Contacts of the helix formed by residues 526 - 546 (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 ARG 526 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476D SER* 4.4 0.2 - - - -
523D LEU 5.4 0.4 + - - -
524D CYS* 4.5 4.2 - - - +
525D GLY* 1.3 70.5 - - - +
527D GLU* 1.3 58.4 + - - +
528D ASN 3.7 1.1 - - - +
529D GLU* 3.8 21.8 - - + -
530D VAL* 3.1 24.8 + - - +
632D VAL* 3.9 17.0 - - + +
635D LEU* 2.9 53.7 + - + +
636D MET* 3.6 22.1 - - + +
639D ASP* 2.8 46.3 + - - +
640D GLU* 4.4 0.8 + - - -
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Residues in contact with GLU 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476D SER* 4.1 11.5 + - - +
477D GLN* 5.9 2.7 - - - -
480D LYS* 3.0 56.8 + - + +
525D GLY 2.5 16.1 + - - +
526D ARG* 1.3 72.7 - - - +
528D ASN* 1.3 61.6 + - + +
529D GLU 3.0 8.7 + - - -
530D VAL* 3.9 0.9 + - - +
531D LYS* 3.7 18.7 + - - +
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Residues in contact with ASN 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525D GLY 4.4 1.4 + - - -
526D ARG* 4.7 0.2 - - - +
527D GLU* 1.3 80.3 - - + +
529D GLU* 1.3 57.0 + - - +
531D LYS* 2.7 29.8 + - - +
532D LEU* 3.3 23.9 - - - +
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Residues in contact with GLU 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526D ARG* 3.8 22.2 - - + +
527D GLU 3.0 0.2 - - - -
528D ASN* 1.3 77.5 - - - +
530D VAL* 1.3 60.9 + - - +
531D LYS 2.9 3.6 - - - -
532D LEU* 2.9 28.1 + - - +
533D LEU* 3.5 19.3 + - - +
628D LYS* 6.0 1.0 - - - -
632D VAL* 3.0 44.4 - - + +
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Residues in contact with VAL 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473D ALA* 3.7 20.9 - - + +
476D SER* 4.0 7.0 - - - +
526D ARG 3.1 21.0 + - - +
527D GLU 3.9 1.5 + - - +
529D GLU* 1.3 73.9 - - - +
531D LYS* 1.3 61.4 + - - +
533D LEU* 3.5 14.8 + - + +
534D VAL* 3.2 26.3 + - + +
632D VAL* 4.0 14.1 - - + +
633D VAL* 3.6 24.2 - - + -
636D MET* 3.5 24.0 - - + -
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Residues in contact with LYS 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527D GLU 3.7 15.0 + - - +
528D ASN* 2.7 39.5 + - - +
529D GLU 2.9 0.2 - - - -
530D VAL* 1.3 79.4 - - - +
532D LEU* 1.3 73.5 + - - +
534D VAL* 3.0 24.4 - - + +
535D GLU* 3.0 41.7 - - + +
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Residues in contact with LEU 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528D ASN* 3.3 17.7 - - - +
529D GLU* 2.9 16.6 + - - +
531D LYS* 1.3 109.8 - - - +
533D LEU* 1.3 63.1 + - + +
535D GLU* 4.1 12.1 - - + +
536D ARG* 3.3 24.4 + - - +
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Residues in contact with LEU 533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529D GLU* 3.5 28.5 + - - +
530D VAL* 3.7 20.2 - - + +
531D LYS 3.2 0.4 - - - -
532D LEU* 1.3 76.5 - - + +
534D VAL* 1.3 55.3 + - - +
536D ARG* 3.2 18.0 + - - +
537D MET* 2.6 40.9 + - + +
628D LYS* 4.1 24.0 - - + +
629D VAL* 3.3 52.0 - - + +
632D VAL* 4.1 9.2 - - + -
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Residues in contact with VAL 534 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470D ASN* 4.3 8.5 - - - +
530D VAL* 3.2 15.6 + - + +
531D LYS* 3.0 28.7 - - + +
533D LEU* 1.3 79.8 - - - +
535D GLU* 1.3 57.3 + - + +
537D MET* 4.1 18.8 - - + +
538D MET* 2.7 63.7 + - + +
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Residues in contact with GLU 535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531D LYS* 3.0 49.3 + - + +
532D LEU* 4.1 16.9 - - + +
533D LEU 3.3 0.2 - - - -
534D VAL* 1.3 83.3 - - + +
536D ARG* 1.3 61.2 + - - +
538D MET* 3.8 13.0 - - - +
539D ALA* 4.2 4.2 + - - +
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Residues in contact with ARG 536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532D LEU* 3.3 16.2 + - + +
533D LEU* 3.2 28.7 + - - +
534D VAL 3.2 0.2 - - - -
535D GLU* 1.3 79.1 - - - +
537D MET* 1.3 75.4 + - - +
538D MET 3.2 0.2 - - - -
539D ALA* 3.1 22.8 - - + +
540D LEU* 4.0 3.2 + - - +
621D LYS* 4.8 3.2 + - - +
625D LEU* 2.8 61.7 + - - +
628D LYS* 5.6 3.4 - - - +
629D VAL* 4.7 0.8 - - - +
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Residues in contact with MET 537 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466D SER* 5.5 7.6 - - - +
470D ASN* 3.2 43.7 - - + +
533D LEU* 2.6 24.4 + - + +
534D VAL* 4.1 17.5 - - + +
536D ARG* 1.3 83.1 - - - +
538D MET* 1.3 69.0 + - - +
539D ALA 2.9 5.4 - - - -
540D LEU* 2.7 38.7 + - + +
541D GLN* 3.0 25.6 + - - -
625D LEU 5.8 3.8 - - - +
629D VAL* 6.0 2.7 - - + -
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Residues in contact with MET 538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467D LYS* 5.8 2.7 - - - -
470D ASN* 5.5 4.7 - - - +
534D VAL* 2.7 48.1 + - + +
535D GLU* 3.8 11.0 - - - +
537D MET* 1.3 84.7 - - + +
539D ALA* 1.3 59.3 + - - +
541D GLN* 3.5 16.2 + - - +
542D THR* 3.4 26.8 + - + +
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Residues in contact with ALA 539 (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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535D GLU 4.2 3.9 + - - +
536D ARG* 3.1 17.1 + - + +
537D MET 2.9 0.2 - - - -
538D MET* 1.3 80.7 - - - +
540D LEU* 1.3 49.9 + - - +
542D THR* 2.8 7.6 + - - -
543D ASP* 2.6 47.8 + - - +
621D LYS* 6.1 1.8 - - - +
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Residues in contact with LEU 540 (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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458D LEU* 6.0 0.4 - - + -
462D ASN* 4.7 10.3 - - - +
466D SER* 6.0 1.3 - - - +
536D ARG* 4.0 2.9 + - - +
537D MET* 2.7 27.3 + - + +
539D ALA* 1.3 70.5 - - - +
541D GLN* 1.3 65.6 + - - +
542D THR 3.0 3.1 + - - -
543D ASP* 3.5 7.0 - - + -
544D ILE* 3.1 43.9 + - + +
618D CYS* 3.6 28.5 - - + +
621D LYS* 3.9 22.1 - - + +
622D ALA* 3.3 37.9 - - + -
625D LEU* 6.1 0.2 - - + -
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Residues in contact with GLN 541 (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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462D ASN* 3.3 26.0 + - - +
466D SER* 5.4 1.8 + - - -
467D LYS* 2.9 54.4 - - - +
470D ASN* 4.0 10.5 - - - +
537D MET* 3.0 21.0 + - - +
538D MET* 3.5 25.4 - - - +
539D ALA 3.3 0.2 - - - -
540D LEU* 1.3 78.5 - - - +
542D THR* 1.3 61.1 + - + +
544D ILE* 3.2 22.1 - - - +
545D VAL* 3.7 11.3 - - - +
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Residues in contact with THR 542 (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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538D MET* 3.4 17.9 + - + +
539D ALA* 2.8 20.8 + - - -
541D GLN* 1.3 81.5 - - + +
543D ASP* 1.3 59.4 + - - +
544D ILE 3.1 2.5 - - - -
545D VAL* 3.0 12.5 - - + +
546D ASP* 2.8 44.8 + - - +
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Residues in contact with ASP 543 (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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539D ALA* 2.6 37.7 + - - +
540D LEU* 3.1 11.4 + - + +
542D THR* 1.3 75.7 + - - +
544D ILE* 1.3 62.1 + - - +
546D ASP* 3.4 22.3 - - - +
547D LEU* 3.6 12.3 - - - +
618D CYS* 4.2 16.2 - - - -
621D LYS* 2.7 29.0 + - - -
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Residues in contact with ILE 544 (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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455D MET* 5.5 0.5 - - - +
458D LEU* 3.3 30.3 - - + -
459D LEU* 6.1 3.6 - - + -
462D ASN* 3.1 38.6 - - - +
540D LEU* 3.1 32.7 + - + +
541D GLN* 3.2 20.9 - - - +
543D ASP* 1.3 74.3 - - - +
545D VAL* 1.3 72.7 + - + +
546D ASP 3.0 4.5 - - - -
547D LEU* 3.0 34.0 + - + +
548D GLN* 3.4 6.3 + - - +
618D CYS* 3.9 9.9 - - + -
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Residues in contact with VAL 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541D GLN 3.7 12.3 - - - +
542D THR* 3.0 31.6 - - + +
544D ILE* 1.3 79.7 - - + +
546D ASP* 1.3 60.9 + - - +
547D LEU 2.9 12.9 + - - +
548D GLN* 3.2 24.1 + - - +
549D ARG* 5.4 0.5 + - - -
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Residues in contact with ASP 546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542D THR* 2.8 34.6 + - - +
543D ASP* 3.4 17.6 - - - +
544D ILE 3.0 0.8 - - - -
545D VAL* 1.3 81.8 - - - +
547D LEU* 1.3 67.3 + - + +
549D ARG* 4.0 6.8 + - - -
614D LYS* 5.9 0.3 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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