Contacts of the helix formed by residues 403 - 408 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172K CYS* 3.9 0.7 - - - -
173K THR* 3.3 34.6 - - - +
175K LYS* 4.5 2.0 - - - -
401K GLN 4.0 0.6 - - - -
402K PHE* 1.3 69.7 - - - +
404K GLY* 1.3 60.9 + - - +
405K GLY 3.1 0.8 - - - +
406K THR 2.9 3.1 + - - -
407K LEU* 2.9 32.8 + - - +
1478R CAP 2.8 21.5 + - - -
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Residues in contact with GLY 404 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E THR* 3.9 13.5 - - - +
66E TRP* 3.9 3.8 - - - -
67E THR* 3.3 24.1 - - - +
69E VAL* 4.2 7.6 - - - -
175K LYS* 4.4 0.6 - - - +
403K GLY* 1.3 71.5 - - - +
405K GLY* 1.3 55.6 + - - +
408K GLY* 2.8 31.9 + - - -
462K TRP* 3.6 0.9 - - - -
1478R CAP 2.7 21.1 + - - -
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Residues in contact with GLY 405 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E TRP* 3.8 18.7 - - - +
382K ILE 4.0 10.7 + - - -
383K HIS* 4.9 2.0 - - - -
402K PHE* 4.0 6.7 - - - -
403K GLY 3.1 4.9 - - - +
404K GLY* 1.3 73.7 - - - +
406K THR* 1.3 58.1 + - - +
416K GLY* 4.4 4.0 - - - +
420K ASN* 3.1 20.4 + - - +
462K TRP* 3.6 28.8 - - - -
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Residues in contact with THR 406 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172K CYS* 3.7 5.8 - - - -
192K CYS* 3.9 14.8 - - - -
197K LEU* 3.9 21.8 - - + +
402K PHE* 2.7 25.1 + - - +
403K GLY 2.9 2.5 + - - -
404K GLY 3.0 0.2 - - - -
405K GLY* 1.3 76.5 - - - +
407K LEU* 1.3 59.8 + - - +
408K GLY 3.1 3.8 - - - -
409K HIS* 3.2 24.2 + - - +
412K GLY 3.8 7.8 - - - +
413K ASN* 3.5 22.9 - - - +
416K GLY* 3.9 3.1 - - - -
417K ALA 3.7 9.4 - - - +
420K ASN* 3.1 16.3 + - - -
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Residues in contact with LEU 407 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E PHE* 4.4 0.2 - - - -
69E VAL* 3.4 17.6 - - + -
70E TRP* 3.1 34.5 + - - +
71E THR* 3.8 15.5 - - + +
172K CYS* 3.5 24.5 - - - -
173K THR 3.6 13.2 - - - +
174K ILE* 4.1 5.4 - - + -
175K LYS* 3.6 28.0 - - + +
188K ALA* 4.3 8.5 - - + -
192K CYS* 4.1 5.4 - - - -
403K GLY 2.9 24.1 + - - +
406K THR* 1.3 76.3 - - - +
408K GLY* 1.3 56.8 + - - +
409K HIS 3.5 0.9 - - - -
413K ASN* 3.4 35.0 - - - +
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Residues in contact with GLY 408 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E PHE* 3.9 2.1 - - - -
15E ALA* 3.5 19.8 - - - +
16E GLY 4.5 0.9 + - - -
67E THR* 4.4 1.3 - - - -
68E THR 3.2 22.9 - - - +
69E VAL* 4.1 0.2 - - - +
404K GLY 2.8 19.6 + - - -
407K LEU* 1.3 78.4 - - - +
409K HIS* 1.3 64.9 + - - +
410K PRO* 4.0 0.3 - - - +
461K VAL* 4.8 0.2 - - - +
462K TRP* 3.5 17.8 - - - -
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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