Contacts of the helix formed by residues 477 - 485 (chain C) in PDB entry 3GJN
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 PRO 477 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458C LYS 3.3 7.4 - - - +
460C VAL* 4.0 11.9 - - + -
464C TRP* 3.7 32.3 - - + +
475C PRO 3.4 5.8 - - - +
476C VAL* 1.4 90.0 - - + +
478C ASP* 1.3 65.9 + - - +
479C ARG* 4.4 4.0 - - + +
480C ILE* 3.2 29.9 + - + +
481C ALA* 3.1 20.8 + - - +
499C PHE* 4.2 6.3 - - + -
509C LEU* 3.7 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 478 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456C LYS 3.4 22.2 - - - +
457C GLY 4.4 0.7 - - - +
458C LYS* 2.6 24.9 + - - +
459C PRO* 3.6 28.9 - - - +
477C PRO* 1.3 70.8 - - - +
479C ARG* 1.3 74.1 + - - +
481C ALA* 3.2 2.6 - - - +
482C ASN* 2.9 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 479 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1058A GLU* 6.3 0.4 - - - +
1059A GLY* 5.4 12.3 - - - +
460C VAL* 5.0 17.8 + - - +
477C PRO* 3.2 3.9 - - + +
478C ASP* 1.3 93.2 + - - +
480C ILE* 1.4 57.2 + - + +
482C ASN* 3.2 16.8 - - - +
483C LYS* 3.1 40.1 + - - +
506C ASP* 3.2 29.3 + - - +
507C PRO* 6.0 2.1 - - - +
508C GLU* 2.9 44.7 - - - +
509C LEU* 5.2 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 480 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C VAL* 4.6 1.6 - - + -
477C PRO* 3.2 22.6 + - + +
479C ARG* 1.4 73.0 - - - +
481C ALA* 1.3 56.4 + - - +
483C LYS* 3.0 10.0 + - + +
484C LEU* 2.8 54.1 + - + +
499C PHE* 4.0 19.5 - - + +
502C GLU* 3.8 32.5 - - + +
503C VAL* 4.1 5.6 - - + -
506C ASP* 3.7 21.3 - - + +
509C LEU* 3.1 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 481 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C GLY 3.7 8.1 - - - +
456C LYS 3.3 30.3 - - - +
457C GLY* 4.0 3.4 - - - +
476C VAL* 4.1 3.7 - - + +
477C PRO 3.1 10.8 + - - +
478C ASP 3.2 10.1 - - - +
480C ILE* 1.3 69.8 - - - +
482C ASN* 1.3 67.4 + - - +
484C LEU 2.8 14.0 + - - -
485C ARG* 3.0 18.2 + - - +
558C MET* 3.6 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 482 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061A ASP* 3.8 40.2 + - - +
1063A SER* 3.6 15.3 - - - +
478C ASP* 2.9 26.7 + - - +
479C ARG* 3.2 19.8 - - - +
481C ALA* 1.3 70.8 - - - +
483C LYS* 1.3 64.9 + - - +
484C LEU 3.3 0.2 + - - -
485C ARG* 3.4 39.6 + - - +
486C ASP* 4.0 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 483 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062A ASP* 2.5 47.6 + - - +
1063A SER* 3.9 18.1 - - - +
1064A PRO* 5.2 4.4 - - + +
515B ARG* 3.8 29.1 - - + +
479C ARG* 3.1 34.0 + - - +
480C ILE* 3.0 14.7 + - + +
482C ASN* 1.3 78.7 - - - +
484C LEU* 1.3 59.2 + - - +
486C ASP* 3.7 10.0 + - - +
487C LYS* 3.3 22.5 + - - +
502C GLU* 3.3 32.5 - - + +
506C ASP* 5.3 4.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 484 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453C ALA* 4.3 2.2 - - + -
476C VAL* 5.6 0.2 - - + -
480C ILE* 2.8 24.7 + - + +
481C ALA 2.8 8.8 + - - +
483C LYS* 1.3 71.4 - - - +
485C ARG* 1.3 59.3 + - - +
486C ASP 3.1 5.2 - - - -
487C LYS* 3.0 45.6 + - + +
489C PHE* 3.1 24.4 - - + -
495C PHE* 3.7 25.4 - - + -
498C LYS* 3.8 27.6 - - + +
499C PHE* 3.8 31.2 - - + +
502C GLU* 4.2 4.3 - - + -
558C MET* 4.0 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 485 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061A ASP* 5.2 3.4 + - - -
1065A SER* 6.3 1.2 - - - -
452C LYS* 5.2 9.7 - - - +
453C ALA* 3.1 27.9 - - - +
454C THR* 4.7 1.1 - - - +
455C GLY 3.0 32.0 + - - +
456C LYS* 3.8 19.6 + - - +
481C ALA* 3.0 12.2 + - - +
482C ASN* 3.4 44.5 + - - +
484C LEU* 1.3 75.2 - - - +
486C ASP* 1.3 60.6 + - - +
487C LYS 3.2 4.3 + - - -
558C MET* 4.2 4.1 - - + +
----------------------------------------------------------
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