Contacts of the helix formed by residues 508 - 525 (chain A) in PDB entry 4FWF
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 PRO 508 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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507A VAL* 1.4 96.7 - - + +
509A LEU* 1.3 63.9 + - - +
510A GLY 3.3 0.2 + - - -
511A GLU* 3.8 32.1 - - + +
512A LYS* 3.1 19.2 + - - +
551A LEU 4.1 0.2 - - - +
552A HIS* 3.7 37.7 - - + +
554A VAL 3.4 7.9 - - - +
772A THR* 3.6 17.2 - - + +
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Residues in contact with LEU 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A LEU* 4.2 7.4 - - + -
494A VAL* 4.1 24.7 - - + -
507A VAL 3.4 2.4 + - - -
508A PRO* 1.3 71.0 - - - +
510A GLY* 1.3 56.8 + - - +
512A LYS* 3.7 0.8 - - - +
513A ILE* 2.9 47.8 + - + +
543A LEU* 3.9 16.8 - - + -
547A CYS* 5.3 0.2 - - - -
551A LEU* 3.7 26.7 - - + +
554A VAL* 2.8 25.5 + - + +
555A SER 4.2 1.3 - - - -
556A ALA* 3.4 16.1 - - - +
559A TRP* 4.0 33.4 - - + +
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Residues in contact with GLY 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A PRO 3.2 0.2 - - - -
509A LEU* 1.3 70.8 - - - +
511A GLU* 1.3 63.1 + - - +
513A ILE* 3.7 6.9 + - - +
514A GLU* 3.4 20.4 + - - +
551A LEU* 2.8 43.6 + - - +
552A HIS* 3.5 17.5 + - - -
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Residues in contact with GLU 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A VAL* 4.5 9.2 - - + +
508A PRO* 3.3 35.8 + - + +
510A GLY* 1.3 71.3 - - - +
512A LYS* 1.3 68.0 + - - +
514A GLU* 3.3 4.5 + - - +
515A GLU* 3.1 25.9 + - - +
552A HIS* 3.3 26.4 + - + +
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Residues in contact with LYS 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A VAL* 3.8 17.3 - - + -
497A TRP* 3.1 64.1 - - + +
507A VAL* 4.2 15.3 - - + +
508A PRO 3.1 14.5 + - - +
509A LEU* 3.7 8.3 - - - +
511A GLU* 1.3 80.2 - - - +
513A ILE* 1.3 64.8 + - - +
515A GLU* 3.3 31.3 + - - +
516A ILE* 3.1 44.2 + - + +
556A ALA* 4.4 2.2 - - + -
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Residues in contact with ILE 513 (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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487A PHE* 5.4 0.9 - - + -
490A LEU* 3.8 29.4 - - + +
491A LEU* 4.3 16.8 - - + -
494A VAL* 4.5 5.8 - - + -
509A LEU* 2.9 50.3 + - + +
510A GLY* 3.8 4.9 - - - +
512A LYS* 1.3 77.7 - - - +
514A GLU* 1.3 62.3 + - + +
516A ILE* 3.2 8.6 + - - +
517A TYR* 2.8 25.7 + - + +
536A LEU* 6.1 1.3 - - + -
540A LEU* 4.0 25.8 - - + -
543A LEU* 4.5 0.9 - - + -
551A LEU* 3.7 24.2 - - + -
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Residues in contact with GLU 514 (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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510A GLY 3.4 11.5 + - - +
511A GLU* 3.3 6.0 + - - +
513A ILE* 1.3 82.1 - - + +
515A GLU* 1.3 57.7 + - - +
517A TYR* 3.2 14.9 - - + +
518A LYS* 2.8 35.2 + - + +
552A HIS* 5.8 3.4 - - + +
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Residues in contact with GLU 515 (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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511A GLU* 3.1 14.0 + - - +
512A LYS* 3.4 37.9 + - - +
514A GLU* 1.3 76.0 - - - +
516A ILE* 1.3 67.3 + - + +
518A LYS* 3.1 8.8 + - - +
519A ALA* 3.0 21.6 + - + +
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Residues in contact with ILE 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A LEU* 4.3 11.9 - - + +
493A VAL* 3.7 41.1 - - + -
494A VAL* 3.7 27.8 - - + +
497A TRP* 5.5 2.0 - - + -
512A LYS* 3.1 30.4 + - + +
513A ILE* 3.6 6.3 - - - +
515A GLU* 1.3 80.6 - - + +
517A TYR* 1.3 62.6 + - - +
519A ALA* 3.5 9.1 + - + +
520A PHE* 3.4 38.2 + - + -
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Residues in contact with TYR 517 (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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486A HIS* 4.3 7.4 - + - -
490A LEU* 4.6 13.7 - - + +
513A ILE* 2.8 16.5 + - + +
514A GLU* 3.2 20.0 - - + +
515A GLU 3.0 0.4 - - - -
516A ILE* 1.3 77.4 - - - +
518A LYS* 1.3 73.2 + - + +
520A PHE* 3.2 13.5 + - - +
521A ILE* 3.1 33.2 + - + +
528A PHE* 3.5 43.0 - + - +
533A GLY* 5.4 5.4 - - - -
536A LEU* 3.9 27.8 - - + -
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Residues in contact with LYS 518 (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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514A GLU* 2.8 19.5 + - + +
515A GLU* 3.1 8.7 + - - +
517A TYR* 1.3 83.9 - - + +
519A ALA* 1.3 56.6 + - - +
521A ILE* 3.4 12.5 + - + +
522A LYS* 3.0 29.6 + - - +
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Residues in contact with ALA 519 (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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515A GLU* 3.0 12.2 + - + +
516A ILE* 3.7 14.6 - - + +
517A TYR 3.2 0.2 - - - -
518A LYS* 1.3 74.7 - - - +
520A PHE* 1.3 60.6 + - + +
522A LYS* 3.4 5.3 + - - +
523A GLU* 2.9 34.2 + - + +
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Residues in contact with PHE 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A HIS* 3.8 28.7 - + + +
489A ALA* 5.3 7.2 - - + -
490A LEU* 4.0 14.4 - - + -
493A VAL* 4.3 18.8 - - + -
516A ILE* 3.4 34.4 + - + -
517A TYR 3.2 7.3 + - - +
519A ALA* 1.3 75.9 - - + +
521A ILE* 1.3 61.8 + - + +
523A GLU* 5.2 2.5 - - + -
524A SER* 2.7 43.3 + - - +
528A PHE* 6.3 0.7 - - + -
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Residues in contact with ILE 521 (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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517A TYR* 3.1 48.2 - - + +
518A LYS* 3.4 14.8 - - + +
520A PHE* 1.3 76.4 - - + +
522A LYS* 1.3 55.9 + - - +
524A SER* 3.5 0.2 + - - -
525A GLY* 2.8 36.9 + - - +
526A ILE 4.0 16.6 - - - +
527A GLN* 3.7 28.9 - - + +
528A PHE* 4.0 25.4 - - + +
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Residues in contact with LYS 522 (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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518A LYS 3.0 14.2 + - - +
519A ALA* 3.8 5.4 - - - +
521A ILE* 1.3 84.7 - - - +
523A GLU* 1.3 65.9 + - + +
524A SER 3.2 0.2 + - - -
525A GLY* 3.3 8.3 + - - -
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Residues in contact with GLU 523 (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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519A ALA* 2.9 19.5 + - + +
520A PHE* 5.2 2.9 - - + -
522A LYS* 1.3 77.0 - - + +
524A SER* 1.3 59.4 + - - +
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Residues in contact with SER 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A PHE* 2.7 27.9 + - - +
522A LYS 4.0 0.2 - - - -
523A GLU* 1.3 78.9 - - - +
525A GLY* 1.3 60.4 + - - +
526A ILE* 3.2 37.7 + - - +
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Residues in contact with GLY 525 (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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521A ILE* 2.8 19.7 + - - +
522A LYS 3.3 7.1 + - - -
524A SER* 1.3 73.1 - - - +
526A ILE* 1.3 64.8 + - - +
527A GLN* 3.7 6.2 + - - +
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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