Contacts of the helix formed by residues 403 - 408 (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 GLY 403 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172O CYS* 4.0 0.4 - - - -
173O THR* 3.2 33.3 - - - +
175O LYS* 4.5 2.0 - - - -
402O PHE* 1.3 70.0 - - - +
404O GLY* 1.3 60.3 + - - +
405O GLY 3.1 1.2 - - - +
406O THR 2.9 2.9 + - - -
407O LEU* 2.9 32.6 + - - +
1476O CAP 2.9 22.5 + - - -
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Residues in contact with GLY 404 (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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175O LYS* 4.4 0.6 - - - +
403O GLY* 1.3 70.1 - - - +
405O GLY* 1.3 56.7 + - - +
406O THR 3.0 0.2 + - - -
408O GLY* 2.8 31.7 + - - -
462O TRP* 3.6 1.0 - - - -
1476O CAP 2.7 19.6 + - - -
65V THR* 4.0 13.0 - - - +
66V TRP* 3.9 4.5 - - - +
67V THR* 3.4 24.0 - - - +
69V VAL* 4.2 8.1 - - - -
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Residues in contact with GLY 405 (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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382O ILE 4.0 10.7 + - - -
383O HIS* 4.9 2.2 - - - -
402O PHE* 4.0 7.6 - - - -
403O GLY 3.1 4.4 - - - +
404O GLY* 1.3 73.6 - - - +
406O THR* 1.3 57.9 + - - +
409O HIS* 5.6 0.2 - - - -
416O GLY* 4.4 4.0 - - - +
420O ASN* 3.2 19.7 + - - +
462O TRP* 3.5 28.2 - - - -
66V TRP* 3.8 20.1 - - - +
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Residues in contact with THR 406 (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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172O CYS* 3.8 4.0 - - - -
192O CYS* 3.9 21.5 - - - -
197O LEU* 3.9 15.8 - - + +
402O PHE* 2.7 24.7 + - - +
403O GLY 2.9 3.1 + - - -
405O GLY* 1.3 76.8 - - - +
407O LEU* 1.3 58.8 + - - +
408O GLY 3.1 4.3 - - - -
409O HIS* 3.2 24.1 + - - +
412O GLY 3.8 7.4 - - - +
413O ASN* 3.5 23.8 - - - +
416O GLY* 3.9 2.9 - - - -
417O ALA 3.7 9.2 - - - +
420O ASN* 3.1 17.4 + - - -
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Residues in contact with LEU 407 (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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172O CYS* 3.5 25.6 - - - -
173O THR 3.5 13.2 - - - +
174O ILE* 4.1 5.8 - - + -
175O LYS* 3.6 28.3 - - + +
188O ALA* 4.3 8.7 - - + -
192O CYS* 4.1 4.0 - - - -
403O GLY 2.9 25.6 + - - +
406O THR* 1.3 75.7 - - - +
408O GLY* 1.3 56.7 + - - +
409O HIS 3.5 0.7 - - - -
413O ASN* 3.3 35.0 - - - +
13V PHE* 4.4 0.2 - - - -
69V VAL* 3.4 17.2 - - + -
70V TRP* 3.2 34.9 + - - +
71V THR* 3.8 15.3 - - + +
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Residues in contact with GLY 408 (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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404O GLY 2.8 20.4 + - - -
407O LEU* 1.3 78.6 - - - +
409O HIS* 1.3 63.9 + - - +
410O PRO* 3.9 0.3 - - - +
461O VAL* 4.8 0.2 - - - +
462O TRP* 3.5 18.1 - - - -
13V PHE* 3.9 2.8 - - - -
15V ALA* 3.4 20.4 - - - +
16V GLY 4.5 1.0 + - - -
67V THR* 4.4 1.3 - - - -
68V THR 3.3 21.5 - - - +
69V VAL* 4.2 0.4 - - - +
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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