Contacts of the helix formed by residues 297 - 303 (chain E) in PDB entry 1UW9
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 MET 297 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270E LEU* 4.0 15.0 - - + +
271E THR* 3.9 22.2 - - + -
296E ALA* 1.3 73.1 - - - +
298E HIS* 1.3 64.5 + - - +
299E ALA 3.2 2.9 - - - -
300E VAL* 3.0 32.1 + - + +
301E ILE* 3.8 10.1 + - + +
1482E EDO 4.1 22.4 - - - -
117K PHE* 4.4 17.9 - - + -
121K VAL* 3.4 25.6 - - + +
122K GLY 2.7 15.2 + - - -
274K PHE* 6.1 0.4 - - - -
301K ILE* 4.4 18.8 - - + -
309K ILE* 4.1 26.2 - - + -
314K LEU* 5.9 0.7 - - + -
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Residues in contact with HIS 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E LEU* 3.7 17.9 - - + +
295E ARG* 2.9 77.7 + - + +
296E ALA* 3.3 1.2 + - - -
297E MET* 1.3 77.1 - - - +
299E ALA* 1.3 71.2 + - + +
301E ILE* 2.9 10.8 + - - +
302E ASP* 2.5 64.3 + - - +
311E PHE* 3.9 6.5 - + + -
314E LEU* 4.1 9.6 - - + +
335E LEU* 5.9 3.2 - - - +
336E GLU 5.7 3.1 - - - -
1477E CAP 4.0 7.6 + - - -
122K GLY 5.0 4.3 - - - -
123K ASN* 5.9 1.1 - - - -
126K GLY* 5.7 3.0 - - - -
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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
----------------------------------------------------------
297E MET* 3.2 1.2 - - - +
298E HIS* 1.3 87.7 - - + +
300E VAL* 1.3 62.4 + - - +
301E ILE 3.1 1.7 + - - -
302E ASP* 3.2 14.4 - - - +
303E ARG* 3.3 14.2 + - + +
122K GLY 5.5 1.8 + - - +
123K ASN 5.1 2.5 - - - +
125K PHE* 3.4 10.8 - - + +
126K GLY* 3.3 37.2 - - - +
307K HIS* 2.8 20.6 + - - -
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Residues in contact with VAL 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297E MET* 3.0 23.3 + - + +
299E ALA* 1.3 76.8 - - - +
301E ILE* 1.3 58.7 + - + +
121K VAL* 3.8 23.8 - - + +
125K PHE* 3.7 30.5 - - + +
300K VAL 4.9 4.7 - - - +
301K ILE* 3.9 20.6 - - + -
307K HIS* 3.5 22.7 - - - -
308K GLY* 3.9 11.4 - - - -
309K ILE* 3.7 29.4 - - + -
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Residues in contact with ILE 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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270E LEU* 4.8 10.1 - - + -
297E MET* 4.2 25.4 - - + +
298E HIS 2.9 6.4 + - - +
300E VAL* 1.3 83.3 - - + +
302E ASP* 1.3 58.3 + - - +
303E ARG 3.7 1.5 + - - -
304E GLN 5.2 0.6 + - - +
307E HIS 3.9 4.7 - - - +
308E GLY* 3.3 10.7 - - - -
309E ILE* 3.1 47.8 + - + +
314E LEU* 4.1 17.0 - - + -
1482E EDO 5.0 7.0 - - - -
297K MET* 4.3 16.4 - - + -
300K VAL* 3.8 17.0 - - + -
301K ILE* 4.0 24.5 - - + -
307K HIS* 5.8 0.4 - - - -
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Residues in contact with ASP 302 (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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134E ARG* 3.0 23.3 + - - -
298E HIS* 2.5 44.1 + - - +
299E ALA* 3.2 15.6 - - - +
301E ILE* 1.3 78.1 - - - +
303E ARG* 1.3 62.5 + - - +
304E GLN 3.6 2.0 - - - -
309E ILE 3.0 22.2 - - - +
310E HIS* 4.8 0.2 - - - -
311E PHE* 3.3 34.6 + - - +
314E LEU* 4.0 4.2 - - + +
473E ASP* 4.1 7.3 - - - +
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Residues in contact with ARG 303 (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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299E ALA* 3.3 21.2 + - - +
301E ILE 3.7 1.0 - - - -
302E ASP* 1.3 82.6 + - - +
304E GLN* 1.3 76.6 + - - +
336E GLU* 3.0 44.7 + - - +
472E ILE* 3.6 21.7 - - + +
473E ASP* 3.5 21.5 + - - +
45K GLN* 4.5 0.6 - - - +
125K PHE 2.9 25.0 + - - +
126K GLY* 3.4 15.6 - - - -
127K PHE 2.9 25.7 + - - -
128K LYS* 3.9 6.1 + - - +
130K LEU* 2.8 32.3 + - - +
131K ARG 4.7 2.0 - - - +
307K HIS* 3.5 11.8 + - + +
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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