Contacts of the strand formed by residues 407 - 412 (chain A) in PDB entry 1A16
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 ASP 407 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A ASP 4.8 0.2 - - - -
274A ARG* 2.8 30.5 + - - -
297A LEU* 3.9 13.2 - - + +
301A LEU* 4.0 6.1 - - + +
381A THR* 3.2 4.7 - - - -
382A VAL* 2.8 34.0 + - + +
405A ILE 4.4 0.2 - - - -
406A GLU* 1.4 72.0 - - - +
408A ASP* 1.3 67.7 + - - +
409A ILE* 4.2 1.1 + - - -
418A ASN* 3.2 24.4 + - - +
420A THR* 2.7 22.0 + - - +
425A LYS* 2.8 31.6 + - - -
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Residues in contact with ASP 408 (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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188A GLY* 4.8 1.8 - - - -
270A GLY* 3.4 6.6 - - - -
271A ASP 2.6 45.7 + - - +
356A LEU* 3.5 26.0 - - + +
380A LEU 3.6 4.5 - - - -
381A THR* 3.5 12.5 - - - +
407A ASP* 1.3 77.8 - - - +
409A ILE* 1.3 62.7 + - - +
418A ASN* 3.6 3.5 - - - +
419A LEU* 2.8 36.8 + - + +
420A THR* 3.1 24.6 + - + +
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Residues in contact with ILE 409 (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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301A LEU* 3.5 28.7 - - + -
304A TYR* 3.7 35.0 - - + -
379A VAL* 3.3 9.9 - - - +
380A LEU* 2.7 56.1 + - + +
382A VAL* 3.7 20.4 - - + -
407A ASP* 4.9 0.7 - - + -
408A ASP* 1.3 80.2 - - - +
410A VAL* 1.3 61.5 + - - +
411A ILE* 4.4 3.6 - - + -
416A ASN* 3.8 20.9 - - + +
417A GLU 3.3 9.0 - - - +
418A ASN* 4.0 10.3 - - - -
419A LEU* 4.4 2.5 - - - +
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Residues in contact with VAL 410 (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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181A ILE* 3.9 36.3 - - + -
377A GLY 4.6 2.5 - - - -
378A MET 3.5 11.0 - - - +
379A VAL* 4.0 12.6 - - + -
409A ILE* 1.3 75.1 - - - +
411A ILE* 1.3 73.9 + - - +
412A THR* 3.8 5.8 - - + +
416A ASN* 3.0 6.2 - - - -
417A GLU* 2.8 66.8 + - + +
419A LEU* 4.2 12.1 - - + -
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Residues in contact with ILE 411 (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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304A TYR* 4.2 6.5 - - + -
305A ARG 4.0 20.2 - - - +
306A PRO* 3.7 33.0 - - + -
374A LEU* 4.1 18.4 - - + -
375A GLU* 3.5 28.5 - - - +
376A PRO* 3.4 0.6 - - - +
377A GLY 3.0 23.2 + - - -
378A MET* 2.9 15.5 + - + +
380A LEU* 3.7 27.6 - - + -
409A ILE* 4.4 0.9 - - + -
410A VAL* 1.3 76.6 - - - +
412A THR* 1.3 61.8 + - - +
415A GLY 3.6 7.6 - - - +
416A ASN* 4.2 9.2 - - + -
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Residues in contact with THR 412 (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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306A PRO* 2.9 27.7 - - - +
376A PRO* 3.9 7.9 - - - -
410A VAL* 3.5 16.8 + - + +
411A ILE* 1.3 76.7 - - - +
413A GLU* 1.3 61.3 + - - +
414A THR* 3.3 3.4 + - - -
415A GLY 2.9 26.3 + - - +
416A ASN* 3.4 3.7 + - - -
417A GLU* 4.0 20.6 - - + +
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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