Contacts of the helix formed by residues 619 - 628 (chain F) in PDB entry 5JLH
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 ASN 619 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414F ALA 3.8 9.9 + - - -
415F LEU* 3.5 29.1 + - - +
418F PRO* 4.0 10.8 - - + +
431F GLN* 3.1 27.7 + - - +
439F ALA* 4.1 21.2 - - + +
443F LEU* 5.5 2.8 - - + +
617F PRO* 4.2 1.9 + - - +
618F LEU* 1.3 80.1 - - - +
620F ASP* 1.3 63.7 + - - +
621F ASN 4.2 2.0 - - - +
622F VAL* 4.0 20.3 - - + +
623F ALA* 3.1 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 620 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 5.8 4.3 - - - +
419F ARG 5.7 2.7 - - - +
420F ILE* 6.4 2.0 - - + -
618F LEU* 3.4 12.0 + - - +
619F ASN* 1.3 71.3 - - - +
621F ASN* 1.3 60.2 + - - +
623F ALA* 3.6 7.8 - - - +
624F ALA* 2.8 29.1 + - - +
664F ARG* 4.9 6.8 - - - +
665F GLY* 4.3 14.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 621 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414F ALA* 3.5 30.4 - - + +
417F THR 5.0 0.6 + - - -
418F PRO* 4.0 10.9 - - + +
419F ARG* 3.6 55.0 + - - +
619F ASN* 3.2 1.0 - - + +
620F ASP* 1.3 76.5 - - - +
622F VAL* 1.3 66.3 + - + +
624F ALA* 3.2 8.8 + - - +
625F LEU* 3.0 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 622 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406F LEU* 4.9 4.7 - - + -
411F PHE* 4.0 20.6 - - + -
414F ALA* 3.6 34.1 - - + +
415F LEU* 3.8 14.6 - - + +
443F LEU* 3.4 33.7 - - + -
619F ASN* 3.6 17.4 + - + +
621F ASN* 1.3 72.5 - - - +
623F ALA* 1.3 65.0 + - - +
625F LEU* 3.0 18.7 + - + +
626F LEU* 3.0 20.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 623 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443F LEU* 4.9 3.0 - - - +
618F LEU* 5.0 10.8 - - + -
619F ASN 3.1 19.1 + - - +
620F ASP* 3.6 10.8 - - - +
622F VAL* 1.3 77.9 - - - +
624F ALA* 1.3 56.0 + - - +
626F LEU* 3.2 14.4 + - - +
627F HIS* 2.9 27.0 + - - +
638F TRP* 4.7 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 624 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620F ASP 2.8 15.7 + - - +
621F ASN* 3.3 14.8 - - - +
623F ALA* 1.3 74.9 - - - +
625F LEU* 1.3 64.3 + - + +
627F HIS* 3.0 20.1 + - - +
628F GLN* 3.1 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 625 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406F LEU* 3.6 25.8 - - + +
410F ASP* 3.9 25.4 - - + +
411F PHE* 3.9 15.0 - - + -
414F ALA* 3.5 31.0 - - + -
621F ASN* 3.0 22.6 + - - +
622F VAL* 3.0 13.7 + - + +
624F ALA* 1.3 77.7 - - + +
626F LEU* 1.3 57.6 - - - +
628F GLN* 2.9 35.8 + - - +
629F SER 3.2 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 626 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375F PHE* 5.8 4.3 - - + -
404F LEU* 3.9 22.4 - - + -
406F LEU* 3.8 25.8 - - + -
443F LEU* 4.2 17.0 - - + -
447F THR* 4.7 3.6 - - - +
622F VAL* 3.0 19.0 + - + +
623F ALA* 3.2 9.4 + - - +
625F LEU* 1.3 74.5 - - - +
627F HIS* 1.3 58.0 + - - +
629F SER* 2.5 35.9 + - - +
634F THR* 4.6 3.7 - - - +
635F ALA* 3.6 9.5 - - - -
638F TRP* 3.2 55.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 627 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623F ALA 2.9 12.4 + - - +
624F ALA* 3.0 14.8 + - - +
626F LEU* 1.3 76.2 - - - +
628F GLN* 1.3 62.3 + - + +
629F SER 3.8 0.3 + - - -
635F ALA* 4.3 13.9 + - - +
638F TRP* 3.2 31.8 + - - +
639F LYS* 4.1 23.5 - - + -
640F ASP 4.7 9.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 628 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405F GLY 5.7 0.2 - - - +
624F ALA* 3.5 20.6 + - - +
625F LEU* 2.9 29.5 + - - +
627F HIS* 1.3 83.6 - - + +
629F SER* 1.3 67.3 + - - +
630F THR* 3.5 1.6 + - - -
----------------------------------------------------------
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