Contacts of the helix formed by residues 597 - 604 (chain T) in PDB entry 5MQF
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 597 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591T CYS 5.2 0.2 - - - +
595T GLY* 3.4 5.2 - - - +
596T LEU* 1.3 92.5 - - + +
598T LYS* 1.3 58.2 + - + +
600T ASN* 4.6 1.5 - - + +
601T ALA* 2.8 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 598 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594T MET 5.6 0.9 - - - +
595T GLY* 2.9 12.4 + - - +
597T PRO* 1.3 77.6 - - + +
599T LEU* 1.3 56.7 + - - +
601T ALA* 4.5 1.8 - - - -
602T ARG* 2.6 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 599 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590T LEU 5.4 0.4 - - - +
591T CYS* 6.1 0.2 - - - -
594T MET* 3.7 22.0 + - + +
595T GLY 2.5 19.8 + - - +
596T LEU* 3.7 10.3 - - - +
598T LYS* 1.3 73.9 - - - +
600T ASN* 1.3 51.5 + - - +
602T ARG* 4.8 0.7 - - - -
603T LEU* 2.6 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 600 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596T LEU* 2.6 21.4 + - + +
597T PRO* 4.6 1.3 - - + +
599T LEU* 1.3 72.8 - - - +
601T ALA* 1.3 59.1 + - - +
603T LEU* 3.7 4.3 - - - +
604T LYS* 2.9 30.0 + - - +
639T LEU* 4.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 601 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597T PRO 2.8 22.5 + - - +
598T LYS* 4.5 2.0 - - - -
600T ASN* 1.3 78.3 - - - +
602T ARG* 1.3 60.1 + - - +
604T LYS* 3.4 17.4 + - - +
605T ASP* 3.8 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 602 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598T LYS* 2.6 25.8 + - + +
599T LEU* 4.6 0.9 - - - +
601T ALA* 1.3 77.4 - - - +
603T LEU* 1.3 61.0 + - - +
604T LYS 3.5 0.2 + - - -
605T ASP* 3.5 6.4 + - - +
606T GLU* 3.4 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 603 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599T LEU 2.6 24.7 + - - +
600T ASN* 3.8 5.8 - - - +
601T ALA 3.3 0.4 - - - -
602T ARG* 1.3 76.1 - - - +
604T LYS* 1.3 63.9 + - - +
605T ASP 3.3 0.2 - - - -
606T GLU* 3.4 18.8 + - + +
608T LEU* 4.0 21.0 + - + +
609T GLN* 4.4 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 604 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600T ASN 2.9 16.4 + - - +
601T ALA* 3.6 10.3 - - - +
602T ARG 3.3 0.4 - - - -
603T LEU* 1.3 78.8 - - - +
605T ASP* 1.3 58.3 + - - +
606T GLU 3.7 0.2 + - - -
607T THR* 4.2 6.2 + - - -
609T GLN* 5.5 7.9 - - - +
610T PRO* 5.5 4.0 - - - +
----------------------------------------------------------
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