Contacts of the strand formed by residues 400 - 409 (chain A) in PDB entry 3F2B
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 VAL 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A ILE* 3.5 31.9 - - + -
375A ILE* 3.2 10.3 - - + +
377A VAL* 4.0 19.5 - - + -
389A ALA* 4.2 4.0 - - + +
393A ALA* 3.6 23.4 - - + +
398A MET* 3.6 3.6 + - + +
399A LYS* 1.3 81.8 - - - +
401A ILE* 1.3 71.7 + - - +
402A TYR* 3.5 48.8 - - + +
811A ILE* 5.0 3.8 - - - +
812A GLY 5.4 1.6 - - - +
814A VAL* 5.6 2.6 + - - +
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Residues in contact with ILE 401 (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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343A VAL* 4.4 4.0 - - + -
345A LEU* 4.3 18.6 - - + -
374A ALA* 4.3 13.7 - - + -
375A ILE 2.8 13.9 + - - +
376A ALA* 3.1 10.4 - - + +
377A VAL 2.8 30.8 + - - -
399A LYS* 5.0 2.7 - - - -
400A VAL* 1.3 77.2 - - - +
402A TYR* 1.3 59.2 + - - +
403A GLY 3.4 0.5 + - - -
624A LEU* 3.9 26.0 - - + -
625A ALA 4.4 2.2 - - - +
808A ALA* 4.0 25.4 - - + +
811A ILE* 3.9 49.6 - - + -
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Residues in contact with TYR 402 (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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377A VAL* 4.9 0.9 - - + +
386A PHE* 3.4 57.0 - + + -
389A ALA* 4.0 5.2 - - + -
390A TYR* 3.3 32.9 + - - -
393A ALA* 4.3 3.5 - - - +
400A VAL* 3.5 40.8 - - + +
401A ILE* 1.3 70.8 - - - +
403A GLY* 1.3 57.9 + - - +
625A ALA* 2.9 37.9 + - + +
631A LEU* 4.7 2.9 - - + -
634A LEU* 3.7 1.3 - - - +
811A ILE* 5.6 0.2 - - - +
814A VAL* 3.4 47.0 + - + +
816A PRO* 3.7 18.4 - - + -
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Residues in contact with GLY 403 (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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377A VAL 2.7 25.9 + - - +
378A THR* 3.9 6.4 - - - -
379A ASP 4.6 0.3 + - - -
382A VAL 4.5 1.9 - - - +
383A VAL* 3.5 5.2 - - - +
386A PHE* 3.2 19.6 - - - -
401A ILE 3.4 1.4 + - - -
402A TYR* 1.3 74.4 - - - +
404A LEU* 1.3 63.6 + - - +
623A LEU 2.8 15.7 - - - -
624A LEU* 4.3 2.2 - - - -
634A LEU* 3.9 5.4 - - - -
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Residues in contact with LEU 404 (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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378A THR* 3.8 9.3 - - - +
379A ASP 3.7 5.6 - - - +
381A ALA* 3.6 41.3 - - - +
382A VAL* 3.6 9.4 - - - +
383A VAL* 4.2 11.0 - - + -
403A GLY* 1.3 76.3 - - - +
405A GLU* 1.3 62.8 + - - +
406A ALA* 3.7 10.7 + - + +
621A VAL 3.6 0.5 - - - +
622A THR* 3.6 1.2 - - - +
623A LEU* 2.7 58.9 + - + +
634A LEU* 4.0 24.9 - - + +
637A LEU* 4.6 13.7 - - + -
638A VAL* 4.7 7.4 - - + +
652A ILE* 4.9 2.9 - - + -
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Residues in contact with GLU 405 (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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6A MG 2.2 31.5 - - - -
7A MG 2.5 16.7 - - - -
346A HIS* 3.1 13.6 + - + +
348A HIS* 2.7 27.1 + - - -
378A THR* 3.7 14.3 + - - +
379A ASP 2.9 16.5 + - - +
380A HIS* 3.6 16.9 + - - +
381A ALA 2.8 28.9 + - - -
404A LEU* 1.3 71.8 - - - +
406A ALA* 1.3 60.2 + - - +
620A HIS* 3.7 19.8 + - + +
621A VAL 3.2 12.3 - - - +
622A THR* 4.6 2.7 - - - +
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Residues in contact with ALA 406 (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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380A HIS* 5.4 0.2 - - - -
381A ALA* 4.9 2.7 - - - +
404A LEU* 3.7 9.8 + - + -
405A GLU* 1.3 75.0 - - - +
407A ASN* 1.3 65.2 + - - +
408A ILE* 3.7 9.3 + - + -
619A PHE 3.4 1.0 - - - +
620A HIS* 3.2 9.2 - - - +
621A VAL* 2.9 32.3 + - + -
623A LEU* 4.0 20.9 - - + -
652A ILE* 3.8 26.2 - - + -
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Residues in contact with ASN 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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380A HIS* 3.2 35.9 + - - -
381A ALA* 4.4 8.9 - - - +
406A ALA* 1.3 73.0 - - - +
408A ILE* 1.3 56.4 + - - +
409A VAL* 5.8 0.9 - - + -
618A PRO* 5.9 4.6 - - + -
619A PHE 3.6 5.8 - - - +
620A HIS* 3.6 19.1 + - - -
649A VAL* 3.5 18.5 - - + +
650A PRO* 2.9 27.6 + - - +
651A ARG* 3.3 7.9 - - + +
652A ILE* 2.5 36.9 + - - +
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Residues in contact with ILE 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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406A ALA* 4.2 9.0 - - + +
407A ASN* 1.3 77.7 - - - +
409A VAL* 1.3 64.1 + - - +
618A PRO* 3.5 1.9 - - - +
619A PHE* 2.8 64.4 + - + +
621A VAL* 3.5 38.8 - - + -
652A ILE* 3.1 25.8 - - + +
654A ARG* 3.7 26.5 - - + +
657A LEU* 4.0 22.4 - - + -
693A PHE* 6.1 0.7 - - + -
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Residues in contact with VAL 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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407A ASN* 5.1 0.7 - - + -
408A ILE* 1.3 82.4 - - - +
410A ASP* 1.3 63.9 + - - +
411A ASP* 5.6 0.9 - - + -
618A PRO* 4.3 25.6 - - + -
619A PHE* 4.7 1.3 - - - -
651A ARG* 3.7 54.1 - - + +
652A ILE 3.1 6.2 + - - -
653A PRO* 3.1 23.6 - - + +
654A ARG 2.8 26.8 + - - -
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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