Contacts of the helix formed by residues 505 - 514 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C PRO* 3.8 15.4 - - + +
250C LEU* 3.4 20.0 - - + -
503C GLU* 3.0 3.0 + - - +
504C TYR* 1.3 95.8 - + + +
506C SER* 1.3 66.6 + - - +
507C HIS 3.3 2.0 - - - -
508C PRO* 3.3 7.4 - - - +
509C ARG* 3.0 23.9 + - - +
546C GLN* 2.6 34.2 + - - -
549C HIS* 3.5 60.9 + + + +
550C ILE* 3.8 10.4 - - + +
576C PRO* 3.5 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 506 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503C GLU* 2.7 38.7 + - - -
505C TYR* 1.3 73.4 - - - +
507C HIS* 1.3 69.1 + - - +
509C ARG* 3.4 2.4 + - - +
510C LEU* 2.9 28.4 + - - +
576C PRO* 3.6 12.7 - - - +
577C PRO* 3.3 29.3 - - - +
578C ASP 4.9 1.6 - - - -
579C VAL* 3.7 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 507 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C HIS* 3.5 26.9 + + + +
350C ASP* 6.1 0.7 - - + -
351C PHE* 3.7 24.9 - + + -
357C THR 4.4 2.2 - - - +
358C LYS* 3.5 31.1 - - + +
359C LEU* 3.1 53.1 + - + +
503C GLU* 4.5 1.2 + - - -
504C TYR 6.1 0.2 - - - -
506C SER* 1.3 87.8 + - - +
508C PRO* 1.3 72.5 - - + +
510C LEU* 3.1 8.2 + - + +
511C PHE* 2.9 24.1 + - - +
579C VAL* 3.7 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 508 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C LEU* 4.1 4.0 - - + -
251C HIS* 3.7 31.2 - - + +
254C MET* 3.8 20.8 - - + +
504C TYR 3.2 22.9 - - - +
505C TYR* 3.3 12.8 - - - +
507C HIS* 1.3 97.5 - - + +
509C ARG* 1.3 54.9 + - - +
511C PHE* 3.5 2.9 + - + +
512C TRP* 2.9 28.6 + - - +
550C ILE* 3.6 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 509 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C TYR 3.0 17.9 + - - +
506C SER* 3.6 5.2 - - - +
507C HIS 3.2 0.2 - - - -
508C PRO* 1.3 72.9 - - - +
510C LEU* 1.3 65.3 + - - +
512C TRP* 3.2 3.8 + - + +
513C LEU* 2.9 52.2 + - + +
550C ILE* 3.1 33.6 + - + +
551C ASP* 2.6 34.5 + - + +
575C PRO* 3.9 20.6 - - - +
576C PRO* 3.5 29.3 + - + -
577C PRO 5.3 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 510 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C LEU* 4.3 9.0 - - + -
361C PRO* 3.9 29.2 - - + -
506C SER 2.9 16.7 + - - +
507C HIS* 3.1 8.3 + - + +
509C ARG* 1.3 76.4 - - - +
511C PHE* 1.3 59.3 + - - +
513C LEU* 3.5 6.3 + - - +
514C SER* 2.6 33.6 + - - -
579C VAL* 4.1 17.9 - - + -
582C LEU* 3.9 22.0 - - + +
583C LYS* 4.2 0.9 - - - +
584C LYS* 3.6 37.7 - - - +
585C ASP* 4.3 1.6 - - + +
588C LEU* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 511 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C HIS* 4.3 6.1 - - + +
254C MET* 3.6 40.6 - - + -
255C TRP* 3.3 51.6 - + - +
258C SER* 3.8 18.8 - - - -
260C ARG* 4.7 2.7 - - + -
507C HIS 2.9 14.8 + - - +
508C PRO 3.6 4.0 - - - +
510C LEU* 1.3 79.2 - - - +
512C TRP* 1.3 64.6 + - - +
514C SER* 3.3 3.6 + - - -
515C GLN* 2.7 51.7 + - - +
523C ILE* 3.8 16.6 - - + -
588C LEU* 3.6 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 512 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C MET* 3.9 20.9 - - + -
508C PRO 2.9 17.5 + - - +
509C ARG* 3.2 7.6 + - - +
511C PHE* 1.3 80.6 - - - +
513C LEU* 1.3 78.1 + - + +
514C SER 3.4 0.9 + - - -
515C GLN* 3.4 14.9 + - - +
520C GLN* 2.9 80.3 + - + +
523C ILE* 3.9 12.1 - - + -
524C VAL* 4.0 11.2 - - + -
550C ILE* 4.8 2.5 - - + -
551C ASP* 3.2 35.9 + - + -
553C THR* 4.9 9.8 - - + -
554C LEU* 3.7 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 513 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509C ARG* 2.9 60.1 + - + +
510C LEU* 4.1 4.0 - - - +
512C TRP* 1.3 93.5 - - + +
514C SER* 1.3 58.7 + - - +
515C GLN 3.3 6.3 + - - +
520C GLN* 4.2 6.6 + - - +
551C ASP* 4.6 2.5 - - - +
583C LYS* 3.4 34.5 - - + +
584C LYS* 4.1 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 514 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510C LEU 2.6 22.8 + - - -
511C PHE 3.6 6.1 - - - -
512C TRP 3.3 0.2 - - - -
513C LEU* 1.3 76.8 - - - +
515C GLN* 1.3 62.7 + - - +
584C LYS* 3.5 19.6 + - - +
585C ASP 2.9 41.9 + - - +
586C PRO* 4.6 1.4 - - - +
588C LEU* 3.7 15.8 - - - +
589C SER* 3.4 17.8 - - - -
592C ALA* 4.6 2.9 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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