Contacts of the helix formed by residues 560 - 575 (chain D) in PDB entry 4E3C
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 LEU 560 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437D ILE* 4.7 3.8 - - + -
440D LEU* 3.7 17.9 - - + +
441D LYS* 3.7 32.4 - - + +
444D CYS* 4.2 11.9 - - + -
559D THR* 1.3 82.2 - - - +
561D ASP* 1.3 62.8 + - - +
562D ASP 3.2 0.3 + - - -
563D LEU* 3.3 8.5 + - + +
564D GLU* 3.2 23.0 + - - +
597D ALA* 3.2 45.8 - - + +
600D SER* 3.7 9.6 + - - +
601D PHE* 4.1 19.7 - - + +
604D LYS* 4.3 13.5 - - + +
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Residues in contact with ASP 561 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441D LYS* 3.8 39.8 + - - +
445D ASN* 4.5 9.7 + - - +
559D THR* 3.1 5.3 + - - +
560D LEU* 1.3 77.8 + - - +
562D ASP* 1.3 61.6 + - - +
564D GLU* 3.9 4.9 + - - +
565D GLU* 3.7 16.3 + - - +
604D LYS* 4.0 20.5 + - - -
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Residues in contact with ASP 562 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559D THR* 2.8 23.6 + - - +
561D ASP* 1.3 77.6 - - - +
563D LEU* 1.3 60.1 + - - +
565D GLU* 3.0 10.0 + - - +
566D GLN* 2.7 56.4 + - - +
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Residues in contact with LEU 563 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437D ILE* 4.6 10.8 - - + -
559D THR 3.0 14.3 + - - +
560D LEU* 3.3 11.9 + - - +
562D ASP* 1.3 79.1 + - - +
564D GLU* 1.3 64.1 + - - +
566D GLN* 3.1 17.8 + - - +
567D ALA* 2.8 27.6 + - - +
593D LEU* 4.5 17.8 - - + +
596D GLN* 3.2 51.1 - - + +
597D ALA* 3.4 17.9 - - + +
600D SER* 4.4 10.1 - - - -
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Residues in contact with GLU 564 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434D TRP* 3.3 14.5 - - + -
437D ILE* 4.0 16.2 - - + +
438D GLN* 3.1 54.9 + - + +
441D LYS* 3.4 39.2 + - + +
560D LEU 3.2 9.2 + - - +
561D ASP 3.9 2.0 - - - +
563D LEU* 1.3 77.3 - - - +
565D GLU* 1.3 63.0 + - - +
567D ALA* 3.7 2.3 + - - +
568D ARG* 2.9 44.6 + - - -
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Residues in contact with GLU 565 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441D LYS* 6.0 0.9 - - - +
561D ASP 3.7 9.4 + - - +
562D ASP* 3.0 9.7 + - - +
564D GLU* 1.3 85.5 + - - +
566D GLN* 1.3 67.2 - - - +
568D ARG* 3.1 35.2 + - + +
569D GLU* 3.3 9.9 + - + +
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Residues in contact with GLN 566 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562D ASP* 2.7 37.4 + - - +
563D LEU* 3.4 12.7 - - - +
565D GLU* 1.3 73.4 - - - +
567D ALA* 1.3 63.0 + - - +
569D GLU* 3.1 26.2 - - + +
570D LEU* 3.3 8.1 - - + +
589D GLU* 5.9 0.8 + - - -
592D ARG* 4.9 5.3 - - - +
593D LEU* 3.3 31.0 - - + +
596D GLN* 5.6 1.2 + - - -
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Residues in contact with ALA 567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434D TRP* 4.2 3.4 - - + -
437D ILE* 4.2 21.3 - - + -
563D LEU 2.8 15.1 + - - +
564D GLU 3.8 4.3 - - - +
566D GLN* 1.3 74.4 - - - +
568D ARG* 1.3 67.6 + - - +
569D GLU 2.9 2.5 - - - -
570D LEU* 2.8 28.1 + - - +
571D TYR* 3.1 21.5 - - + -
590D MET* 4.5 3.6 - - - -
593D LEU* 3.8 17.4 - - + +
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Residues in contact with ARG 568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D PHE* 6.1 5.6 - - + -
112D GLU* 5.5 7.6 + - - +
434D TRP* 3.1 38.5 - - + -
438D GLN* 4.7 2.0 - - - +
441D LYS* 5.4 2.2 - - - +
564D GLU* 2.9 33.0 + - - +
565D GLU* 3.1 25.2 + - - +
567D ALA* 1.3 77.8 - - - +
569D GLU* 1.3 62.1 + - - +
570D LEU 3.1 1.0 + - - -
571D TYR* 3.1 25.8 + - + +
572D ARG* 3.1 17.5 + - + +
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Residues in contact with GLU 569 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565D GLU* 3.3 8.9 + - + +
566D GLN* 3.1 20.7 + - + +
567D ALA 2.8 1.6 + - - -
568D ARG* 1.3 79.0 - - - +
570D LEU* 1.3 61.1 + - + +
572D ARG* 3.4 41.1 + - - +
573D ARG* 2.8 45.1 + - - +
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Residues in contact with LEU 570 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430D TRP* 3.6 25.2 - - + -
566D GLN* 3.3 16.4 - - + +
567D ALA* 2.8 30.7 + - - +
569D GLU* 1.3 73.2 - - + +
571D TYR* 1.3 53.2 + - - +
573D ARG* 3.0 13.7 + - - +
574D LEU* 2.7 36.4 + - - +
589D GLU* 4.3 32.1 - - + +
590D MET* 3.3 29.4 - - + -
593D LEU* 4.1 10.3 - - + -
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Residues in contact with TYR 571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D PHE* 6.1 5.2 - - + -
430D TRP* 2.9 42.2 + + + -
431D GLY* 3.4 8.7 - - - -
434D TRP* 2.9 52.2 + + + +
567D ALA 3.1 25.6 - - - -
568D ARG* 3.3 13.9 - - + +
570D LEU* 1.3 74.0 - - - +
572D ARG* 1.3 58.7 + - - +
574D LEU* 2.9 7.0 + - - +
575D ARG* 2.7 70.3 + - - +
590D MET* 3.3 25.5 - - + -
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Residues in contact with ARG 572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D PHE* 4.9 16.4 - - + -
568D ARG* 3.1 19.1 + - + +
569D GLU* 3.4 37.1 + - - +
571D TYR* 1.3 79.5 - - - +
573D ARG* 1.3 79.9 + - - +
575D ARG* 5.4 0.2 - - - -
576D GLU* 3.0 64.2 + - - +
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Residues in contact with ARG 573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569D GLU* 2.8 59.9 + - - +
570D LEU* 3.0 14.8 + - - +
571D TYR 3.0 0.6 - - - -
572D ARG* 1.3 98.5 - - - +
574D LEU* 1.3 57.4 + - - +
576D GLU* 4.1 0.8 - - - -
577D LYS* 3.2 38.7 + - + +
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Residues in contact with LEU 574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424D PHE* 6.5 0.2 - - + -
426D LEU* 3.4 34.3 - - + +
427D ARG* 4.8 19.5 - - + -
430D TRP* 3.6 25.4 - - + -
570D LEU 2.7 14.0 + - - +
571D TYR* 3.8 5.4 - - - +
573D ARG* 1.3 77.7 - - - +
575D ARG* 1.3 62.7 + - - +
576D GLU 2.9 4.3 - - - -
577D LYS* 2.9 45.8 + - + +
582D ARG* 5.5 12.7 - - + +
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Residues in contact with ARG 575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D PHE* 4.0 38.0 - - + +
114D CYS* 3.0 35.4 - - - +
115D CYS 5.0 0.8 - - - +
427D ARG* 3.6 59.7 + - + +
428D LYS* 5.3 0.8 - - - +
431D GLY* 4.2 0.2 - - - -
571D TYR* 2.7 62.5 + - - +
574D LEU* 1.3 78.4 - - + +
576D GLU* 1.3 60.0 + - + +
577D LYS 4.7 1.7 - - - +
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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