Contacts of the helix formed by residues 509 - 523 (chain E) in PDB entry 4K4I
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 SER 509 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420E ARG* 3.3 24.1 - - - +
508E GLY* 1.3 75.5 + - - -
510E ALA* 1.3 66.1 + - - +
511E HIS* 2.9 6.4 + - - +
512E PHE* 2.9 15.5 + - - +
513E ASN* 2.9 20.3 + - - +
573E ARG 2.8 19.5 + - - -
574E ASP* 2.7 27.3 + - - -
601E 1RY 4.6 1.8 - - - -
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Residues in contact with ALA 510 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509E SER* 1.3 73.8 - - - +
511E HIS* 1.3 68.7 + - + +
513E ASN* 3.3 4.3 + - - +
514E ARG* 3.2 25.8 + - - +
601E 1RY 3.7 61.3 + - + +
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Residues in contact with HIS 511 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277E LEU* 4.2 14.7 - - + +
280E ALA* 3.6 31.6 - - + +
281E LYS* 5.1 9.0 - - + -
284E ASN* 3.5 28.2 + - - +
509E SER* 2.9 6.7 + - - +
510E ALA* 1.3 80.8 - - + +
512E PHE* 1.3 66.4 + - - +
514E ARG* 3.0 31.2 + - + +
515E SER* 3.0 27.5 + - - +
574E ASP 4.6 3.8 - - - +
575E TRP* 5.5 1.6 - - - -
576E LEU 5.6 0.2 - - - -
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Residues in contact with PHE 512 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504E LEU* 4.4 9.9 - - + -
508E GLY 4.1 7.9 - - - -
509E SER* 2.9 14.9 + - - +
511E HIS* 1.3 73.8 - - - +
513E ASN* 1.3 75.6 + - - +
515E SER* 3.1 13.5 + - - -
516E MET* 3.2 35.4 + - + +
560E PHE* 3.8 24.9 - + - -
568E ARG* 3.9 6.5 - - - -
573E ARG* 3.3 55.6 - - + +
574E ASP 4.0 3.3 + - - +
575E TRP* 3.4 25.2 - - - +
576E LEU* 3.6 28.3 - - + +
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Residues in contact with ASN 513 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504E LEU* 4.0 13.8 - - - +
505E TYR* 2.9 39.4 + - - +
508E GLY* 3.8 6.4 - - - -
509E SER 2.9 17.3 + - - +
510E ALA 3.7 6.7 - - - +
511E HIS 3.3 0.4 - - - -
512E PHE* 1.3 83.4 - - - +
514E ARG* 1.3 58.5 + - - +
516E MET* 3.7 7.4 - - - +
517E ARG* 3.1 38.6 + - - +
601E 1RY 3.1 27.3 + - - +
5F G 4.4 6.5 - - - +
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Residues in contact with ARG 514 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274E TRP* 5.1 2.4 - - - -
277E LEU* 3.9 28.2 - - - +
281E LYS* 5.4 6.1 - - - +
510E ALA* 3.2 15.8 + - - +
511E HIS* 3.0 33.3 + - + +
513E ASN* 1.3 73.4 - - - +
515E SER* 1.3 68.8 + - - +
517E ARG 4.1 0.2 - - - -
518E ALA* 3.2 21.7 + - - +
601E 1RY 5.8 1.0 + - - -
5F G 2.8 107.4 + - + +
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Residues in contact with SER 515 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E LYS* 5.7 7.6 - - - +
511E HIS* 3.0 13.4 + - - +
512E PHE 3.1 7.8 + - - -
514E ARG* 1.3 77.2 - - - +
516E MET* 1.3 63.5 + - - +
518E ALA* 2.9 8.8 + - - +
519E LEU* 2.8 23.7 + - - +
576E LEU* 3.6 32.0 + - - +
577E GLU* 5.6 1.9 + - - +
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Residues in contact with MET 516 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504E LEU* 4.1 24.2 - - + -
512E PHE* 3.2 42.6 - - + +
513E ASN* 3.7 8.5 - - - +
515E SER* 1.3 73.2 - - - +
517E ARG* 1.3 67.8 + - - +
519E LEU* 2.7 23.0 + - - +
520E ALA* 2.8 13.2 + - - +
527E LEU* 4.0 17.9 - - + -
559E VAL* 4.5 8.1 - - + -
560E PHE* 4.3 17.5 - - + -
563E LEU* 4.2 22.2 - - + +
565E LEU* 4.1 20.4 - - + -
576E LEU* 4.4 8.5 - - + +
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Residues in contact with ARG 517 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505E TYR* 3.4 23.0 - - - +
513E ASN* 3.1 20.3 + - - +
514E ARG 4.1 0.2 - - - +
516E MET* 1.3 77.3 - - - +
518E ALA* 1.3 56.2 + - - +
520E ALA* 3.7 3.2 + - - +
521E LYS* 3.2 26.7 + - - +
526E SER* 5.6 0.2 - - - -
527E LEU* 3.2 40.3 + - + +
528E SER* 3.5 8.5 - - - -
529E GLU* 2.9 39.4 + - - +
5F G 3.4 49.6 - - - +
6F G 3.0 52.9 + - - -
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Residues in contact with ALA 518 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514E ARG 3.2 14.3 + - - +
515E SER* 2.9 11.1 + - - +
516E MET 2.8 3.6 + - - -
517E ARG* 1.3 71.4 - - - +
519E LEU* 1.3 63.7 + - - +
521E LYS* 3.3 12.1 + - - +
522E THR* 3.1 28.8 + - - +
4F C 6.4 2.0 - - - -
5F G 4.3 15.6 - - - -
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Residues in contact with LEU 519 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515E SER 2.8 11.5 + - - +
516E MET* 2.7 14.4 + - - +
518E ALA* 1.3 71.5 - - - +
520E ALA* 1.3 61.5 + - - +
522E THR* 2.3 33.1 + - - +
523E LYS* 3.3 31.0 - - - +
563E LEU* 3.5 31.9 - - + +
565E LEU* 3.6 37.9 - - + -
576E LEU* 4.4 11.0 - - + -
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Residues in contact with ALA 520 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516E MET 2.8 13.2 + - - +
517E ARG 3.8 8.5 - - - +
519E LEU* 1.3 74.5 - - - +
521E LYS* 1.3 61.7 + - - +
523E LYS 3.0 6.9 + - - -
525E MET* 2.9 40.1 + - + +
526E SER 4.1 8.7 - - - +
527E LEU* 4.1 18.4 - - + +
532E LEU* 4.5 0.7 - - + -
563E LEU* 3.5 26.0 - - + -
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Residues in contact with LYS 521 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517E ARG 3.2 15.3 + - - +
518E ALA* 3.3 9.4 + - - +
520E ALA* 1.3 78.8 - - - +
522E THR* 1.3 63.4 + - - +
523E LYS 3.3 0.5 + - - -
524E GLY* 3.4 11.8 + - - -
525E MET 3.5 7.8 + - - +
526E SER* 5.4 0.4 - - - +
538E ARG* 3.4 42.7 + - - +
3F G 4.0 3.0 + - - -
4F C 2.0 39.8 + - - -
5F G 4.5 4.5 - - - +
6F G 3.3 28.0 + - - +
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Residues in contact with THR 522 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518E ALA 3.1 18.3 + - - +
519E LEU* 2.3 28.6 + - - +
521E LYS* 1.3 78.3 - - - +
523E LYS* 1.3 62.9 + - - +
524E GLY 3.3 4.2 + - - -
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Residues in contact with LYS 523 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519E LEU* 3.3 29.8 - - + +
520E ALA 3.0 4.0 + - - +
522E THR* 1.3 80.8 - - - +
524E GLY* 1.3 50.3 + - - +
525E MET* 2.8 55.8 + - + +
534E THR* 5.1 2.3 - - - +
562E LEU 5.4 0.2 + - - -
563E LEU 2.5 31.8 + - - -
564E GLY* 4.3 4.6 + - - -
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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