Contacts of the helix formed by residues 671 - 683 (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 ILE 671 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308J ARG* 4.5 2.5 - - - +
312J GLU 5.6 6.3 - - - +
446J THR* 3.1 29.2 - - - +
447J TYR* 4.1 33.8 + - + +
664L HIS* 3.5 24.4 + - + +
670L SER* 1.3 68.8 - - - +
672L MET* 1.3 73.2 + - + +
673L SER 3.0 2.7 - - - -
674L ILE* 3.0 36.2 + - + +
675L ASP* 3.7 3.8 + - - +
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Residues in contact with MET 672 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670L SER* 3.3 17.2 - - - +
671L ILE* 1.3 86.2 - - + +
673L SER* 1.3 56.3 + - - +
675L ASP* 3.6 8.6 + - - +
676L LYS* 3.0 28.7 + - - +
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Residues in contact with SER 673 (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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633L ASN* 2.7 41.1 + - - +
636L CYS* 5.9 3.8 - - - -
637L MET* 6.1 0.9 - - - +
660L LEU* 5.3 0.6 - - - +
669L ILE* 4.6 10.8 - - - -
670L SER* 3.3 9.2 + - - -
671L ILE 3.0 1.2 - - - -
672L MET* 1.3 76.8 - - - +
674L ILE* 1.3 59.7 + - - +
675L ASP 3.3 0.2 - - - -
676L LYS* 3.7 13.2 - - - +
677L ALA* 2.8 33.5 + - - +
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Residues in contact with ILE 674 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443J LEU* 5.5 0.7 - - + -
446J THR* 5.7 2.7 - - + +
447J TYR* 4.2 9.0 - - + +
457J LEU* 3.9 19.9 - - + +
657L MET* 5.2 3.6 - - + +
660L LEU* 4.1 29.2 - - + +
661L VAL* 5.1 12.1 - - + +
664L HIS* 3.5 26.0 - - + -
669L ILE* 3.8 16.4 - - + -
670L SER 3.6 5.2 - - - +
671L ILE* 3.0 44.0 + - + +
673L SER* 1.3 73.8 - - - +
675L ASP* 1.3 63.8 + - - +
678L VAL* 3.0 39.7 + - + +
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Residues in contact with ASP 675 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447J TYR* 3.9 9.0 + - - +
453J ALA* 4.3 11.8 - - - +
456J ARG* 3.1 32.0 + - - +
457J LEU* 3.0 30.1 - - - +
671L ILE 3.7 2.9 + - - +
672L MET* 3.6 11.4 + - - +
674L ILE* 1.3 78.6 - - - +
676L LYS* 1.3 57.4 + - - +
677L ALA 3.2 0.2 + - - -
678L VAL* 3.2 3.6 + - - +
679L THR* 2.9 35.1 + - - -
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Residues in contact with LYS 676 (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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637L MET* 3.8 31.4 - - + +
672L MET 3.0 19.0 + - - +
673L SER* 4.0 13.0 - - - +
674L ILE 3.5 0.2 - - - -
675L ASP* 1.3 76.6 - - - +
677L ALA* 1.3 60.2 + - - +
679L THR* 3.6 8.2 - - - -
680L LYS* 3.3 33.2 + - + +
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Residues in contact with ALA 677 (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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636L CYS* 4.7 16.6 - - + +
637L MET* 5.2 4.5 - - + +
640L VAL* 4.4 7.0 - - + +
656L PHE* 4.6 7.2 - - + -
660L LEU* 4.1 26.5 - - + -
673L SER* 2.8 23.1 + - - +
676L LYS* 1.3 70.3 - - - +
678L VAL* 1.3 65.8 + - - +
679L THR 3.1 1.3 - - - -
680L LYS* 3.1 11.1 + - - +
681L LEU* 3.0 22.7 + - - +
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Residues in contact with VAL 678 (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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457J LEU* 4.7 11.2 - - + +
656L PHE* 5.2 3.1 - - + -
657L MET* 3.6 48.5 - - + -
660L LEU* 4.0 15.5 - - + -
674L ILE* 3.0 27.6 + - + +
675L ASP 3.9 2.5 - - - +
677L ALA* 1.3 75.1 - - - +
679L THR* 1.3 61.2 + - - +
681L LEU* 3.5 7.3 + - + +
682L ARG* 3.2 53.0 + - + +
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Residues in contact with THR 679 (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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456J ARG* 3.7 24.5 + - - +
675L ASP* 2.9 20.3 + - - -
676L LYS* 3.6 12.1 - - - +
678L VAL* 1.3 73.3 - - - +
680L LYS* 1.3 58.8 + - + +
682L ARG* 3.0 6.3 + - - +
683L GLU* 2.6 52.8 + - + +
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Residues in contact with LYS 680 (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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637L MET* 3.8 28.4 - - + +
640L VAL* 3.9 13.2 - - + -
641L GLU* 3.3 39.8 + - - +
676L LYS* 3.3 20.8 + - + +
677L ALA* 3.1 9.2 + - - +
679L THR* 1.3 79.6 - - + +
681L LEU* 1.3 59.4 + - - +
683L GLU* 4.1 17.5 + - - +
684L MET* 3.4 31.9 + - + +
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Residues in contact with LEU 681 (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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640L VAL* 4.4 16.8 - - + +
644L GLY* 3.9 33.0 - - - +
647L ILE* 4.5 9.9 - - + -
648L ILE* 3.8 13.6 - - + +
653L CYS* 4.3 28.7 - - + +
656L PHE* 3.9 20.6 - - + -
657L MET* 5.2 6.3 - - + -
677L ALA 3.0 12.3 + - - +
678L VAL* 3.6 10.3 - - - +
679L THR 3.1 0.2 - - - -
680L LYS* 1.3 76.8 - - - +
682L ARG* 1.3 70.3 + - + +
683L GLU 3.3 0.2 - - - -
684L MET* 3.2 29.9 + - + +
685L GLN* 3.7 5.7 - - - +
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Residues in contact with ARG 682 (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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456J ARG* 2.6 30.9 + - - +
457J LEU* 3.4 20.2 + - - +
458J ILE 4.0 2.8 + - - -
459J GLY* 3.6 18.4 - - - -
653L CYS* 6.5 0.7 - - + -
657L MET* 4.6 7.4 - - - +
678L VAL* 3.2 35.6 + - + +
679L THR* 3.0 6.2 + - - +
681L LEU* 1.3 82.5 - - + +
683L GLU* 1.3 62.2 - - - +
684L MET 3.2 0.7 - - - -
685L GLN* 3.0 43.2 + - - +
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Residues in contact with GLU 683 (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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679L THR* 2.6 36.5 + - + +
680L LYS* 4.1 17.7 + - - +
682L ARG* 1.3 73.5 - - - +
684L MET* 1.3 55.8 + - - +
685L GLN 3.3 4.7 + - - +
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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
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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