - + +
361A LEU* 3.8 14.6 - - + -
362A ALA* 4.3 5.8 - - + +
365A LEU* 3.7 13.6 - - + +
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Residues in contact with GLU 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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255A VAL* 4.7 0.2 - - + -
259A MET* 3.7 31.2 - - + +
297A SER* 2.8 31.4 + - - +
298A LYS* 3.6 40.0 + - - +
300A LEU* 1.3 74.0 - - - +
302A LEU* 1.3 57.3 + - - +
304A LEU* 3.4 6.4 + - - +
305A ALA 3.0 21.8 + - - -
357A ASN* 4.5 7.0 + - - -
361A LEU* 4.0 23.7 - - + +
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Residues in contact with LEU 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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239A PHE* 5.1 1.1 - - + -
242A LEU* 3.4 34.1 - - + -
255A VAL* 4.0 12.1 - - + +
258A LEU* 3.7 34.3 - - + -
259A MET* 4.2 17.4 - - + -
262A LEU* 4.4 4.7 - - + -
284A VAL* 4.6 12.3 - - + -
298A LYS 3.0 15.7 + - - +
299A VAL* 3.6 6.1 - - - +
301A GLU* 1.3 77.0 - - - +
303A LEU* 1.3 58.2 + - - +
305A ALA* 3.1 6.3 + - - +
306A PHE* 2.9 50.6 + - + -
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Residues in contact with LEU 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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281A LEU* 3.8 29.4 - - + -
284A VAL* 4.3 13.9 - - + -
285A LEU* 4.2 10.8 - - + -
288A LEU* 3.9 28.9 - - + -
299A VAL* 3.1 25.5 + - + +
300A LEU* 3.8 6.1 - - - +
301A GLU 3.3 0.2 - - - -
302A LEU* 1.3 75.8 - - - +
304A LEU* 1.3 57.1 + - - +
306A PHE* 3.4 13.9 + - + +
307A CYS* 3.2 30.3 + - - -
316A LEU* 3.8 16.2 - - + +
320A MET* 5.9 0.2 - - + -
365A LEU* 3.8 27.8 - - + -
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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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300A LEU 3.1 15.8 + - - +
301A GLU* 3.6 8.5 - - - +
302A LEU 3.2 0.2 - - - -
303A LEU* 1.3 74.4 - - - +
305A ALA* 1.3 62.6 + - - +
307A CYS* 3.3 13.5 + - - +
308A SER* 3.3 11.8 + - - -
361A LEU* 3.4 44.2 - - + +
364A GLU* 3.7 25.8 - - + +
365A LEU* 3.6 34.5 - - + +
368A GLU* 4.1 13.8 - - + +
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Residues in contact with ALA 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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259A MET* 3.8 32.1 - - + +
262A LEU* 4.0 21.5 - - + +
301A GLU 3.0 14.1 + - - +
302A LEU 3.1 9.2 + - - +
304A LEU* 1.3 73.9 - - - +
306A PHE* 1.3 62.4 + - - +
308A SER* 2.6 28.1 + - - -
309A VAL* 3.9 3.5 + - - +
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Residues in contact with PHE 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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239A PHE* 4.1 16.2 - + - -
258A LEU* 4.2 2.5 - - + -
262A LEU* 3.7 23.6 - - + -
271A LEU* 3.8 17.3 - - + -
277A PHE* 4.0 15.9 - + - -
281A LEU* 3.9 30.5 - - + -
284A VAL* 5.0 4.0 - - + -
302A LEU* 2.9 46.4 + - + -
303A LEU* 3.5 19.5 - - + +
304A LEU 3.3 0.2 - - - -
305A ALA* 1.3 74.8 - - - +
307A CYS* 1.3 58.8 + - - +
309A VAL* 2.9 26.2 + - - +
312A LEU* 3.4 34.3 - - + +
313A ARG* 3.7 1.9 + - - -
316A LEU* 4.8 6.5 - - + -
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Residues in contact with CYS 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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303A LEU 3.2 25.9 + - - -
304A LEU* 3.3 10.2 + - - +
306A PHE* 1.3 76.8 - - - +
308A SER* 1.3 61.1 + - - +
309A VAL 3.2 6.4 + - - +
310A THR* 4.4 1.0 + - - -
313A ARG* 3.5 33.6 + - + +
316A LEU* 3.7 19.7 - - - -
365A LEU* 3.7 10.3 - - - -
368A GLU* 3.6 45.6 - - + +
369A ILE* 5.0 1.8 - - - -
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Residues in contact with SER 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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262A LEU* 5.4 4.0 + - - +
304A LEU 3.3 7.9 + - - -
305A ALA* 2.6 24.3 + - - +
307A CYS* 1.3 78.1 - - - +
309A VAL* 1.3 62.9 + - - +
310A THR* 3.9 2.8 + - - -
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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