Contacts of the helix formed by residues 505 - 515 (chain D) in PDB entry 1GGE
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 TYR 505 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247D PRO* 3.8 15.1 - - + +
250D LEU* 3.4 11.2 - - + -
503D GLU* 3.0 3.8 + - - +
504D TYR* 1.3 93.2 - + + +
506D SER* 1.3 67.1 + - - +
507D HIS 3.4 2.0 - - - -
508D PRO* 3.2 7.5 - - - +
509D ARG* 3.0 23.6 + - - +
546D GLN* 2.7 39.0 + - - -
549D HIS* 3.6 55.7 + + + +
550D ILE* 3.8 16.4 - - + +
576D PRO* 3.6 12.2 - - + +
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Residues in contact with SER 506 (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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350D ASP* 6.2 0.2 - - - +
503D GLU* 2.8 37.3 + - - -
505D TYR* 1.3 73.4 - - - +
507D HIS* 1.3 68.2 + - - +
509D ARG* 3.4 3.2 + - - +
510D LEU* 2.9 28.2 + - - +
576D PRO* 3.6 12.7 - - - +
577D PRO* 3.3 29.0 - - - +
578D ASP 4.9 1.1 - - - -
579D VAL* 3.7 11.5 - - - +
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Residues in contact with HIS 507 (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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251D HIS* 3.5 21.8 + - + +
350D ASP* 6.0 0.9 - - + -
351D PHE* 3.5 30.6 - + + -
357D THR 4.5 0.4 - - - +
358D LYS* 3.5 30.2 - - + +
359D LEU* 3.1 54.6 + - + +
503D GLU* 4.4 1.0 + - - -
506D SER* 1.3 84.8 + - - +
508D PRO* 1.3 76.1 - - + +
510D LEU* 3.0 9.4 + - + +
511D PHE* 2.8 23.0 + - - +
579D VAL* 3.6 19.9 - - + +
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Residues in contact with PRO 508 (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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250D LEU* 4.1 3.8 - - + -
251D HIS* 3.7 35.6 - - + +
254D MET* 3.9 16.8 - - + +
504D TYR 3.2 24.0 - - - +
505D TYR* 3.2 13.7 - - - +
507D HIS* 1.3 96.6 - - + +
509D ARG* 1.3 56.6 + - - +
511D PHE* 3.3 3.2 + - + +
512D TRP* 2.9 27.7 + - - +
550D ILE* 3.6 25.1 - - + -
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Residues in contact with ARG 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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505D TYR 3.0 14.3 + - - +
506D SER 3.6 4.5 - - - +
508D PRO* 1.3 75.6 - - - +
510D LEU* 1.3 65.9 + - - +
512D TRP* 3.2 4.3 + - - +
513D LEU* 2.9 60.1 + - + +
550D ILE* 3.0 35.0 + - - +
551D ASP* 2.9 32.6 + - + +
575D PRO* 3.9 21.0 - - - +
576D PRO* 3.6 30.9 + - + -
577D PRO 5.2 2.9 - - - -
578D ASP* 5.1 6.7 + - - +
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Residues in contact with LEU 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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359D LEU* 4.3 8.5 - - + -
361D PRO* 4.0 23.8 - - + -
506D SER 2.9 14.8 + - - +
507D HIS* 3.0 10.7 + - + +
509D ARG* 1.3 75.7 - - - +
511D PHE* 1.3 57.8 + - - +
513D LEU* 3.6 5.8 + - - +
514D SER* 2.6 34.4 + - - +
579D VAL* 3.9 26.9 - - + +
582D LEU* 4.2 16.6 - - + +
583D LYS 4.4 0.7 - - - -
584D LYS* 3.6 37.7 - - - +
585D ASP* 4.0 2.5 - - + +
588D LEU* 3.9 16.6 - - + -
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Residues in contact with PHE 511 (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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251D HIS* 4.2 6.3 - - + +
254D MET* 3.6 34.5 - - + -
255D TRP* 3.3 56.3 - + - +
258D SER* 3.7 20.0 - - - -
260D ARG* 4.7 2.9 - - + -
507D HIS 2.8 13.2 + - - +
508D PRO* 3.5 7.9 - - + +
510D LEU* 1.3 76.5 - - - +
512D TRP* 1.3 65.8 + - - +
514D SER* 3.1 6.9 + - - -
515D GLN* 3.0 50.5 + - - +
523D ILE* 3.6 23.6 - - + -
588D LEU* 3.7 19.5 - - + +
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Residues in contact with TRP 512 (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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254D MET* 3.9 16.8 - - + -
508D PRO 2.9 17.3 + - - +
509D ARG* 3.5 6.5 - - - +
511D PHE* 1.3 81.2 - - - +
513D LEU* 1.3 80.8 + - + +
515D GLN* 3.2 16.9 + - - +
520D GLN* 2.9 83.5 + - + +
523D ILE* 4.1 9.6 - - + -
524D VAL* 3.9 13.7 - - + -
550D ILE* 5.0 2.0 - - + -
551D ASP* 3.2 33.4 + - + -
553D THR* 4.5 12.4 - - + -
554D LEU* 3.7 42.2 - - + -
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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
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509D ARG* 2.9 60.9 + - + +
510D LEU* 4.1 5.6 - - - +
512D TRP* 1.3 95.9 - - + +
514D SER* 1.3 58.7 + - - +
515D GLN 3.3 5.5 + - - +
520D GLN* 4.1 6.0 + - - +
551D ASP* 4.6 2.5 - - - +
578D ASP* 5.4 3.4 - - - +
583D LYS* 3.6 32.5 - - + +
584D LYS* 3.8 14.9 - - - +
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Residues in contact with SER 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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510D LEU* 2.6 22.1 + - - +
511D PHE 3.1 6.8 + - - -
513D LEU* 1.3 74.5 - - - +
515D GLN* 1.3 63.3 + - - +
584D LYS* 3.5 11.7 - - - +
585D ASP 2.8 41.8 + - - -
586D PRO* 4.6 4.0 - - - +
588D LEU* 3.8 16.4 - - - +
589D SER* 3.3 18.4 - - - -
592D ALA* 4.6 5.0 - - - +
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Residues in contact with GLN 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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258D SER* 5.2 2.4 - - - -
260D ARG* 5.8 0.7 + - - +
511D PHE* 3.0 48.5 + - + +
512D TRP 3.2 10.2 + - - +
513D LEU 4.1 3.8 - - - +
514D SER* 1.3 83.7 - - - +
516D THR* 1.3 66.6 + - - +
517D PRO* 4.5 1.0 - - - +
519D GLU* 3.4 36.5 - - + +
520D GLN* 3.9 19.0 + - + +
523D ILE* 3.8 20.9 - - + +
588D LEU* 3.1 29.3 + - - +
589D SER* 3.7 5.0 - - - -
590D LEU* 4.4 0.7 + - - +
592D ALA* 5.8 0.2 - - - -
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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