Contacts of the helix formed by residues 485 - 492 (chain A) in PDB entry 1GPU
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 GLU 485 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ASN* 4.5 0.7 - - - +
447A SER* 4.6 8.6 + - - +
484A ILE* 1.3 76.1 + - - +
486A THR* 1.3 68.7 + - - +
487A LEU 3.5 1.6 - - - -
488A ALA* 3.3 5.7 + - - +
489A HIS* 2.9 27.0 + - - +
619A ALA* 4.4 1.1 - - - -
454B ARG* 2.9 48.3 + - - +
489B HIS* 4.1 24.7 + - + +
492B SER* 3.4 37.7 - - - +
493B LEU* 3.5 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LEU* 3.5 42.4 - - + +
444A ASN* 4.0 8.0 + - - -
447A SER* 3.9 16.5 + - - +
483A PRO* 3.3 31.5 - - - +
484A ILE 3.5 1.6 + - - -
485A GLU* 1.3 84.7 + - - +
487A LEU* 1.3 63.0 + - - +
489A HIS* 3.3 4.9 - - - +
490A PHE* 3.3 42.9 + - + -
618A LEU* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LEU* 4.0 26.5 - - + -
484A ILE 5.0 0.2 + - - -
485A GLU 3.5 0.2 - - - -
486A THR* 1.3 75.2 - - - +
488A ALA* 1.3 61.0 + - - +
489A HIS 3.2 0.2 + - - -
490A PHE* 3.3 3.2 + - + +
491A ARG* 2.8 64.7 + - - +
498A VAL* 3.5 25.1 - - + +
500A ARG* 3.6 32.1 - - + +
523A ILE* 5.4 1.3 - - + -
525A ALA* 4.3 10.8 - - + -
616A GLU* 3.9 3.1 - - - +
618A LEU* 3.9 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ILE 5.2 0.8 + - - +
485A GLU 3.3 11.0 + - - +
487A LEU* 1.3 77.1 - - - +
489A HIS* 1.3 58.7 + - - +
491A ARG* 3.4 2.4 + - - +
492A SER* 2.7 33.8 + - - -
619A ALA* 4.5 7.6 - - + -
621A THR* 3.6 12.1 - - - +
622A CYS* 3.7 26.8 - - + +
489B HIS* 5.4 0.4 - - - -
492B SER* 3.4 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A SER* 4.9 7.8 + - - -
450A ALA* 4.1 19.3 - - + +
485A GLU 2.9 13.5 + - - +
486A THR* 3.3 11.8 - - - +
488A ALA* 1.3 75.7 - - - +
490A PHE* 1.3 92.9 + + - +
492A SER* 3.1 22.5 + - - -
493A LEU* 3.4 5.7 + - + +
447B SER* 5.6 3.6 + - - -
485B GLU* 4.1 20.8 + - + +
489B HIS* 3.4 63.6 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LEU* 5.7 0.7 - - + -
446A VAL* 4.0 30.7 - - + -
447A SER* 4.8 5.2 - - - -
450A ALA* 4.8 6.3 - - + -
453A VAL* 3.5 33.7 - - + -
454A ARG 5.7 0.2 - - - -
486A THR* 3.3 39.1 + - + +
487A LEU* 4.2 1.6 - - + +
489A HIS* 1.3 107.9 - + - +
491A ARG* 1.3 64.5 + - - +
492A SER 3.1 1.8 - - - -
493A LEU* 3.1 22.9 + - + +
496A ILE* 3.1 27.9 - - + +
498A VAL* 3.9 19.3 - - + -
523A ILE* 3.4 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A LEU* 2.8 46.9 + - - +
488A ALA* 3.8 5.4 - - - +
490A PHE* 1.3 76.9 - - - +
492A SER* 1.3 60.1 + - - +
493A LEU 3.3 4.0 - - - +
496A ILE 5.7 0.7 - - - -
498A VAL* 4.2 28.4 + - + +
500A ARG* 4.9 4.0 - - - +
562A THR* 4.0 8.1 + - - +
588A LEU 5.1 0.6 + - - -
589A PRO 5.7 0.8 + - - -
591A PHE* 3.6 60.7 - - + +
616A GLU* 2.9 42.2 + - - -
622A CYS* 3.6 25.9 - - + -
623A TRP* 3.9 0.2 - - - +
625A LYS* 5.2 5.4 + - - -
621B THR* 3.8 11.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A ALA 2.7 17.0 + - - -
489A HIS* 3.1 10.9 + - - -
490A PHE 3.1 0.6 - - - -
491A ARG* 1.3 77.5 - - - +
493A LEU* 1.3 59.2 + - - +
494A PRO* 3.6 7.6 - - - +
622A CYS* 5.2 1.2 - - - +
484B ILE* 4.4 0.2 - - - +
485B GLU* 3.3 17.8 + - - +
488B ALA* 3.5 21.6 - - - +
492B SER* 5.5 0.5 + - - -
619B ALA* 3.8 13.4 - - - +
621B THR* 2.5 37.6 + - - +
634B ASP* 5.2 1.2 - - - +
----------------------------------------------------------
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