Contacts of the helix formed by residues 296 - 309 (chain A) in PDB entry 4U7D
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 ASN 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A PRO* 3.4 5.0 - - - +
295A SER* 1.3 78.7 - - - +
297A THR* 1.3 58.8 + - - +
298A GLU* 2.7 37.4 + - - +
299A ASP* 3.1 35.4 + - + +
300A PHE* 3.0 26.2 + - - +
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Residues in contact with THR 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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294A PRO 5.3 0.9 - - - +
295A SER 4.1 8.5 - - - +
296A ASN* 1.3 73.6 + - - +
298A GLU* 1.3 61.9 + - - +
300A PHE* 3.7 12.6 - - + +
301A ILE* 3.3 29.6 + - - +
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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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296A ASN* 2.7 17.4 + - - +
297A THR* 1.3 74.4 + - - +
299A ASP* 1.3 62.1 + - - +
300A PHE 3.2 0.4 - - - -
301A ILE* 3.5 8.3 + - - +
302A GLU* 3.1 32.5 + - + +
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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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294A PRO* 4.6 8.5 - - + -
296A ASN* 3.1 35.7 + - + +
298A GLU* 1.3 77.3 - - - +
300A PHE* 1.3 57.7 + - - +
302A GLU* 3.4 10.2 + - - +
303A ASP* 2.8 38.0 + - - +
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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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293A LYS* 3.6 28.3 - - + -
294A PRO* 3.2 25.4 - - + +
296A ASN 3.0 16.7 + - - +
297A THR* 3.7 13.2 - - + +
298A GLU 3.2 0.4 - - - -
299A ASP* 1.3 74.6 - - - +
301A ILE* 1.3 66.5 + - + +
303A ASP* 3.3 4.3 + - + +
304A ILE* 3.2 27.3 + - + +
389A HIS* 3.2 43.3 - + - -
417A TYR* 3.3 60.8 - + + -
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Residues in contact with ILE 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 THR 3.3 15.8 + - - +
298A GLU* 3.6 10.5 - - - +
300A PHE* 1.3 78.3 - - + +
302A GLU* 1.3 63.3 + - - +
304A ILE* 3.0 20.5 + - + +
305A VAL* 3.1 18.2 + - + +
330A VAL* 3.8 31.6 - - + +
333A SER* 3.6 34.5 - - - +
334A LEU* 4.4 10.3 - - + -
337A LEU* 3.5 28.5 - - + -
389A HIS* 5.6 2.5 - - - +
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Residues in contact with GLU 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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298A GLU* 3.1 21.2 + - + +
299A ASP* 3.5 13.2 - - - +
300A PHE 3.3 0.2 - - - -
301A ILE* 1.3 79.3 - - + +
303A ASP* 1.3 63.3 + - - +
304A ILE 3.4 0.2 + - - -
305A VAL* 3.7 6.8 + - - +
306A LYS* 3.4 37.9 + - - +
337A LEU* 5.3 7.6 - - + -
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Residues in contact with ASP 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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291A ARG* 5.7 1.0 + - - +
294A PRO* 3.7 18.9 - - - +
299A ASP* 2.8 22.9 + - - +
300A PHE* 3.5 11.4 - - + +
301A ILE 3.2 0.4 - - - -
302A GLU* 1.3 78.9 - - - +
304A ILE* 1.3 63.5 + - - +
306A LYS* 3.6 12.7 + - - +
307A LEU* 3.6 22.4 + - - +
417A TYR* 4.5 15.1 - - - +
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Residues in contact with ILE 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 PHE* 3.2 41.9 + - + +
301A ILE* 3.0 17.6 + - + +
303A ASP* 1.3 74.0 - - - +
305A VAL* 1.3 62.2 + - - +
306A LYS 3.1 1.6 - - - -
307A LEU* 2.8 28.4 + - - +
308A ILE* 3.0 33.7 + - + +
319A ILE* 4.5 17.3 - - + -
330A VAL* 5.3 2.7 - - + -
334A LEU* 4.1 12.6 - - + -
387A ILE* 4.8 15.9 - - + -
389A HIS* 4.5 12.8 - - + -
417A TYR* 4.5 12.6 - - + +
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Residues in contact with VAL 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 ILE 3.3 14.6 - - - +
302A GLU* 4.1 5.8 - - - +
303A ASP 3.6 0.2 - - - -
304A ILE* 1.3 75.9 - - - +
306A LYS* 1.3 58.3 + - + +
308A ILE* 3.8 7.6 - - - -
309A ASN* 3.0 50.1 + - - +
334A LEU* 3.9 20.4 - - + -
337A LEU* 3.9 36.8 - - + +
339A ILE* 4.3 9.9 - - + -
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Residues in contact with LYS 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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302A GLU* 3.4 25.6 + - - +
303A ASP* 3.8 13.9 - - - +
304A ILE 3.1 1.2 + - - -
305A VAL* 1.3 74.9 - - + +
307A LEU* 1.3 62.5 + - + +
309A ASN* 3.9 2.0 - - - -
310A GLY* 3.0 24.8 + - - +
311A ARG 4.4 0.2 + - - -
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Residues in contact with LEU 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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291A ARG* 4.0 20.9 - - - +
303A ASP 3.6 11.8 + - - +
304A ILE* 2.8 12.7 + - - +
306A LYS* 1.3 76.3 - - + +
308A ILE* 1.3 61.6 + - + +
310A GLY 3.0 5.9 + - - -
311A ARG* 3.1 44.9 + - + +
312A TYR* 3.0 37.8 + - + -
387A ILE* 4.7 12.3 - - + -
415A ILE* 4.6 12.6 - - + -
417A TYR* 3.5 24.9 - - + +
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Residues in contact with ILE 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ILE* 3.0 37.7 + - + +
305A VAL* 4.0 4.7 - - - +
307A LEU* 1.3 77.9 - - + +
309A ASN* 1.3 61.2 + - - +
310A GLY 3.3 0.2 - - - -
312A TYR* 3.1 33.6 - - + +
313A LYS* 3.2 4.2 + - - -
319A ILE* 4.7 8.7 - - + -
334A LEU* 4.7 3.8 - - + -
339A ILE* 3.7 31.9 - - + -
366A GLN* 3.3 32.4 + - - +
367A VAL* 4.2 18.4 - - + -
385A PHE* 4.5 16.2 - - + -
387A ILE* 5.3 2.2 - - + -
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Residues in contact with ASN 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A VAL* 3.0 39.8 + - - +
306A LYS* 3.9 2.5 - - - +
308A ILE* 1.3 79.3 - - - +
310A GLY* 1.3 60.6 + - - +
313A LYS* 4.0 12.8 - - - +
337A LEU 5.1 3.6 + - - -
339A ILE* 3.8 19.2 - - - +
366A GLN* 5.3 0.7 - - - +
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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