Contacts of the helix formed by residues 411 - 418 (chain A) in PDB entry 1U67
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 THR 411 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A TYR* 5.1 11.0 - - + -
283A SER* 3.4 47.1 - - - +
285A MET* 6.3 0.7 - - - -
296A PRO* 6.0 0.4 - - - +
409A PHE 3.4 6.4 + - - -
410A ASN* 1.3 86.3 + - - +
412A SER* 1.3 65.0 + - - +
413A MET* 2.9 7.0 + - - +
414A LEU* 3.4 15.4 + - - +
415A VAL* 4.4 5.0 + - - +
1D NAG 4.7 0.4 - - - +
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Residues in contact with SER 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A ASN* 3.4 2.8 + - - -
411A THR* 1.3 79.1 - - - +
413A MET* 1.3 51.6 + - - +
414A LEU 3.4 0.4 + - - -
415A VAL* 3.4 5.6 + - - +
416A ASP* 2.7 41.2 + - - +
1D NAG 4.5 15.2 - - - -
2D NDG 5.6 6.3 - - - -
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Residues in contact with MET 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A PRO* 3.9 12.8 - - + -
397A VAL* 4.7 9.2 - - - -
402A TYR* 3.2 42.2 - - + -
406A GLN 3.9 8.3 - - - +
407A PHE* 3.4 39.3 - - + -
410A ASN* 3.0 19.8 + - - +
411A THR 2.9 2.4 + - - +
412A SER* 1.3 76.4 - - - +
414A LEU* 1.3 60.8 + - - +
417A TYR* 3.1 45.9 + - + +
422A LEU* 4.5 7.5 - - + +
1D NAG 3.2 21.9 + - - +
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Residues in contact with LEU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A TYR* 4.0 20.6 + - + -
285A MET* 5.1 3.1 - - - -
296A PRO* 4.2 15.0 - - + +
299A MET* 3.2 35.9 - - + -
300A LEU* 3.5 44.6 - - + +
303A THR* 3.8 9.4 - - - +
411A THR 3.4 8.8 + - - +
413A MET* 1.3 78.4 - - - +
415A VAL* 1.3 61.4 + - + +
417A TYR* 4.8 0.2 - - - +
418A GLY* 3.1 24.7 + - - -
419A VAL* 4.7 8.7 - - + +
422A LEU* 4.9 9.5 - - + +
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Residues in contact with VAL 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A LEU* 3.8 25.4 - - + -
258A ASN* 3.0 34.8 + - - +
262A TYR* 3.7 33.2 + - + -
283A SER* 6.6 0.4 - - - -
285A MET* 4.6 14.1 - - + -
411A THR 5.2 4.5 - - - +
412A SER* 3.4 6.7 + - - +
414A LEU* 1.3 78.0 - - + +
416A ASP* 1.3 64.1 + - - +
418A GLY* 4.3 1.9 + - - -
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Residues in contact with ASP 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A SER* 2.7 23.0 + - - +
413A MET 3.7 0.7 - - - +
414A LEU 3.2 0.2 - - - -
415A VAL* 1.3 81.1 - - - +
417A TYR* 1.3 66.5 + - + +
418A GLY* 4.6 0.2 - - - -
1D NAG 3.5 20.0 - - - +
2D NDG 5.8 4.0 - - - +
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Residues in contact with TYR 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A VAL* 3.8 25.8 - - + -
400A GLN* 3.4 12.0 - - + +
402A TYR* 2.2 49.4 + + - -
413A MET* 3.1 37.9 + - + +
416A ASP* 1.3 81.6 - - + +
418A GLY* 1.3 63.7 + - - +
421A ALA* 3.7 21.3 - - + +
422A LEU* 3.9 26.9 - - + +
1D NAG 3.9 9.2 - - - -
2D NDG 5.3 0.8 + - - -
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Residues in contact with GLY 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A GLU* 5.9 3.4 - - - -
262A TYR* 3.9 12.3 - - - -
414A LEU 3.1 18.7 + - - -
415A VAL 5.0 0.9 - - - -
416A ASP 3.4 2.6 - - - -
417A TYR* 1.3 77.6 - - - +
419A VAL* 1.3 71.7 + - - +
420A GLU* 3.5 4.0 + - - -
421A ALA 3.7 1.0 + - - -
422A LEU* 2.9 19.7 + - - +
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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