Contacts of the helix formed by residues 290 - 303 (chain A) in PDB entry 4PED
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 290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A PHE 3.6 3.0 + - - -
289A ILE* 1.3 72.7 - - - +
291A PRO* 1.3 72.4 - - - +
292A HIS* 2.8 47.3 + - - +
293A LEU* 2.9 27.1 + - + +
294A ALA 3.0 10.6 + - - -
383A ASN 5.3 1.2 + - - -
384A MSE 4.0 34.2 + - - +
386A PRO* 6.1 1.0 - - - +
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Residues in contact with PRO 291 (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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285A ASP* 5.6 7.6 - - - +
286A ASP 6.1 0.4 - - - +
289A ILE 3.1 8.7 - - - +
290A ASN* 1.3 86.3 - - - +
292A HIS* 1.3 69.6 + - + +
294A ALA* 3.4 8.4 + - + +
295A LYS* 3.0 25.1 + - - +
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Residues in contact with HIS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ALA* 6.3 2.0 - - + -
290A ASN* 2.8 23.2 + - - +
291A PRO* 1.3 80.5 - - + +
293A LEU* 1.3 54.7 + - - +
295A LYS* 3.4 7.4 + - + +
296A ILE* 3.0 36.2 + - + +
384A MSE 4.2 20.2 - - + +
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Residues in contact with LEU 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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263A ILE* 6.2 1.3 - - + -
267A LEU* 5.9 0.4 - - + -
283A ILE* 4.0 31.9 - - + -
289A ILE* 4.4 6.5 - - + -
290A ASN* 2.9 22.2 + - + +
292A HIS* 1.3 75.0 - - - +
294A ALA* 1.3 65.4 + - - +
296A ILE* 3.3 8.7 + - + +
297A PHE* 3.0 49.0 + - + -
379A LEU* 4.5 12.6 - - + -
382A SER* 5.1 1.3 - - - +
384A MSE 3.6 45.4 - - + +
385A LEU* 4.7 6.3 - - + -
386A PRO* 4.4 8.1 - - + -
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Residues in contact with ALA 294 (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 ILE* 4.6 7.6 - - - -
284A GLN* 3.6 33.7 - - - +
285A ASP* 3.7 16.6 - - + +
289A ILE* 4.0 6.8 - - + +
290A ASN 3.0 10.8 + - - +
291A PRO* 3.8 11.0 - - + +
292A HIS 3.4 0.2 - - - -
293A LEU* 1.3 76.2 - - - +
295A LYS* 1.3 58.0 + - - +
297A PHE* 3.3 3.7 + - - +
298A GLU* 3.0 35.6 + - - +
301A ARG* 4.9 0.2 + - - -
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Residues in contact with LYS 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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291A PRO 3.0 17.0 + - - +
292A HIS* 3.8 8.3 - - + +
293A LEU 3.2 0.2 - - - -
294A ALA* 1.3 74.1 - - - +
296A ILE* 1.3 61.8 + - + +
298A GLU* 3.3 18.5 + - + +
299A ARG* 2.9 41.6 + - + +
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Residues in contact with ILE 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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260A ALA* 4.0 31.4 - - + +
263A ILE* 4.0 24.5 - - + -
264A VAL* 3.9 16.1 - - + +
267A LEU* 3.6 30.1 - - + -
292A HIS* 3.0 21.3 + - + +
293A LEU* 3.5 8.3 - - + +
295A LYS* 1.3 76.7 - - + +
297A PHE* 1.3 61.7 + - + +
299A ARG* 3.1 5.0 + - - +
300A VAL* 2.9 27.4 + - - +
384A MSE 3.9 27.8 - - + -
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Residues in contact with PHE 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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267A LEU* 4.2 19.5 - - + -
274A ALA* 3.2 36.1 - - + -
275A LEU* 4.2 15.7 - - + +
277A LEU* 5.7 2.0 - - + -
278A GLY* 3.9 17.5 - - - -
283A ILE* 3.8 24.2 - - + +
293A LEU* 3.0 45.8 + - + +
294A ALA 3.8 4.3 - - - +
296A ILE* 1.3 81.9 - - + +
298A GLU* 1.3 61.4 + - - +
300A VAL* 3.3 8.8 + - + +
301A ARG* 3.0 42.7 + - - +
379A LEU* 4.3 19.5 - - + -
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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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285A ASP* 3.8 27.0 + - - +
294A ALA* 3.0 23.2 + - + +
295A LYS* 3.3 19.4 + - - +
297A PHE* 1.3 74.4 - - - +
299A ARG* 1.3 59.2 + - + +
301A ARG* 3.2 25.1 + - - +
302A GLN* 2.9 37.0 + - - +
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Residues in contact with ARG 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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261A GLU* 2.9 37.9 + - - +
264A VAL* 3.8 17.5 - - + +
295A LYS* 2.9 31.5 + - + +
296A ILE* 3.1 8.7 + - - +
298A GLU* 1.3 75.3 - - + +
300A VAL* 1.3 60.1 + - - +
302A GLN* 2.8 53.7 + - - +
303A SER* 2.8 53.1 + - - +
306A PHE* 5.6 10.7 - - - -
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Residues in contact with VAL 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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264A VAL* 4.1 17.3 - - + +
267A LEU* 3.8 36.3 - - + -
268A CYS* 4.4 4.3 - - - -
271A ARG* 2.9 49.0 + - + +
274A ALA* 4.8 4.7 - - + -
275A LEU* 3.9 23.3 - - + -
296A ILE 2.9 18.7 + - - +
297A PHE* 3.3 10.5 + - + +
299A ARG* 1.3 74.8 - - - +
301A ARG* 1.3 64.1 + - - +
303A SER* 3.2 10.8 + - - -
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Residues in contact with ARG 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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271A ARG* 3.5 9.8 + - - +
275A LEU* 3.6 24.2 - - + +
278A GLY* 5.9 3.0 - - - -
279A GLN* 6.2 0.4 - - - +
283A ILE 3.4 23.8 + - - -
284A GLN* 5.1 4.2 - - - +
294A ALA 4.9 0.4 + - - -
297A PHE* 3.0 27.8 + - - +
298A GLU* 3.4 43.3 - - - +
300A VAL* 1.3 76.5 - - - +
302A GLN* 1.3 64.1 + - - +
303A SER 3.2 0.7 + - - -
304A ALA* 3.2 16.1 + - - +
338A ALA* 3.7 18.1 + - + +
454A ASP* 4.1 23.8 + - - +
490A ASN* 5.7 0.6 + - - -
492A SER* 4.5 16.0 - - - +
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Residues in contact with GLN 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* 2.9 21.9 + - - +
299A ARG* 2.8 52.0 + - - +
301A ARG* 1.3 76.8 - - - +
303A SER* 1.3 56.4 + - - +
304A ALA* 3.0 2.9 + - - -
305A ASP* 3.0 37.2 - - - +
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Residues in contact with SER 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A VAL* 4.1 2.9 - - - +
268A CYS* 3.5 23.7 - - - -
271A ARG* 3.9 3.8 - - - -
299A ARG* 2.8 42.9 + - - +
300A VAL 3.5 6.7 - - - -
301A ARG 3.1 1.4 - - - -
302A GLN* 1.3 73.6 - - - +
304A ALA* 1.3 59.8 + - - +
305A ASP 2.9 6.1 - - - +
306A PHE* 2.9 31.4 + - - +
307A MSE 3.5 11.6 - - - +
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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