Contacts of the helix formed by residues 433 - 448 (chain A) in PDB entry 6F3T
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 LYS 433 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431A GLU* 4.4 12.3 - - + +
432A LEU* 1.3 76.8 - - - +
434A ASP* 1.3 66.0 + - - +
435A SER* 3.1 16.4 - - - +
436A ASP* 3.0 45.1 + - - +
437A LYS* 3.2 13.4 + - - +
554A ASP* 2.9 29.6 + - - -
556A ASN* 4.8 4.5 - - - +
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Residues in contact with ASP 434 (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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432A LEU 4.8 0.3 - - - +
433A LYS* 1.3 74.2 - - - +
435A SER* 1.3 60.2 + - - +
437A LYS* 3.0 41.1 + - - +
438A LEU* 3.4 11.8 + - - +
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Residues in contact with SER 435 (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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433A LYS* 3.8 15.8 - - - +
434A ASP* 1.3 77.0 - - - +
436A ASP* 1.3 74.7 + - - +
438A LEU* 3.4 16.7 + - - +
439A ASP* 3.4 13.0 + - - +
554A ASP* 5.6 1.6 - - - +
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Residues in contact with ASP 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A GLU 4.6 1.7 - - - +
432A LEU* 3.7 24.8 - - + +
433A LYS* 3.0 50.5 + - - +
435A SER* 1.3 79.6 + - - +
437A LYS* 1.3 57.4 + - - +
439A ASP* 3.3 7.3 + - - +
440A LYS* 3.0 35.8 + - + +
554A ASP* 3.9 17.6 - - - +
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Residues in contact with LYS 437 (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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432A LEU* 3.7 40.1 + - + -
433A LYS 3.2 7.1 + - - +
434A ASP* 3.0 34.5 + - - +
435A SER 3.2 0.8 - - - -
436A ASP* 1.3 76.5 - - - +
438A LEU* 1.3 61.7 + - - +
440A LYS* 3.4 8.4 + - - +
441A ILE* 3.3 28.6 + - + +
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Residues in contact with LEU 438 (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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434A ASP 3.4 8.4 + - - +
435A SER* 3.4 12.0 + - - +
436A ASP 3.3 0.6 - - - -
437A LYS* 1.3 79.5 - - - +
439A ASP* 1.3 62.9 + - - +
441A ILE* 3.2 19.6 - - + +
442A MET* 3.1 40.1 + - + +
508A LYS* 3.0 40.4 - - + +
509A GLN* 4.2 17.3 - - - +
510A ALA* 5.2 1.8 - - - +
513A LEU* 5.8 1.8 - - + -
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Residues in contact with ASP 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A SER 3.4 9.3 + - - +
436A ASP* 3.3 9.9 + - - +
438A LEU* 1.3 79.8 - - - +
440A LYS* 1.3 58.2 + - + +
442A MET* 3.3 6.1 + - - +
443A ASN* 2.8 27.4 + - - +
508A LYS* 2.9 29.3 + - + +
553A PRO 4.5 6.9 - - - +
555A ARG* 3.4 24.7 + - - +
787A ARG* 3.4 24.1 + - - -
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Residues in contact with LYS 440 (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 GLU* 4.5 19.1 + - - +
380A PRO* 5.4 3.2 - - - +
432A LEU* 3.9 28.6 - - + +
436A ASP* 3.0 24.9 + - - +
437A LYS* 3.7 8.5 - - - +
438A LEU 3.2 0.4 - - - -
439A ASP* 1.3 76.3 - - + +
441A ILE* 1.3 61.5 + - + +
443A ASN* 3.4 12.4 + - + +
444A MET* 2.9 28.2 + - - +
596A TYR* 5.5 10.3 - - - -
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Residues in contact with ILE 441 (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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437A LYS* 3.3 13.9 + - + +
438A LEU* 3.2 27.4 - - + +
440A LYS* 1.3 75.7 - - + +
442A MET* 1.3 67.2 + - + +
444A MET* 3.1 11.6 + - - -
445A LYS* 2.9 51.3 + - - +
513A LEU* 4.2 30.3 - - + -
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Residues in contact with MET 442 (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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438A LEU* 3.1 30.3 + - + +
439A ASP* 3.3 15.0 + - - +
441A ILE* 1.3 80.8 - - + +
443A ASN* 1.3 61.7 + - - +
445A LYS* 3.3 6.7 + - - +
446A GLU* 3.0 28.5 + - + +
508A LYS* 4.1 34.5 - - + +
509A GLN 5.3 1.1 - - - +
512A ASP* 5.0 8.7 - - + +
513A LEU* 4.2 27.1 - - - -
516A ILE* 3.7 30.0 - - + +
787A ARG* 4.2 4.9 - - - +
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Residues in contact with ASN 443 (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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439A ASP 2.8 16.7 + - - +
440A LYS* 3.6 13.8 - - + +
442A MET* 1.3 74.6 - - - +
444A MET* 1.3 63.9 + - - +
446A GLU* 3.1 5.0 + - - +
447A THR* 3.0 26.6 + - - -
450A ARG* 4.1 6.8 + - - -
480A ASP* 3.7 7.7 + - - -
721A ARG* 4.8 3.4 - - - +
787A ARG* 3.5 46.3 - - - +
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Residues in contact with MET 444 (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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440A LYS 2.9 14.9 + - - +
441A ILE* 3.1 15.9 + - - +
443A ASN* 1.3 76.0 - - - +
445A LYS* 1.3 78.5 + - + +
447A THR* 3.3 22.2 + - - +
448A THR* 3.6 10.9 + - - +
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Residues in contact with LYS 445 (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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441A ILE* 2.9 41.5 + - - +
442A MET* 3.7 5.6 - - - +
444A MET* 1.3 91.9 - - - +
446A GLU* 1.3 62.6 + - - +
448A THR* 3.0 27.6 + - - +
449A LYS* 4.7 0.9 - - - +
513A LEU* 4.3 22.0 - - + -
516A ILE* 3.8 28.3 - - + +
517A ASP* 5.9 2.2 - - - +
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Residues in contact with GLU 446 (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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442A MET* 3.0 18.7 + - + +
443A ASN 3.1 9.4 + - - +
445A LYS* 1.3 75.4 - - - +
447A THR* 1.3 65.6 + - - +
449A LYS* 3.7 6.5 + - - +
450A ARG 3.5 12.1 + - - -
516A ILE* 4.7 19.0 - - + +
521A ASP* 4.9 3.5 - - - +
523A VAL* 6.1 0.9 - - - +
787A ARG* 3.7 42.3 - - + +
788A ARG* 2.9 47.8 + - - +
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Residues in contact with THR 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ASN* 3.0 14.6 + - - -
444A MET* 3.5 13.1 + - - -
445A LYS 3.2 0.6 - - - -
446A GLU* 1.3 77.3 - - - +
448A THR* 1.3 56.0 + - + +
449A LYS 2.7 14.6 + - - -
450A ARG* 2.8 56.6 + - + +
722A ASP* 5.5 0.9 - - - +
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Residues in contact with THR 448 (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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444A MET 3.6 10.0 + - - +
445A LYS* 3.0 19.9 + - - +
447A THR* 1.3 74.5 - - + +
449A LYS* 1.3 73.3 + - - +
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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