Contacts of the helix formed by residues 589 - 602 (chain L) in PDB entry 5LS6
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 589 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115J PRO* 4.0 15.9 - - + +
116J LEU* 5.1 1.3 - - + -
117J GLN* 3.8 31.9 - - + +
118J GLN* 5.7 3.6 - - - +
587L LYS* 4.3 7.2 - - + -
588L ASP* 1.4 90.5 - - - +
590L GLU* 1.3 69.1 + - + +
591L TRP* 3.2 30.3 - - + +
592L LEU* 3.0 33.8 + - + +
593L ARG* 3.5 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 590 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115J PRO* 5.9 3.1 - - + -
269K ARG* 4.3 11.1 + - - +
292K GLN* 5.0 1.2 - - - +
293K LYS* 2.9 39.7 + - - +
295K HIS* 3.3 20.5 + - - +
588L ASP 2.9 9.0 + - - -
589L PRO* 1.3 72.8 - - + +
591L TRP* 1.3 66.0 + - + +
592L LEU 3.4 0.2 + - - -
593L ARG* 3.4 29.7 + - - +
594L GLU* 3.5 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 591 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114J SER* 4.2 9.6 - - - -
115J PRO* 2.6 49.4 + - + +
116J LEU* 3.5 19.3 - - + -
120J PHE* 3.5 32.1 - + - -
680J LYS* 4.1 13.2 - - + -
232K VAL* 3.4 22.4 - - + -
295K HIS* 3.6 36.8 - + + -
296K PHE* 3.8 14.1 - + + -
589L PRO* 3.4 17.1 - - + +
590L GLU* 1.3 81.8 - - + +
592L LEU* 1.3 87.7 + - + +
594L GLU* 3.2 7.8 + - - +
595L LYS* 3.0 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 592 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J LEU* 5.3 2.5 - - + -
118J GLN* 5.9 4.0 - - - +
120J PHE* 3.6 32.5 - - + -
291J LYS* 6.1 0.4 - - - -
295J PHE* 3.7 26.2 - - + -
588L ASP* 5.1 2.9 - - - +
589L PRO* 3.0 30.1 + - + +
591L TRP* 1.3 92.8 - - + +
593L ARG* 1.3 66.1 - - - +
595L LYS* 3.2 11.5 + - + +
596L THR* 3.2 16.6 + - - -
622L MET* 3.6 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 593 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588L ASP* 3.4 50.6 + - - +
589L PRO 3.5 1.4 + - - +
590L GLU* 3.4 28.2 + - - +
591L TRP 3.3 0.4 - - - -
592L LEU* 1.3 79.8 - - - +
594L GLU* 1.3 62.8 + - + +
596L THR* 3.3 2.1 + - - -
597L ILE* 3.1 32.5 + - + +
619L LEU* 3.4 35.6 - - + +
622L MET* 4.5 15.9 - - + -
623L LYS* 5.4 17.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 594 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269K ARG* 5.9 3.8 + - - +
296K PHE* 3.5 28.4 - - + +
590L GLU 3.5 8.4 + - - +
591L TRP* 3.2 11.8 + - - +
593L ARG* 1.3 78.0 - - - +
595L LYS* 1.3 50.4 + - - +
597L ILE* 3.3 15.3 + - + +
598L THR* 2.8 53.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 595 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120J PHE* 5.1 8.0 - - + -
295J PHE* 4.0 16.4 - - + -
232K VAL* 4.2 19.5 - - + +
233K GLU* 4.4 12.8 + - - -
296K PHE* 4.4 15.7 - - + -
591L TRP* 3.0 30.4 + - + +
592L LEU* 3.2 13.7 + - + +
594L GLU* 1.3 71.4 - - - +
596L THR* 1.3 60.8 + - - +
598L THR* 2.7 23.7 + - - +
599L GLN* 2.8 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 596 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292J TYR 4.6 1.3 - - - +
293J ASP 4.9 2.2 - - - +
295J PHE* 3.0 22.0 - - + -
592L LEU 3.2 5.7 + - - -
593L ARG 3.8 4.9 - - - -
595L LYS* 1.3 74.2 - - - +
597L ILE* 1.3 60.1 + - + +
599L GLN* 2.8 8.7 + - + -
600L ILE* 2.7 48.5 + - + +
615L LYS* 5.5 1.3 - - - -
618L ASN* 3.1 40.4 - - + +
619L LEU* 6.4 1.6 - - - -
622L MET* 3.0 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 597 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593L ARG* 3.1 28.3 + - + +
594L GLU* 3.6 15.9 - - + +
596L THR* 1.3 78.8 - - - +
598L THR* 1.3 63.5 + - + +
601L GLU* 3.5 14.6 + - + +
615L LYS* 3.4 38.9 - - + +
619L LEU* 4.1 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 598 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296K PHE* 5.8 8.8 - - + -
345K PRO* 6.5 0.9 - - + -
594L GLU* 2.8 33.5 + - + +
595L LYS* 2.7 29.2 + - - +
597L ILE* 1.3 77.8 - - + +
599L GLN* 1.3 51.8 + - - +
601L GLU* 3.0 10.5 + - - +
602L GLU* 2.8 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 599 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293J ASP* 3.5 25.8 - - - +
294J CYS 5.4 0.5 - - - +
295J PHE* 3.3 29.3 - - - -
595L LYS* 2.8 42.7 + - - +
596L THR* 2.8 10.4 + - - +
598L THR* 1.3 71.0 + - - +
600L ILE* 1.3 61.5 + - + +
602L GLU* 3.4 21.7 - - + +
603L PHE* 3.3 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 600 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284J LEU* 4.9 1.6 - - + -
292J TYR* 3.7 27.4 - - + +
293J ASP* 4.5 9.6 - - + -
596L THR* 2.7 35.6 + - + +
599L GLN* 1.3 71.6 - - + +
601L GLU* 1.3 62.9 + - - +
602L GLU 3.3 0.5 + - - -
603L PHE* 3.4 21.9 + - + +
606L VAL* 5.5 0.2 - - - +
611L LYS* 3.7 34.9 - - + +
614L MET* 4.2 23.8 - - + -
615L LYS* 3.3 34.1 - - + -
618L ASN* 4.1 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 601 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597L ILE* 3.5 11.7 + - + +
598L THR* 3.0 13.3 + - - +
600L ILE* 1.3 78.6 - - - +
602L GLU* 1.3 60.1 + - - +
603L PHE 3.2 1.2 + - - +
608L GLU 4.8 6.4 - - - +
611L LYS* 3.5 29.4 + - - +
612L GLU* 5.0 1.0 - - - +
615L LYS* 3.3 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 602 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346K SER* 5.2 14.1 - - - -
598L THR* 2.8 27.3 + - - +
599L GLN* 3.4 25.1 - - + +
600L ILE 3.2 0.4 - - - -
601L GLU* 1.3 74.0 - - - +
603L PHE* 1.3 57.1 + - + +
604L SER* 3.1 8.8 + - - -
----------------------------------------------------------
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