Contacts of the strand formed by residues 407 - 419 (chain A) in PDB entry 6T3C
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 GLU 407 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368A ILE 3.5 10.8 - - - +
369A ASP* 4.2 10.7 - - + -
405A THR* 2.9 16.8 + - - -
406A GLU* 1.3 81.4 - - + +
408A VAL* 1.3 64.2 + - - +
409A LEU* 3.8 31.7 - - + +
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Residues in contact with VAL 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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367A GLY* 3.0 4.5 - - - -
368A ILE* 2.8 59.7 + - + +
381A VAL* 4.4 2.7 - - + -
402A LYS* 3.7 27.1 - - + -
403A PRO 3.7 6.7 - - - +
404A PHE* 4.4 4.5 - - + -
405A THR* 3.7 31.9 - - - +
407A GLU* 1.3 78.3 - - - +
409A LEU* 1.4 64.7 + - - +
410A TRP* 3.6 25.5 - - + -
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Residues in contact with LEU 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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366A ARG* 3.5 22.2 - - + +
367A GLY* 4.8 1.8 - - - -
402A LYS* 4.2 15.2 - - - +
407A GLU* 3.8 35.2 + - + +
408A VAL* 1.4 77.9 - - - +
410A TRP* 1.3 66.3 + - - +
411A ASN* 5.3 4.7 - - + +
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Residues in contact with TRP 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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365A ILE* 3.6 18.4 - - + +
366A ARG 2.8 9.1 + - - -
367A GLY* 4.1 7.9 - - - -
368A ILE* 3.8 16.8 - - + -
381A VAL* 3.6 27.6 - - + -
382A PHE* 4.1 0.7 - - - -
383A VAL* 3.6 30.1 - - + -
399A THR* 3.7 25.4 + - + -
400A SER* 2.8 40.8 + - - -
402A LYS* 3.4 23.2 - - + +
408A VAL* 3.6 37.9 - - + -
409A LEU* 1.3 74.3 - - - +
411A ASN* 1.4 68.2 + - - +
412A VAL* 3.2 27.4 - - + +
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Residues in contact with ASN 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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364A LYS* 3.4 30.9 - - - +
365A ILE 3.1 11.1 + - - -
366A ARG* 3.2 37.2 + - - +
409A LEU* 5.9 4.1 - - + +
410A TRP* 1.4 77.2 - - - +
412A VAL* 1.4 58.6 + - - +
413A TRP* 4.2 1.2 + - - -
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Residues in contact with VAL 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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364A LYS* 3.3 4.5 - - - -
365A ILE* 2.8 37.8 + - + +
399A THR* 5.0 9.9 - - + -
400A SER* 5.6 2.5 - - - +
410A TRP* 3.2 39.9 - - + +
411A ASN* 1.4 74.3 - - - +
413A TRP* 1.4 73.7 + - - +
414A LEU* 3.5 16.9 + - + +
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Residues in contact with TRP 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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362A ARG* 3.3 74.6 - - + +
363A VAL 3.7 3.6 - - - -
364A LYS* 3.5 58.2 - - + +
411A ASN 4.2 1.3 + - - -
412A VAL* 1.4 79.3 - - - +
414A LEU* 1.3 59.1 + - - +
415A GLU* 3.6 6.9 + - + +
519A LEU* 3.9 34.3 - - + -
521A ASP* 4.6 15.9 - - + -
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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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362A ARG* 3.3 4.1 - - - -
363A VAL* 2.8 42.1 + - + +
365A ILE* 3.7 27.4 - - + -
383A VAL* 5.1 1.1 - - + +
385A ALA* 3.9 24.7 - - + +
397A ARG* 4.2 26.0 - - + +
398A ARG* 3.4 23.1 - - - +
399A THR* 4.0 17.3 - - + -
412A VAL* 4.2 15.0 - - + +
413A TRP* 1.3 69.3 - - - +
415A GLU* 1.3 62.9 + - - +
416A PHE* 3.6 6.8 + - + -
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Residues in contact with GLU 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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360A LYS* 3.9 28.9 + - + +
361A PHE 4.3 4.5 - - - +
362A ARG* 3.9 18.4 - - + -
397A ARG* 3.1 28.2 + - - +
413A TRP* 3.6 7.2 + - + +
414A LEU* 1.3 72.0 - - - +
416A PHE* 1.3 67.2 + - - +
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Residues in contact with PHE 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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360A LYS* 3.6 24.8 - - - +
361A PHE* 2.8 40.2 + + + +
363A VAL* 3.6 26.7 - - + -
385A ALA* 3.6 31.9 - - + -
387A ILE* 3.7 23.8 - - + -
395A CYS* 3.6 24.9 - - + -
397A ARG* 3.6 34.1 - - + -
414A LEU* 3.6 11.4 - - + -
415A GLU* 1.3 76.3 - - - +
417A SER* 1.3 61.0 + - - +
418A ILE* 3.3 14.3 - - + +
429A LEU* 4.3 0.7 - - + -
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Residues in contact with SER 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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360A LYS* 4.2 20.1 - - - +
394A LEU 4.9 2.9 + - - -
395A CYS* 3.1 28.1 - - - +
397A ARG* 4.1 14.2 - - - +
416A PHE* 1.3 70.9 - - - +
418A ILE* 1.3 64.6 + - - +
419A LYS* 3.6 4.7 + - - +
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Residues in contact with ILE 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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360A LYS* 3.8 1.1 - - - -
361A PHE* 2.9 26.0 + - + +
387A ILE* 4.2 14.8 - - + -
394A LEU* 4.1 23.1 - - + +
395A CYS* 3.8 24.2 - - + -
416A PHE* 3.8 12.2 - - + +
417A SER* 1.3 83.0 + - - +
419A LYS* 1.3 71.0 + - - +
422A ASP* 3.8 23.1 - - + +
423A LEU* 4.3 13.7 - - + -
599A GLY* 3.7 28.5 - - - +
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Residues in contact with LYS 419 (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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358A ASP* 3.7 33.7 + - - +
359A ARG 3.4 8.7 - - - +
360A LYS* 3.9 18.6 - - + +
361A PHE* 4.2 1.1 - - - -
417A SER 4.6 3.6 - - - +
418A ILE* 1.3 89.4 - - - +
420A ILE* 1.4 66.4 + - - +
421A LYS* 3.3 23.8 - - + +
422A ASP* 3.3 31.6 + - - +
423A LEU* 3.5 5.2 + - - +
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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