Contacts of the helix formed by residues 670 - 683 (chain F) 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 SER 670 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308D ARG* 4.4 8.1 - - - +
633F ASN* 3.6 11.9 + - - +
664F HIS* 3.7 0.4 - - - -
669F ILE* 1.3 76.1 - - - +
671F ILE* 1.3 66.1 + - - +
672F MET* 3.4 32.0 + - - +
673F SER* 2.9 27.5 + - - -
674F ILE* 3.9 4.7 - - - +
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Residues in contact with ILE 671 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D ARG* 4.8 1.0 - - - +
312D GLU 5.2 10.8 - - - +
446D THR* 3.1 30.1 - - - +
447D TYR* 3.3 50.2 + - + -
664F HIS* 3.3 24.4 + - + +
670F SER* 1.3 72.4 - - - +
672F MET* 1.3 68.8 + - + +
674F ILE* 3.1 29.0 + - + +
675F ASP 3.8 0.5 + - - -
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Residues in contact with MET 672 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670F SER* 3.1 16.8 - - - +
671F ILE* 1.3 83.7 - - + +
673F SER* 1.3 59.5 + - - +
675F ASP* 3.6 6.7 + - - +
676F LYS* 2.9 31.8 + - + +
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Residues in contact with SER 673 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633F ASN* 2.6 36.1 + - - +
636F CYS* 5.5 6.1 - - - -
637F MET* 5.8 6.6 - - - -
660F LEU* 4.7 0.8 - - - +
669F ILE* 4.3 15.5 - - - -
670F SER* 2.9 14.3 + - - -
672F MET* 1.3 77.1 - - - +
674F ILE* 1.3 58.2 + - - +
676F LYS* 4.1 9.4 - - - +
677F ALA* 2.9 34.2 + - - +
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Residues in contact with ILE 674 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446D THR* 5.3 2.7 - - + +
447D TYR* 3.6 9.0 - - + +
457D LEU* 3.5 26.0 - - + -
657F MET* 4.8 6.7 - - + -
660F LEU* 3.9 37.9 - - + +
661F VAL* 4.6 10.5 - - + +
664F HIS* 3.7 27.4 - - + -
669F ILE* 4.2 3.1 - - + -
670F SER 3.9 2.9 - - - +
671F ILE* 3.1 42.1 + - + +
673F SER* 1.3 77.8 - - - +
675F ASP* 1.3 58.7 + - - +
678F VAL* 3.0 39.3 + - + +
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Residues in contact with ASP 675 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447D TYR* 3.8 10.7 + - + +
453D ALA* 6.1 1.6 - - + -
456D ARG* 3.2 36.7 + - - +
457D LEU* 3.0 31.9 - - + +
671F ILE 3.8 0.4 + - - +
672F MET* 3.6 8.4 + - - +
674F ILE* 1.3 78.2 - - - +
676F LYS* 1.3 59.5 + - - +
678F VAL* 3.3 1.8 + - - +
679F THR* 2.9 40.1 + - - -
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Residues in contact with LYS 676 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637F MET* 3.8 40.4 - - + +
672F MET* 2.9 20.1 + - + +
673F SER* 4.1 8.7 - - - +
675F ASP* 1.3 76.9 + - - +
677F ALA* 1.3 60.0 + - - +
679F THR* 3.9 6.6 + - - +
680F LYS* 3.4 32.1 + - + +
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Residues in contact with ALA 677 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636F CYS* 4.8 12.1 - - + +
637F MET* 5.3 6.9 - - + +
640F VAL* 4.1 10.3 - - + +
656F PHE* 4.3 13.0 - - + -
660F LEU* 4.0 21.1 - - + -
673F SER* 2.9 20.0 + - - +
676F LYS* 1.3 74.3 - - - +
678F VAL* 1.3 58.5 + - - +
679F THR 3.1 1.6 - - - -
680F LYS* 3.2 8.0 + - - +
681F LEU* 3.0 29.3 + - - +
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Residues in contact with VAL 678 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457D LEU* 4.8 6.5 - - + +
656F PHE* 4.9 5.6 - - + -
657F MET* 3.4 50.3 - - + -
660F LEU* 3.9 13.5 - - + -
674F ILE* 3.0 27.1 + - + +
675F ASP* 4.0 4.5 - - - +
677F ALA* 1.3 74.5 - - - +
679F THR* 1.3 61.6 + - - +
681F LEU* 4.4 7.9 - - + -
682F ARG* 3.2 52.6 + - + +
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Residues in contact with THR 679 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456D ARG* 3.9 23.4 + - - +
675F ASP* 2.9 27.9 + - - -
676F LYS* 3.9 7.4 - - - +
677F ALA 3.1 0.2 - - - -
678F VAL* 1.3 77.7 - - - +
680F LYS* 1.3 53.9 + - + +
682F ARG* 3.3 4.8 + - - +
683F GLU* 2.7 51.0 + - + +
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Residues in contact with LYS 680 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637F MET* 4.4 16.8 - - + -
640F VAL* 3.9 16.2 - - + -
641F GLU* 3.0 44.3 + - - +
676F LYS* 3.4 27.0 + - + +
677F ALA* 3.2 6.5 + - - +
679F THR* 1.3 78.4 - - + +
681F LEU* 1.3 58.6 + - - +
683F GLU* 4.0 19.9 - - - +
684F MET* 3.5 30.0 + - - +
428G GLU* 4.4 14.5 + - - -
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Residues in contact with LEU 681 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640F VAL* 4.4 15.9 - - + +
644F GLY* 3.6 39.9 - - - +
647F ILE* 4.2 10.3 - - + -
648F ILE* 3.7 15.3 - - + +
653F CYS* 4.3 32.8 - - + +
656F PHE* 3.9 21.5 - - + -
657F MET* 5.9 1.3 - - + -
677F ALA 3.0 15.9 + - - +
678F VAL* 3.9 8.7 - - + +
680F LYS* 1.3 73.9 - - - +
682F ARG* 1.3 73.1 + - + +
683F GLU 3.2 0.2 - - - -
684F MET* 3.1 23.0 + - - +
685F GLN* 3.8 0.8 + - - +
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Residues in contact with ARG 682 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456D ARG* 2.7 31.7 + - - +
457D LEU* 3.1 22.0 + - - +
458D ILE 4.2 7.5 + - - -
459D GLY* 4.1 8.0 - - - -
653F CYS* 6.0 4.0 - - - +
657F MET* 3.6 15.3 - - - +
678F VAL* 3.2 34.9 + - + +
679F THR* 4.1 2.7 - - - +
681F LEU* 1.3 83.2 - - + +
683F GLU* 1.3 61.5 + - - +
684F MET 3.2 0.9 - - - -
685F GLN* 3.1 40.5 + - - +
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Residues in contact with GLU 683 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679F THR* 2.7 28.6 + - + +
680F LYS* 4.0 23.0 - - - +
681F LEU 3.2 0.4 - - - -
682F ARG* 1.3 77.9 - - - +
684F MET* 1.3 56.4 + - - +
685F GLN 3.5 1.0 + - - -
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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