Contacts of the helix formed by residues 296 - 301 (chain E) in PDB entry 5U07
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 PHE 296 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E HIS* 3.6 31.2 - + - -
232E TYR* 3.2 21.4 + - + +
285E HIS* 4.4 13.2 - + - -
294E ILE* 3.9 14.1 - - + -
295E SER* 1.3 77.2 - - - +
297E ALA* 1.3 64.4 + - - +
298E PRO* 3.3 3.1 - - - -
299E ALA* 3.0 22.0 + - + +
300E PHE* 3.9 6.4 - - - -
318E LEU* 3.8 30.5 - - + -
321E TYR* 3.9 25.4 - + + -
322E ALA* 4.2 26.5 - - + -
325E LEU* 3.8 20.9 - - + -
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Residues in contact with ALA 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E TYR* 3.3 11.9 + - - +
192E PHE* 4.2 16.5 - - + -
232E TYR* 4.1 13.9 - - + -
295E SER* 3.3 8.4 + - - +
296E PHE* 1.3 77.2 - - - +
298E PRO* 1.3 67.3 - - + +
299E ALA 3.0 1.2 + - - -
300E PHE* 3.0 16.3 + - - +
301E GLU 3.6 2.1 + - - -
13F PRO* 3.5 36.6 - - + -
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Residues in contact with PRO 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E TYR* 3.7 8.7 - - - +
295E SER 3.9 10.3 - - - +
296E PHE* 3.5 3.6 - - - -
297E ALA* 1.3 94.5 - - + +
299E ALA* 1.3 61.1 + - - +
300E PHE 3.1 1.1 + - - -
301E GLU* 3.2 16.4 + - + +
302E THR* 4.8 0.9 + - - +
321E TYR* 3.6 21.6 - - + +
11F THR* 3.2 24.0 - - - +
13F PRO* 5.4 0.9 - - + -
279F THR* 3.4 28.5 - - + +
282F ASP* 3.8 16.8 - - - +
311F THR* 4.9 4.7 + - - +
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Residues in contact with ALA 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296E PHE* 3.0 19.3 + - + +
297E ALA 3.0 1.2 + - - -
298E PRO* 1.3 79.5 - - - +
300E PHE* 1.3 74.1 + - + +
301E GLU 3.7 0.5 + - - -
302E THR* 4.3 10.4 + - - +
317E GLU* 4.6 15.3 - - - +
318E LEU* 5.0 1.6 - - - -
321E TYR* 3.5 41.4 - - + -
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Residues in contact with PHE 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ILE* 4.0 17.7 - - + -
30E TYR* 4.0 1.5 - - - -
35E ARG* 3.2 20.1 + - - -
192E PHE* 4.2 12.8 - + + -
194E VAL* 3.6 39.5 - - + +
232E TYR* 3.6 40.6 - + + -
296E PHE 3.9 15.5 - - - -
297E ALA* 3.0 10.1 + - - +
299E ALA* 1.3 82.0 - - + +
301E GLU* 1.3 63.2 + - - +
302E THR 3.2 12.0 + - - +
304E LEU* 5.6 2.5 - - + -
314E ALA* 3.9 26.2 - - + -
317E GLU* 4.3 11.7 - - + -
318E LEU* 4.3 14.4 - - + -
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Residues in contact with GLU 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E TYR* 3.6 29.6 - - + +
31E GLY* 3.2 32.9 - - - +
35E ARG* 4.1 2.8 + - - -
297E ALA 3.6 1.6 + - - -
298E PRO* 3.2 17.3 + - + +
300E PHE* 1.3 78.9 - - - +
302E THR* 1.3 68.2 + - - +
303E ALA 3.3 3.1 + - - -
11F THR* 4.8 2.0 - - + -
230F THR* 4.2 11.3 - - + +
309F GLY* 3.4 2.8 - - - -
310F TYR* 2.4 36.9 + - - +
311F THR* 3.2 37.8 + - + +
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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