Contacts of the helix formed by residues 610 - 625 (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 GLU 610 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261J THR* 4.4 14.6 + - - +
262J PRO 4.9 2.6 - - - +
264J ILE* 5.9 1.6 - - - +
277J SER 3.7 18.4 - - - +
280J SER* 2.8 31.8 + - - -
281J PHE* 3.7 16.4 - - + -
606L VAL* 3.8 8.7 - - + -
607L ASN* 3.2 36.6 + - + +
609L GLY* 1.3 70.7 - - - -
611L LYS* 1.3 64.8 + - - +
613L VAL* 3.1 11.4 - - - +
614L MET* 3.0 27.8 + - + +
655L ASN* 3.2 20.6 - - - +
658L LEU* 4.7 2.6 - - - +
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Residues in contact with LYS 611 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600L ILE* 3.8 34.3 - - + +
601L GLU* 3.5 29.1 + - - +
603L PHE 3.0 28.2 + - - -
606L VAL* 3.6 34.5 + - + +
607L ASN 3.2 11.4 + - - +
608L GLU* 3.2 16.4 - - - +
610L GLU* 1.3 77.0 - - - +
612L GLU* 1.3 58.9 + - - +
614L MET* 2.9 6.8 + - - +
615L LYS* 2.8 38.5 + - - +
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Residues in contact with GLU 612 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601L GLU* 5.0 1.2 - - - +
608L GLU 3.8 1.9 + - - +
609L GLY 3.7 16.0 - - - +
610L GLU 3.5 0.4 - - - -
611L LYS* 1.3 78.3 - - - +
613L VAL* 1.3 56.6 + - - +
615L LYS* 3.4 29.5 + - - +
616L LEU* 3.2 48.8 + - + +
650L LYS* 3.0 38.5 + - - +
652L LEU* 4.1 19.3 - - + -
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Residues in contact with VAL 613 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281J PHE* 4.0 16.8 - - + -
292J TYR* 5.5 0.4 - - - -
609L GLY 3.9 3.9 + - - +
610L GLU* 3.1 21.9 - - - +
612L GLU* 1.3 76.1 - - - +
614L MET* 1.3 65.2 + - - +
616L LEU* 4.3 4.0 - - + +
617L TRP* 3.1 24.1 + - - +
639L PHE* 4.6 14.6 - - + -
647L ILE* 5.3 3.6 - - + -
652L LEU* 4.6 11.6 - - + +
655L ASN* 3.9 24.7 - - + +
656L PHE* 4.1 28.3 - - + +
659L HIS* 4.4 10.3 + - + -
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Residues in contact with MET 614 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280J SER* 3.6 43.1 - - - +
281J PHE* 4.5 6.3 - - + +
284J LEU* 4.0 30.5 - - + -
292J TYR* 3.6 40.2 - - + -
600L ILE* 4.2 18.8 - - + -
603L PHE* 6.3 1.1 - - - -
606L VAL* 4.3 15.3 - - + -
610L GLU* 3.0 19.5 + - + +
611L LYS 2.9 7.2 + - - +
613L VAL* 1.3 78.7 - - + +
615L LYS* 1.3 52.9 + - - +
617L TRP* 3.4 1.6 - - - +
618L ASN* 2.8 41.2 + - - +
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Residues in contact with LYS 615 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596L THR* 5.5 1.1 - - - -
597L ILE* 3.4 46.0 - - + +
600L ILE* 3.3 31.1 - - + +
601L GLU* 3.3 32.7 + - - +
608L GLU 5.0 0.8 + - - -
611L LYS* 2.8 19.1 + - - +
612L GLU* 3.4 43.4 + - - +
614L MET* 1.3 73.3 - - - +
616L LEU* 1.3 59.3 + - + +
618L ASN* 3.0 8.3 + - - +
619L LEU* 2.8 42.0 + - + +
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Residues in contact with LEU 616 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612L GLU* 3.2 43.0 + - + +
613L VAL* 4.3 3.6 - - - +
615L LYS* 1.3 78.6 - - + +
617L TRP* 1.3 60.5 + - - +
619L LEU* 4.2 13.2 - - + -
620L HIS* 3.1 22.0 + - - +
639L PHE* 3.4 13.3 - - + -
643L TYR* 3.6 35.5 - - + -
646L LYS* 3.9 25.8 - - + +
647L ILE* 4.6 15.0 - - + +
650L LYS* 4.7 10.1 - - + +
652L LEU* 4.6 11.7 - - + -
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Residues in contact with TRP 617 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285J PHE* 4.3 3.2 - - - -
290J PHE 2.9 28.2 + - - -
292J TYR* 3.7 23.8 - + + -
613L VAL 3.1 19.0 + - - +
614L MET 3.4 3.4 - - - +
616L LEU* 1.3 73.6 - - - +
618L ASN* 1.3 56.6 + - - +
620L HIS* 2.7 28.3 + - - +
621L VAL* 2.8 37.3 + - + +
632L MET* 4.1 8.1 - - - -
635L ALA* 3.9 18.4 - - + -
636L CYS* 3.8 22.4 - - - -
639L PHE* 3.5 53.9 - + + -
659L HIS* 3.2 30.5 - + + -
663L MET* 3.7 20.0 - - + -
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Residues in contact with ASN 618 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291J LYS* 3.6 13.0 - - - +
292J TYR* 2.7 55.8 + - - +
293J ASP 4.3 1.2 + - - -
295J PHE* 5.8 0.2 - - - -
596L THR* 3.1 33.0 - - + +
600L ILE* 4.1 2.2 - - - +
614L MET 2.8 24.1 + - - +
615L LYS* 3.0 5.1 + - - +
617L TRP* 1.3 70.6 - - - +
619L LEU* 1.3 62.3 + - + +
621L VAL* 3.2 10.0 - - - +
622L MET* 3.0 34.9 + - + +
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Residues in contact with LEU 619 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593L ARG* 3.4 45.6 - - + +
596L THR* 6.4 1.3 - - - -
597L ILE* 4.1 28.7 - - + -
615L LYS* 2.8 31.1 + - + +
616L LEU* 3.8 20.0 - - + +
618L ASN* 1.3 73.2 - - - +
620L HIS* 1.3 51.9 + - - +
622L MET* 3.1 8.9 + - - +
623L LYS* 2.8 35.7 + - - +
643L TYR* 4.0 15.9 - - + +
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Residues in contact with HIS 620 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616L LEU 3.1 11.9 + - - +
617L TRP* 2.7 20.7 + - - +
619L LEU* 1.3 73.9 - - - +
621L VAL* 1.3 63.6 + - - +
623L LYS* 3.0 14.5 + - - +
624L HIS* 3.1 50.2 + + - +
626L PHE* 4.0 20.7 - + - -
635L ALA 3.3 26.5 + - - -
638L LEU* 3.7 18.1 + - + +
639L PHE* 3.8 28.6 + + + +
642L ASN* 4.4 2.2 + - - -
643L TYR* 3.9 27.1 + + + -
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Residues in contact with VAL 621 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289J CYS 5.2 1.1 - - - +
290J PHE* 4.3 15.9 - - + +
291J LYS* 3.8 30.2 - - + -
617L TRP* 2.8 55.0 + - + +
618L ASN* 3.2 23.1 - - - +
620L HIS* 1.3 73.4 - - - +
622L MET* 1.3 52.3 + - - +
625L GLY* 2.7 33.4 + - - -
626L PHE* 3.7 28.2 + - + +
632L MET* 4.9 0.2 - - + -
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Residues in contact with MET 622 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291J LYS* 3.7 34.5 - - + +
295J PHE* 4.1 4.3 - - + -
588L ASP* 2.7 27.7 - - - +
592L LEU* 3.6 27.8 - - + -
593L ARG* 4.5 19.7 - - + -
596L THR* 3.0 33.7 - - + +
618L ASN* 3.0 32.6 + - + +
619L LEU* 3.1 7.4 + - - +
621L VAL* 1.3 73.3 - - - +
623L LYS* 1.3 63.4 + - - +
624L HIS 3.6 0.2 + - - -
625L GLY* 3.9 7.3 + - - -
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Residues in contact with LYS 623 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588L ASP* 3.7 8.3 + - - +
593L ARG* 5.4 14.8 - - - +
619L LEU 2.8 13.8 + - - +
620L HIS* 3.0 10.7 + - - +
622L MET* 1.3 79.0 - - - +
624L HIS* 1.3 78.6 + - + +
642L ASN* 5.6 1.3 - - - +
643L TYR* 3.8 22.7 - - + +
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Residues in contact with HIS 624 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597J LYS* 5.1 7.1 + - - -
620L HIS* 3.1 43.2 + + - -
623L LYS* 1.3 94.7 - - + +
625L GLY* 1.3 63.9 + - - +
626L PHE* 3.2 33.9 + + + -
638L LEU* 4.1 19.2 - - + +
642L ASN* 3.8 17.0 + - - -
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Residues in contact with GLY 625 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597J LYS* 5.2 6.6 + - - -
621L VAL 2.7 21.2 + - - -
622L MET* 4.2 8.3 - - - -
623L LYS 3.6 1.4 - - - -
624L HIS* 1.3 75.7 - - - +
626L PHE* 1.3 65.3 + - - +
627L ILE* 3.5 12.8 + - - +
631L GLN* 5.0 0.7 + - - -
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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
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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) + - + + + + + -
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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