Contacts of the helix formed by residues 503 - 518 (chain D) in PDB entry 2GL7
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 HIS 503 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458D GLU* 2.5 40.9 + - - +
501D PRO* 3.2 13.0 + - + -
502D SER* 1.3 72.3 - - - +
504D TRP* 1.3 62.4 + - - +
505D PRO* 3.5 6.3 - - + -
506D LEU* 3.5 2.9 + - - +
507D ILE* 3.1 30.0 + - - +
562D GLU* 3.1 32.3 - - - +
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Residues in contact with TRP 504 (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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503D HIS* 1.3 70.4 - - - +
505D PRO* 1.3 69.1 - - + +
507D ILE* 3.8 26.7 - - + +
508D LYS* 2.9 31.5 + - - +
539D LEU* 4.2 24.9 - - + -
542D ARG* 5.0 13.5 - - + -
543D ALA* 4.8 2.0 - - + -
546D ASP* 5.4 4.9 + - - -
561D VAL* 3.8 31.4 - - + +
562D GLU* 3.9 10.2 + - - +
564D VAL* 3.8 20.0 - - + +
566D MET* 3.7 31.2 - - + +
569D ILE* 3.3 42.0 - - + -
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Residues in contact with PRO 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458D GLU* 5.5 0.4 - - - +
462D GLU* 3.1 27.1 - - - +
503D HIS* 3.5 6.7 - - + -
504D TRP* 1.3 96.0 - - + +
506D LEU* 1.3 61.3 + - - +
508D LYS* 3.3 5.4 + - + +
509D ALA* 3.1 23.2 + - - +
562D GLU* 3.7 35.2 - - + +
564D VAL* 3.7 12.5 - - + -
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Residues in contact with LEU 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456D ASP 6.3 0.4 - - - -
458D GLU* 3.4 34.9 + - + +
461D THR* 3.5 45.3 - - - +
462D GLU* 4.2 14.2 + - + +
465D ILE* 4.4 3.6 - - + -
497D LEU* 4.1 18.4 - - + +
502D SER* 3.4 26.5 - - - +
503D HIS 3.5 3.9 + - - +
504D TRP 3.4 0.2 - - - -
505D PRO* 1.3 79.4 - - - +
507D ILE* 1.3 57.6 + - - +
509D ALA* 3.5 4.5 + - + +
510D THR* 2.8 47.2 + - - +
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Residues in contact with ILE 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497D LEU 4.0 3.8 - - - +
498D LEU* 3.9 19.7 - - + +
499D HIS 5.5 0.4 - - - +
502D SER* 3.4 30.3 - - - +
503D HIS 3.1 26.1 + - - +
504D TRP* 3.8 31.9 - - + +
506D LEU* 1.3 73.5 - - - +
508D LYS* 1.3 60.5 - - - +
510D THR* 3.2 6.0 + - - -
511D VAL* 2.8 42.3 + - + +
535D ARG* 4.9 3.4 - - - +
539D LEU* 3.8 31.6 - - + -
569D ILE* 5.1 2.7 - - + -
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Residues in contact with LYS 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469D ARG* 4.7 8.3 + - - +
504D TRP 2.9 18.4 + - - +
505D PRO* 3.6 6.5 - - + +
507D ILE* 1.3 77.3 - - - +
509D ALA* 1.3 64.5 + - - +
511D VAL* 3.3 7.0 + - - +
512D GLY* 3.1 18.4 + - - -
564D VAL* 4.3 18.2 - - + -
568D GLU* 2.8 55.4 + - + +
569D ILE* 4.8 11.4 - - + +
17E GLU* 2.8 37.8 + - - -
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Residues in contact with ALA 509 (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 GLU* 4.5 4.7 - - + +
465D ILE* 3.8 14.1 - - + +
466D CYS* 3.5 31.6 - - - +
469D ARG* 3.7 18.3 - - - +
505D PRO 3.1 13.8 + - - +
506D LEU* 3.7 6.7 - - - +
508D LYS* 1.3 80.0 - - - +
510D THR* 1.3 56.1 + - - +
512D GLY* 3.1 3.3 + - - -
513D LEU* 3.0 26.5 + - - +
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Residues in contact with THR 510 (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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465D ILE* 3.7 15.0 - - + +
494D VAL* 3.2 32.3 - - + +
497D LEU* 4.0 11.3 - - + +
498D LEU* 3.2 25.6 - - + -
506D LEU* 2.8 36.9 + - - +
507D ILE* 3.7 5.6 - - - -
509D ALA* 1.3 74.0 - - - +
511D VAL* 1.3 65.7 + - - +
513D LEU* 3.4 2.3 + - - +
514D ILE* 3.1 23.6 + - + +
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Residues in contact with VAL 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498D LEU* 4.4 7.6 - - + -
507D ILE* 2.8 37.3 + - + +
508D LYS* 3.6 7.0 - - - +
510D THR* 1.3 72.7 - - - +
512D GLY* 1.3 66.9 + - - +
514D ILE* 3.2 6.7 + - - +
515D ARG* 2.9 23.2 + - - +
536D LEU* 4.1 16.6 - - + -
539D LEU* 4.5 1.6 - - + -
569D ILE* 5.8 3.1 - - + -
572D GLY* 3.4 38.6 - - - +
573D CYS* 3.5 23.3 - - - +
576D ALA* 4.5 2.3 - - + +
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Residues in contact with GLY 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469D ARG* 4.2 9.9 - - - -
508D LYS 3.1 13.0 + - - -
509D ALA 3.1 5.3 + - - -
511D VAL* 1.3 76.3 - - - +
513D LEU* 1.3 60.3 + - - +
515D ARG* 3.2 18.8 - - - +
516D ASN* 3.2 8.5 + - - -
572D GLY* 6.1 0.6 - - - -
14E ALA* 3.6 29.0 - - - +
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Residues in contact with LEU 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465D ILE* 3.9 24.0 - - + -
468D LEU* 3.8 31.4 - - + +
469D ARG* 4.2 13.7 - - + +
472D THR* 3.6 23.6 - - + +
485D VAL* 5.2 2.9 - - + -
494D VAL* 3.7 32.1 - - + -
509D ALA 3.0 12.3 + - - +
510D THR 3.8 5.8 - - - +
511D VAL 3.3 0.2 - - - -
512D GLY* 1.3 74.8 - - - +
514D ILE* 1.3 58.0 + - - +
516D ASN* 3.1 3.9 + - - +
517D LEU* 2.9 47.4 + - + +
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Residues in contact with ILE 514 (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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494D VAL* 3.5 24.5 - - + -
495D VAL* 4.4 12.8 - - + -
498D LEU* 3.6 43.7 - - + -
510D THR 3.1 16.3 + - - +
511D VAL* 3.7 6.1 - - - +
513D LEU* 1.3 71.3 - - - +
515D ARG* 1.3 67.2 + - - +
517D LEU* 3.3 9.3 + - + +
518D ALA* 3.0 23.6 + - - +
527D LEU* 4.5 23.3 - - + +
532D ALA* 5.0 4.5 - - + -
536D LEU* 4.3 21.3 - - + -
576D ALA* 4.7 3.1 - - + -
580D LEU* 4.8 5.6 - - + -
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Residues in contact with ARG 515 (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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511D VAL 2.9 12.7 + - - +
512D GLY* 3.2 12.6 - - - +
514D ILE* 1.3 79.3 - - - +
516D ASN* 1.3 61.2 + - - +
518D ALA* 3.4 13.9 + - - +
519D LEU* 3.7 10.4 + - - +
571D GLU* 3.1 40.3 + - - -
572D GLY* 4.2 11.0 - - - -
575D GLY* 3.7 13.4 - - - -
576D ALA* 3.9 30.2 - - + +
579D ILE* 4.0 20.4 - - + +
613D VAL* 3.9 18.4 - - - +
13E GLY* 4.4 13.3 + - - +
14E ALA* 4.0 30.1 - - - +
15E ASN 5.2 1.4 - - - +
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Residues in contact with ASN 516 (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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469D ARG* 3.0 18.9 - - - +
472D THR* 3.3 26.9 - - - +
473D SER* 2.9 25.5 + - - -
482D GLN* 3.5 11.0 - - - +
512D GLY 3.2 9.1 + - - +
513D LEU 3.1 7.2 + - - +
515D ARG* 1.3 75.8 - - - +
517D LEU* 1.3 63.9 + - - +
518D ALA 3.1 2.0 - - - -
519D LEU* 3.2 26.5 + - - +
13E GLY* 3.0 15.4 - - - -
14E ALA 2.9 30.6 + - - +
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Residues in contact with LEU 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472D THR* 4.2 4.0 - - + -
482D GLN* 3.8 22.2 - - - +
485D VAL* 3.7 38.6 - - + -
491D LEU* 3.7 22.4 - - + -
494D VAL* 4.4 11.0 - - + -
513D LEU* 2.9 44.3 + - + +
514D ILE* 3.3 11.4 + - + +
516D ASN* 1.3 74.6 - - - +
518D ALA* 1.3 60.2 + - - +
519D LEU 3.2 0.4 - - - -
520D CYS* 3.3 7.6 + - - +
523D ASN* 2.9 35.5 - - - +
527D LEU* 4.5 7.0 - - + -
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Residues in contact with ALA 518 (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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514D ILE 3.0 17.0 + - - +
515D ARG* 3.5 9.6 - - - +
516D ASN 3.1 0.6 - - - -
517D LEU* 1.3 74.2 - - - +
519D LEU* 1.3 56.2 + - - +
520D CYS 3.1 7.2 - - - -
524D HIS* 2.9 30.2 + - - -
527D LEU* 4.3 6.5 - - + -
576D ALA 4.7 0.4 - - - +
579D ILE* 3.2 20.5 - - + +
580D LEU* 3.7 32.1 - - + +
582D ARG* 5.3 0.5 - - - -
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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