Contacts of the helix formed by residues 295 - 311 (chain A) in PDB entry 4U1D
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 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A PHE* 3.2 21.6 + - + +
293A SER* 2.2 27.6 + - - +
294A GLY* 1.3 80.7 - - - +
296A PRO* 1.3 68.3 - - - +
297A LEU 3.3 1.8 - - - -
298A LEU* 3.8 26.2 - - + +
299A HIS* 3.3 14.4 + - - +
346A ASP* 3.9 16.1 - - - +
348A HIS* 2.4 26.1 + - - +
352A TYR* 5.1 4.9 + - - +
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Residues in contact with PRO 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A PHE 5.1 0.2 - - - +
294A GLY 3.6 10.0 - - - +
295A ASP* 1.3 82.8 - - - +
297A LEU* 1.3 73.4 + - + +
299A HIS* 3.3 11.4 - - + +
300A THR* 3.3 24.9 + - - -
331A SER 4.9 1.2 - - - +
334A SER 5.5 0.7 - - - +
335A THR* 3.6 36.8 + - + +
336A GLN* 4.5 14.6 - - + +
352A TYR* 5.3 2.9 - - - +
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ASP 3.3 0.2 - - - -
296A PRO* 1.3 82.3 - - + +
298A LEU* 1.3 66.8 + - - +
300A THR* 3.4 2.9 + - - +
301A THR* 3.1 25.6 + - - -
335A THR* 3.9 26.2 - - + +
338A ASP* 4.8 5.4 - - - +
352A TYR* 3.7 25.8 - - + +
360A LYS* 4.5 9.6 - - - -
361A PRO* 3.4 33.7 - - + +
362A THR 4.3 8.1 - - - +
363A ARG* 4.4 4.3 - - - -
366A MET* 3.7 39.5 - - + +
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A PHE* 3.4 44.8 - - + -
295A ASP* 3.6 23.9 + - + +
296A PRO 3.4 0.4 - - - -
297A LEU* 1.3 77.3 - - - +
299A HIS* 1.3 56.8 + - - +
301A THR* 3.2 6.9 + - - -
302A ALA* 2.8 32.9 + - - +
348A HIS* 4.1 9.0 - - + +
351A MET* 3.6 32.3 - - + +
352A TYR* 3.5 43.1 - - + +
355A LEU* 4.6 8.9 - - + +
357A LEU* 5.7 0.4 - - + -
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Residues in contact with HIS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A VAL* 3.0 30.4 + - + +
290A PHE* 3.7 15.4 - - + +
291A PHE* 3.8 33.8 - + + +
295A ASP 3.3 12.4 + - - +
296A PRO* 3.3 15.0 - - + +
298A LEU* 1.3 79.2 - - - +
300A THR* 1.3 61.8 + - - +
302A ALA* 3.5 4.3 + - - +
303A TRP* 3.1 51.1 + + - -
327A THR* 5.5 1.4 - - - +
331A SER* 3.8 28.7 - - - -
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Residues in contact with THR 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A PRO 3.3 13.1 + - - -
297A LEU* 3.9 6.5 - - - -
298A LEU 3.3 0.2 - - - -
299A HIS* 1.3 75.2 - - - +
301A THR* 1.3 66.9 + - - +
303A TRP* 3.2 6.6 + - - +
304A LYS* 2.9 25.2 + - + +
328A ILE* 3.7 24.0 - - + +
331A SER* 2.8 38.1 + - - +
332A ALA* 4.1 6.3 + - + -
335A THR* 4.3 1.7 + - - -
366A MET* 4.0 27.1 - - + +
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Residues in contact with THR 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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297A LEU 3.1 8.5 + - - -
298A LEU* 3.2 10.2 + - - -
300A THR* 1.3 76.5 - - - +
302A ALA* 1.3 56.7 + - - +
304A LYS* 3.0 14.7 + - + +
305A LYS* 2.8 35.0 + - + +
355A LEU* 3.4 26.5 - - + -
357A LEU* 3.8 33.6 - - + +
366A MET* 3.3 25.3 - - - +
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Residues in contact with ALA 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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283A TYR* 3.9 6.6 - - - +
286A LEU* 3.7 29.6 - - + +
287A VAL* 3.6 22.4 - - + +
290A PHE* 4.5 2.5 - - + -
298A LEU 2.8 19.5 + - - +
299A HIS 3.8 1.6 - - - +
301A THR* 1.3 73.4 - - - +
303A TRP* 1.3 61.6 + - - +
305A LYS* 3.4 8.6 + - - +
306A PHE* 3.0 22.9 + - - +
355A LEU* 4.2 9.2 - - + +
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Residues in contact with TRP 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU* 6.3 2.7 - - + -
287A VAL* 3.4 25.3 - - + +
299A HIS* 3.1 51.6 + + - -
300A THR* 3.3 12.1 - - - +
302A ALA* 1.3 77.7 - - - +
304A LYS* 1.3 55.9 + - - +
306A PHE* 3.2 23.6 + + - +
307A TYR* 2.8 29.2 + - + +
324A TYR* 3.8 44.6 - + + -
327A THR* 3.5 29.2 - - + +
328A ILE* 3.7 30.7 - - + -
331A SER* 5.1 2.9 - - - -
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Residues in contact with LYS 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A THR* 2.9 24.1 + - + +
301A THR* 3.0 11.9 + - + +
303A TRP* 1.3 73.6 - - - +
305A LYS* 1.3 61.6 + - + +
307A TYR* 3.2 7.0 + - - +
308A LYS* 2.9 31.7 + - - +
328A ILE* 4.0 18.6 - - + -
366A MET* 3.7 37.9 + - - +
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Residues in contact with LYS 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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264A PHE* 6.3 1.1 - - - -
283A TYR* 3.4 53.9 - - + -
301A THR* 2.8 19.2 + - + +
302A ALA 3.7 5.8 - - - +
304A LYS* 1.3 75.7 - - + +
306A PHE* 1.3 60.9 + - - +
308A LYS* 3.9 7.3 + - - +
309A LEU* 3.5 21.0 + - - +
354A LEU 5.6 0.4 - - - -
355A LEU* 2.8 54.6 + - + +
356A ASN* 4.1 8.6 - - - +
357A LEU* 5.1 1.8 - - - +
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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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280A ALA* 3.4 33.7 - - + -
283A TYR* 4.0 13.7 - - + +
284A GLU* 3.5 42.0 - - + +
287A VAL* 5.4 1.3 - - + -
302A ALA 3.0 14.3 + - - +
303A TRP* 3.5 27.1 - + - +
305A LYS* 1.3 76.9 - - - +
307A TYR* 1.3 63.1 + - - +
309A LEU* 3.2 4.4 + - - +
310A TYR* 2.8 52.2 + + + +
324A TYR* 3.5 36.6 - + - -
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Residues in contact with TYR 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 TRP* 2.8 17.2 + - + +
304A LYS* 3.2 5.6 + - - +
306A PHE* 1.3 82.0 - - + +
308A LYS* 1.3 65.9 + - - +
310A TYR* 3.8 3.8 - + - +
311A SER* 3.1 29.8 + - - -
321A PHE* 3.3 39.8 - + - +
324A TYR* 3.8 31.9 - + + -
325A SER* 2.7 29.7 + - - -
328A ILE* 3.7 18.8 - - + -
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Residues in contact with LYS 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 LYS 2.9 16.8 + - - +
305A LYS* 4.0 7.4 - - - +
307A TYR* 1.3 79.5 - - - +
309A LEU* 1.3 58.8 + - - +
311A SER* 3.0 18.2 + - - -
312A THR* 3.8 10.4 - - - +
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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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276A PRO* 3.6 29.2 - - + +
279A LEU* 3.8 14.6 - - + -
280A ALA* 3.4 40.8 - - + +
283A TYR* 4.1 13.0 - - + -
305A LYS 3.5 12.3 + - - +
306A PHE 3.2 5.1 + - - +
307A TYR 3.1 0.6 - - - -
308A LYS* 1.3 78.1 - - - +
310A TYR* 1.3 58.8 + - - +
311A SER 3.3 1.8 - - - -
312A THR* 3.2 29.0 + - + +
313A ASN* 5.2 0.5 - - - +
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Residues in contact with TYR 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ALA* 5.8 4.2 - - + +
306A PHE* 2.8 42.3 + + + +
307A TYR* 3.3 5.4 + + - +
309A LEU* 1.3 74.0 - - - +
311A SER* 1.3 57.4 + - - +
312A THR 3.0 10.1 + - - -
313A ASN* 3.3 36.4 + - + +
315A ARG 3.6 5.4 + - - -
316A ALA* 3.5 24.8 - - + +
320A GLU* 2.5 41.8 + - + -
321A PHE* 3.9 14.9 - + - -
324A TYR* 3.7 29.2 - + - -
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Residues in contact with SER 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A TYR* 3.1 19.5 + - - -
308A LYS* 3.0 21.1 + - - +
310A TYR* 1.3 76.6 - - - +
312A THR* 1.3 61.7 + - - +
313A ASN 3.4 3.2 - - - +
321A PHE* 3.7 28.3 - - - -
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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
------------------------------------------------------------
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