Contacts of the helix formed by residues 296 - 301 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I HIS* 3.6 30.3 - + - -
232I TYR* 3.3 22.7 + - + +
285I HIS* 4.4 10.1 - + - -
289I ARG* 4.0 22.9 - - - -
294I ILE* 3.9 10.8 - - + -
295I SER* 1.3 78.6 - - - +
297I ALA* 1.3 63.6 + - - +
298I PRO* 3.3 2.9 - - - -
299I ALA* 3.1 20.7 + - + +
300I PHE* 3.7 6.8 - - - -
318I LEU* 4.0 26.9 - - + -
321I TYR* 3.9 16.2 - + + -
322I ALA* 4.0 29.2 - - + -
325I LEU* 3.6 28.9 - - + -
335I ARG* 5.7 0.4 - - - -
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Residues in contact with ALA 297 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E PRO* 3.5 37.5 - - + -
30I TYR* 3.3 11.2 + - - -
192I PHE* 4.1 19.9 - - + -
232I TYR* 4.0 12.7 - - + -
295I SER* 3.3 7.2 + - - +
296I PHE* 1.3 77.4 - - - +
298I PRO* 1.3 67.4 - - + +
300I PHE* 3.0 18.4 + - - +
301I GLU 3.6 1.6 + - - -
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Residues in contact with PRO 298 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E THR* 3.3 24.0 - - + +
13E PRO* 5.5 0.9 - - + -
279E THR* 3.5 25.4 - - + +
282E ASP* 3.9 15.0 - - - +
311E THR* 5.6 2.1 - - - +
30I TYR* 4.0 7.6 - - - +
295I SER 3.9 10.3 - - - +
296I PHE 3.5 3.6 - - - -
297I ALA* 1.3 93.5 - - + +
299I ALA* 1.3 60.7 + - - +
301I GLU* 3.0 20.6 + - + +
302I THR* 5.9 0.5 - - - +
321I TYR* 3.2 26.8 - - + +
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Residues in contact with ALA 299 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296I PHE* 3.1 19.1 + - + +
297I ALA 3.0 1.0 + - - -
298I PRO* 1.3 80.2 - - - +
300I PHE* 1.3 74.8 + - + +
301I GLU 3.4 0.7 + - - -
302I THR* 4.3 10.0 + - - +
317I GLU* 4.4 15.2 - - - +
318I LEU* 4.9 2.0 - - - -
321I TYR* 3.4 42.5 - - + -
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Residues in contact with PHE 300 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I ILE* 5.2 2.7 - - + -
30I TYR* 4.3 0.9 - - - -
35I ARG* 2.8 41.2 + - - +
192I PHE* 4.3 7.9 - + + -
194I VAL* 3.4 40.7 - - + +
232I TYR* 3.6 40.2 - + + -
296I PHE 3.7 17.0 - - - -
297I ALA* 3.0 11.1 + - - +
299I ALA* 1.3 83.7 - - + +
301I GLU* 1.3 56.8 + - - +
302I THR 3.3 10.8 + - - +
304I LEU* 5.7 0.4 - - + -
314I ALA* 4.1 17.0 - - + -
317I GLU* 3.8 21.8 - - + -
318I LEU* 4.1 26.7 - - + -
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Residues in contact with GLU 301 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E THR* 3.8 22.0 - - + -
195E HIS* 5.2 1.0 - - - -
229E GLY* 5.6 1.8 - - - -
230E THR* 4.8 6.6 + - - +
282E ASP* 5.9 0.2 - - - +
309E GLY* 3.8 9.1 - - - -
310E TYR* 4.1 19.0 + - - +
311E THR* 4.2 32.3 - - + +
30I TYR* 2.8 38.9 + - - +
31I GLY* 3.4 27.7 + - - +
35I ARG* 3.3 12.0 + - - -
297I ALA 3.6 0.4 + - - -
298I PRO* 3.0 19.7 + - + +
299I ALA 3.4 0.2 - - - -
300I PHE* 1.3 78.1 - - - +
302I THR* 1.3 57.1 + - + +
303I ALA 3.3 1.4 + - - -
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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