Contacts of the strand formed by residues 405 - 412 (chain A) in PDB entry 3Q0F
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 LEU 405 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397A TYR* 3.9 23.1 - - + -
398A MET 3.3 3.4 - - - +
399A LYS* 4.1 28.7 - - + -
404A GLU* 1.3 77.4 - - - +
406A VAL* 1.3 61.5 + - - +
451A THR* 3.6 35.4 - - - +
454A LEU* 3.8 22.2 - - + -
455A ALA* 3.8 15.3 - - + -
458A ASN* 2.9 33.5 + - - +
10C G 4.8 4.7 - - - +
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Residues in contact with VAL 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ILE* 4.2 17.0 - - + -
397A TYR* 3.6 3.8 - - - -
398A MET* 2.9 52.8 + - + +
400A ASP* 4.2 26.9 - - + +
404A GLU* 3.7 2.2 + - + +
405A LEU* 1.3 80.8 - - - +
407A ALA* 1.3 67.2 + - - +
408A THR* 4.0 0.5 - - - +
455A ALA* 3.7 5.4 - - - -
458A ASN* 4.5 6.7 - - + -
459A SER* 3.9 8.5 - - - +
462A LYS* 4.4 25.6 - - + -
464A ASN* 4.2 4.9 - - - +
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Residues in contact with ALA 407 (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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395A ILE* 4.6 5.6 - - + -
396A ASP 3.4 9.2 - - - +
397A TYR* 3.8 4.0 - - - -
406A VAL* 1.3 75.3 - - - +
408A THR* 1.3 62.1 + - - +
409A SER 4.7 2.5 - - - +
455A ALA* 3.4 6.8 + - + +
456A LEU* 3.7 40.4 - - + +
459A SER* 3.2 13.3 + - - +
464A ASN* 3.0 25.8 + - - -
466A VAL* 4.1 8.5 - - + +
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Residues in contact with THR 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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362A GLN* 3.7 12.9 + - - +
363A ILE 3.9 6.1 - - - +
364A ILE* 3.9 26.9 - - + +
365A GLY 5.2 1.0 + - - -
396A ASP* 2.6 28.9 + - - -
397A TYR* 3.6 2.5 + - - -
398A MET* 3.9 24.5 - - + -
406A VAL 4.0 1.8 - - - +
407A ALA* 1.3 79.5 - - - +
409A SER* 1.3 64.4 + - - +
464A ASN* 4.9 0.2 - - - +
465A PRO 4.5 5.0 - - - +
466A VAL* 3.9 4.4 - - - -
467A ARG* 3.1 45.0 + - - +
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Residues in contact with SER 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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387A ILE 3.1 25.0 + - - -
388A HIS* 3.1 22.8 - - - -
395A ILE* 4.3 0.5 - - - +
396A ASP* 2.9 42.2 + - - +
407A ALA* 3.8 1.1 - - - +
408A THR* 1.3 84.9 + - - +
410A ILE* 1.3 70.3 + - - +
466A VAL* 3.8 3.4 - - - +
467A ARG* 3.2 17.9 + - - -
469A ILE* 4.8 1.8 - - - -
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Residues in contact with ILE 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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388A HIS* 4.4 0.2 - - - -
394A GLY 3.1 9.2 - - - +
395A ILE* 4.5 6.1 - - + -
407A ALA* 5.3 0.4 - - + -
409A SER* 1.3 81.7 - - - +
411A VAL* 1.3 65.6 + - - +
412A SER 5.2 0.7 - - - +
426A LEU* 4.5 5.6 - - + -
428A TYR* 3.8 45.8 - - + -
456A LEU* 4.2 22.0 - - + -
466A VAL* 4.2 4.5 - - + -
467A ARG 2.9 6.0 + - - +
468A VAL* 3.6 23.1 - - + -
469A ILE* 3.0 30.1 + - - +
513A LEU* 3.7 30.3 - - + -
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Residues in contact with VAL 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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379A ARG* 4.0 22.9 - - - +
382A LEU* 4.4 5.2 - - + -
388A HIS* 3.5 33.7 - - + +
394A GLY* 2.9 12.3 + - - +
410A ILE* 1.3 77.2 - - - +
412A SER* 1.3 62.5 + - - +
413A SER* 3.7 20.7 + - - +
428A TYR* 2.9 20.8 + - - -
469A ILE* 3.4 19.1 - - + +
486A TYR* 4.1 22.7 - - + -
6B G 3.9 9.7 - - + -
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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
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410A ILE* 4.2 1.2 - - - +
411A VAL* 1.3 72.3 - - - +
413A SER* 1.3 55.2 + - - +
418A ASP* 2.5 26.8 + - - -
420A LEU* 3.4 21.4 - - - +
426A LEU* 4.3 16.1 - - - +
428A TYR* 4.1 9.0 - - - -
468A VAL* 5.5 1.1 - - - -
469A ILE 2.7 12.5 + - - -
470A ARG* 3.2 12.4 - - - +
471A GLY 2.8 27.8 + - - +
6B G 3.9 3.4 - - - -
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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