Contacts of the helix formed by residues 297 - 303 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270O LEU* 3.9 14.4 - - + +
271O THR* 3.9 21.1 - - + -
296O ALA* 1.3 74.5 - - - +
298O HIS* 1.3 65.3 + - - +
299O ALA 3.2 3.4 - - - -
300O VAL* 3.0 29.7 + - + +
301O ILE* 3.8 10.1 + - + +
1484O EDO 4.2 20.4 - - - -
117V PHE* 4.4 17.9 - - + -
121V VAL* 3.4 26.2 - - + +
122V GLY* 2.7 15.0 + - - -
270V LEU* 6.5 0.2 - - + -
274V PHE* 6.1 0.9 - - - -
301V ILE* 4.2 23.1 - - + -
309V ILE* 4.1 26.2 - - + -
314V LEU* 5.8 0.4 - - + -
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Residues in contact with HIS 298 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270O LEU* 3.7 18.6 - - + +
295O ARG* 2.9 76.0 + - + +
296O ALA 3.3 1.2 + - - -
297O MET* 1.3 77.4 - - - +
299O ALA* 1.3 69.0 + - + +
301O ILE* 2.9 12.0 + - - +
302O ASP* 2.4 61.6 + - - +
311O PHE* 3.9 6.3 - - + -
314O LEU* 4.1 9.4 - - + -
335O LEU* 6.0 2.4 - - - +
336O GLU 5.7 0.7 - - - -
1476O CAP 4.0 7.5 + - - -
1483O EDO 3.6 11.0 - - - -
122V GLY 5.1 4.5 - - - -
123V ASN* 6.0 1.3 - - - -
126V GLY* 5.7 3.2 - - - -
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Residues in contact with ALA 299 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297O MET 3.1 1.4 + - - -
298O HIS* 1.3 87.3 - - + +
300O VAL* 1.3 62.1 - - - +
301O ILE 3.1 2.1 + - - -
302O ASP* 3.3 15.0 - - - +
303O ARG* 3.3 13.3 + - + +
122V GLY 5.4 2.2 + - - +
123V ASN* 5.1 2.5 - - - +
125V PHE* 3.4 9.0 - - + +
126V GLY* 3.3 37.5 - - - +
307V HIS* 2.8 21.5 + - - -
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Residues in contact with VAL 300 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297O MET* 3.0 23.5 + - + +
299O ALA* 1.3 76.8 - - - +
301O ILE* 1.3 58.2 + - + +
121V VAL* 3.8 23.6 - - + +
125V PHE* 3.8 31.7 - - + +
300V VAL 4.9 3.8 - - - +
301V ILE* 3.8 21.8 - - + +
307V HIS* 3.6 21.8 - - - -
308V GLY* 4.0 11.0 - - - -
309V ILE* 3.8 28.5 - - + -
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Residues in contact with ILE 301 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270O LEU* 4.8 8.5 - - + -
297O MET* 4.2 26.2 - - + +
298O HIS 2.9 7.0 + - - +
300O VAL* 1.3 81.6 - - + +
302O ASP* 1.3 60.7 + - - +
303O ARG 3.7 1.1 - - - -
304O GLN 5.1 0.3 + - - +
307O HIS 3.8 5.2 - - - +
308O GLY* 3.3 10.0 - - - -
309O ILE* 3.2 54.8 + - + +
314O LEU* 4.1 17.5 - - + -
1484O EDO 4.8 8.5 - - - -
297V MET* 4.2 16.2 - - + -
300V VAL* 3.8 16.6 - - + +
301V ILE* 3.9 23.6 - - + -
307V HIS* 5.7 0.7 - - - -
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Residues in contact with ASP 302 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134O ARG* 3.0 22.6 + - - +
298O HIS* 2.4 44.4 + - - +
299O ALA* 3.3 14.9 - - - +
301O ILE* 1.3 77.0 - - - +
303O ARG* 1.3 63.4 + - - +
304O GLN 3.6 2.0 - - - -
309O ILE 3.0 22.2 - - - +
310O HIS* 4.8 0.3 - - - -
311O PHE* 3.2 35.0 + - - +
314O LEU* 4.2 3.6 - - + -
473O ASP* 4.1 7.8 - - - +
1483O EDO 4.3 7.7 + - - -
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Residues in contact with ARG 303 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299O ALA* 3.3 21.1 + - - +
301O ILE 3.7 0.8 - - - -
302O ASP* 1.3 81.8 + - - +
304O GLN* 1.3 75.0 + - - +
336O GLU* 2.9 43.7 + - - +
472O ILE* 3.6 21.4 - - + +
473O ASP* 3.5 22.2 + - - +
1483O EDO 6.0 0.7 - - - -
45V GLN* 4.5 0.6 - - - +
125V PHE 2.9 24.8 + - - +
126V GLY* 3.4 16.1 - - - -
127V PHE 2.9 26.3 + - - -
128V LYS* 4.0 7.1 + - - +
130V LEU* 2.8 31.7 + - - +
131V ARG 4.7 1.5 - - - +
307V HIS* 3.5 12.1 + - + +
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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