Contacts of the helix formed by residues 522 - 535 (chain D) in PDB entry 3GEB
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 CYS 522 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293D ARG* 4.8 2.9 - - + +
294D TYR* 3.2 20.6 - - + +
424D TRP* 3.9 8.5 - - - -
520D ILE* 3.3 7.9 + - - +
521D SER* 1.3 85.6 - - - +
523D HIS* 1.3 67.2 - - - +
524D ALA* 3.2 16.4 - - - +
525D ASP* 3.2 33.4 + - - +
526D LEU 3.3 7.8 + - - -
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Residues in contact with HIS 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D PHE* 6.5 0.2 - + - -
294D TYR* 3.1 20.9 + + + -
421D THR 3.6 18.4 + - - -
422D ASP* 3.1 27.6 + - + -
424D TRP* 3.6 35.8 - + + -
427D HIS* 2.8 35.1 + + - -
522D CYS* 1.3 75.7 - - - +
524D ALA* 1.3 63.2 + - - +
526D LEU* 3.0 19.8 + - + +
527D GLU* 3.1 23.8 + - + +
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Residues in contact with ALA 524 (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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531A HIS* 3.8 17.1 - - + -
522D CYS* 3.2 14.6 - - - +
523D HIS* 1.3 78.3 - - - +
525D ASP* 1.3 52.8 + - - +
527D GLU* 3.2 10.8 + - - +
528D ALA* 2.8 33.8 + - - +
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Residues in contact with ASP 525 (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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531A HIS* 2.9 21.1 + - - -
535A LEU* 3.7 26.1 - - + +
519D ARG 3.6 16.1 - - - +
520D ILE* 3.8 10.9 - - + +
521D SER* 3.0 30.8 + - - -
522D CYS* 3.2 25.2 + - - +
524D ALA* 1.3 73.4 - - - +
526D LEU* 1.3 60.6 + - - +
528D ALA* 3.6 2.4 - - - +
529D LEU* 2.9 28.1 + - - +
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Residues in contact with LEU 526 (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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273D TRP* 5.7 2.9 - - + -
278D THR 4.1 11.9 - - - +
424D TRP* 3.3 53.4 - - + +
427D HIS* 4.1 15.3 - - + +
428D SER* 3.9 24.5 - - - +
431D ALA* 5.0 5.4 - - + -
520D ILE* 4.1 14.5 - - + +
522D CYS 3.3 6.0 + - - +
523D HIS* 3.0 16.5 + - - +
525D ASP* 1.3 79.6 - - - +
527D GLU* 1.3 57.0 + - - +
529D LEU* 3.2 12.7 + - + +
530D ARG* 2.9 28.2 + - + +
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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
----------------------------------------------------------
427D HIS* 3.8 16.9 + - + -
523D HIS* 3.1 36.5 + - + +
524D ALA* 3.7 10.3 - - - +
526D LEU* 1.3 74.5 - - - +
528D ALA* 1.3 64.5 + - - +
530D ARG* 2.8 44.0 + - - +
531D HIS* 3.1 23.4 + - - +
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Residues in contact with ALA 528 (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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518A TRP* 6.0 0.2 - - - -
528A ALA 5.8 0.9 - - - +
531A HIS* 3.8 22.0 - - + +
532A ALA* 5.3 7.7 - - + +
535A LEU* 3.8 19.5 - - + -
518D TRP* 4.8 3.0 - - + -
524D ALA 2.8 16.6 + - - +
525D ASP 3.6 6.3 - - - +
526D LEU 3.2 0.2 - - - -
527D GLU* 1.3 77.1 - - - +
529D LEU* 1.3 58.0 + - - +
531D HIS* 3.3 10.2 + - - +
532D ALA* 3.0 26.2 + - - +
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Residues in contact with LEU 529 (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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273D TRP* 4.0 22.2 - - + -
431D ALA* 5.2 0.7 - - + -
500D ILE* 3.8 31.2 - - + -
518D TRP* 3.6 26.2 - - + -
520D ILE* 3.8 11.4 - - + -
525D ASP 2.9 14.8 + - - +
526D LEU* 3.3 12.8 - - + +
528D ALA* 1.3 74.2 - - - +
530D ARG* 1.3 67.1 + - - +
532D ALA* 2.8 16.7 + - - +
533D LEU* 2.9 21.9 + - + +
538D LEU* 3.2 35.0 - - + -
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Residues in contact with ARG 530 (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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427D HIS* 3.2 45.0 + - - +
430D LYS* 3.6 35.1 - - + +
431D ALA* 4.3 22.7 - - + +
434D LEU* 4.3 2.9 - - + +
526D LEU 2.9 14.0 + - - +
527D GLU* 2.8 55.7 + - - +
528D ALA 3.5 0.2 - - - -
529D LEU* 1.3 72.3 - - - +
531D HIS* 1.3 57.2 + - - +
533D LEU* 3.3 7.1 + - - +
534D GLU* 3.0 43.6 + - + +
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Residues in contact with HIS 531 (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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518A TRP* 3.4 31.7 - + - -
528A ALA* 4.8 10.3 + - + +
527D GLU 3.1 17.4 + - - +
528D ALA* 3.5 8.4 + - - +
529D LEU 3.0 0.2 - - - -
530D ARG* 1.3 77.7 - - - +
532D ALA* 1.3 62.3 + - - +
534D GLU* 3.3 14.6 + - + +
535D LEU* 3.2 57.3 + - + +
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Residues in contact with ALA 532 (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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518A TRP* 5.1 2.7 - - + -
532A ALA* 5.3 3.1 - - + -
518D TRP* 3.8 26.7 - - + -
528D ALA 3.0 12.2 + - - +
529D LEU 2.8 10.0 + - - +
531D HIS* 1.3 79.6 - - - +
533D LEU* 1.3 60.4 + - - +
535D LEU* 3.6 0.8 + - - -
536D GLU 3.3 1.9 + - - -
537D TYR* 2.9 49.1 + - + +
538D LEU* 3.1 11.3 + - + -
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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
----------------------------------------------------------
271D PHE* 3.9 25.1 - - + -
273D TRP* 4.9 0.9 - - + -
431D ALA* 3.8 33.7 - - + +
434D LEU* 3.8 18.7 - - + +
435D ILE* 3.8 22.0 - - + -
438D ARG* 2.8 24.7 + - - +
529D LEU* 2.9 30.6 + - + +
530D ARG* 3.5 7.0 - - - +
532D ALA* 1.3 75.4 - - - +
534D GLU* 1.3 65.2 + - - +
536D GLU* 3.1 4.0 + - - +
538D LEU* 3.3 31.0 - - + +
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Residues in contact with GLU 534 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519C ARG* 3.2 38.5 + - - -
430D LYS* 5.3 8.3 - - - +
434D LEU* 3.8 21.5 - - + +
530D ARG* 3.0 34.1 + - + +
531D HIS* 3.3 19.7 - - + +
533D LEU* 1.3 79.5 - - - +
535D LEU* 1.3 64.9 + - + +
536D GLU* 3.2 12.8 + - - +
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Residues in contact with LEU 535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A PRO* 3.4 14.0 - - - +
517A PHE 4.1 20.4 + - - +
518A TRP* 3.7 34.1 - - + -
519A ARG 5.3 2.0 - - - +
531D HIS* 3.2 48.0 + - + +
532D ALA 3.6 0.9 + - - +
534D GLU* 1.3 81.4 - - + +
536D GLU* 1.3 70.7 + - - +
537D TYR* 2.9 15.6 + - + +
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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
------------------------------------------------------------
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