Contacts of the helix formed by residues 589 - 602 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A PRO* 3.5 30.5 - - + +
116A LEU* 4.8 2.5 - - + -
117A GLN* 3.9 33.0 - - + +
587C LYS* 4.3 12.1 - - + -
588C ASP* 1.4 90.6 - - - +
590C GLU* 1.3 69.6 + - + +
591C TRP* 3.1 14.5 + - + +
592C LEU* 3.1 32.8 + - + +
593C ARG 3.8 1.7 + - - -
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Residues in contact with GLU 590 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PRO* 6.0 3.8 - - + -
269B ARG* 4.6 11.1 + - - +
293B LYS* 3.2 25.8 + - - +
295B HIS* 3.0 34.6 - - - -
587C LYS* 5.9 4.3 - - - -
588C ASP 2.9 8.8 + - - -
589C PRO* 1.3 71.3 - - + +
591C TRP* 1.3 66.1 + - + +
593C ARG* 3.0 41.6 + - - +
594C GLU* 3.7 3.0 + - - +
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Residues in contact with TRP 591 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A SER* 3.8 12.7 - - - -
115A PRO* 2.8 31.8 + - + +
116A LEU* 3.5 24.5 - - + -
120A PHE* 3.7 39.0 - + - -
680A LYS* 3.9 12.1 - - + -
232B VAL* 3.3 22.7 - - + -
295B HIS* 3.6 47.1 - + + -
296B PHE* 4.1 8.6 - + + -
589C PRO* 3.1 13.0 + - + +
590C GLU* 1.3 81.0 - - + +
592C LEU* 1.3 88.3 + - + +
594C GLU* 2.9 9.6 + - - +
595C LYS* 2.9 36.8 + - + +
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Residues in contact with LEU 592 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 4.4 7.2 - - + -
118A GLN* 6.1 1.8 - - - +
120A PHE* 3.9 18.6 - - + -
291A LYS* 5.9 1.1 - - - -
295A PHE* 3.5 27.8 - - + -
588C ASP* 5.0 4.5 - - - +
589C PRO* 3.1 28.2 + - + +
591C TRP* 1.3 113.0 - - + +
593C ARG* 1.3 54.0 + - - +
595C LYS* 3.4 3.4 + - + +
596C THR* 2.8 32.6 + - - -
622C MET* 3.7 24.0 - - + -
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Residues in contact with ARG 593 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588C ASP* 2.8 53.6 + - - +
589C PRO 4.3 1.1 - - - +
590C GLU* 3.0 22.2 + - - +
592C LEU* 1.3 78.5 - - - +
594C GLU* 1.3 61.4 + - - +
595C LYS 3.4 0.2 + - - -
596C THR* 3.4 6.0 + - - -
597C ILE* 3.1 31.8 + - + +
619C LEU* 3.6 32.1 - - + +
622C MET* 4.7 7.9 - - - -
623C LYS* 4.9 22.3 - - - +
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Residues in contact with GLU 594 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ARG* 6.3 1.6 - - - +
296B PHE* 4.0 22.8 - - + -
590C GLU 3.7 2.3 + - - +
591C TRP* 2.9 11.4 + - - +
593C ARG* 1.3 79.0 - - - +
595C LYS* 1.3 57.4 + - - +
597C ILE* 3.4 21.4 + - + +
598C THR* 3.0 48.5 + - - +
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Residues in contact with LYS 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PHE* 4.6 12.8 - - + -
295A PHE* 4.1 15.5 - - + -
232B VAL* 4.4 8.3 - - + -
233B GLU* 4.1 20.2 + - - -
296B PHE* 3.9 20.1 - - + -
591C TRP* 2.9 27.6 + - + +
592C LEU* 3.7 12.8 - - - +
593C ARG 3.2 0.4 - - - -
594C GLU* 1.3 75.3 - - - +
596C THR* 1.3 53.6 + - - +
598C THR* 2.9 9.0 + - - +
599C GLN* 2.8 65.1 + - + +
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Residues in contact with THR 596 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A TYR 4.5 2.9 - - - +
293A ASP 4.6 3.1 - - - +
295A PHE* 3.8 15.8 - - + -
592C LEU 2.8 17.2 + - - -
593C ARG* 3.4 5.0 + - - -
594C GLU 3.4 0.2 - - - -
595C LYS* 1.3 75.5 - - - +
597C ILE* 1.3 58.2 + - - +
599C GLN* 3.0 4.6 + - + -
600C ILE* 2.7 48.6 + - + +
615C LYS* 6.2 1.3 - - - -
618C ASN* 3.2 37.5 - - + +
619C LEU* 6.0 3.4 - - - -
622C MET* 3.2 23.1 - - + +
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Residues in contact with ILE 597 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593C ARG* 3.1 26.4 + - + +
594C GLU* 3.6 26.7 - - + +
596C THR* 1.3 78.9 - - - +
598C THR* 1.3 62.1 + - + +
601C GLU* 3.3 22.6 + - + +
615C LYS* 3.5 39.4 - - + +
619C LEU* 4.4 28.5 - - + -
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Residues in contact with THR 598 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B PHE* 4.9 11.5 - - + -
594C GLU* 3.0 33.8 + - - +
595C LYS* 2.9 22.2 + - - +
597C ILE* 1.3 80.2 - - + +
599C GLN* 1.3 54.6 + - - +
600C ILE 3.3 0.2 + - - -
601C GLU* 3.3 7.4 + - - +
602C GLU* 3.0 36.7 + - - +
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Residues in contact with GLN 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PHE* 5.8 0.6 - - - -
293A ASP* 3.4 32.4 - - + +
294A CYS 5.0 0.5 - - - +
295A PHE* 3.1 33.1 - - - -
595C LYS* 2.8 47.7 + - + +
596C THR* 3.0 5.5 + - + +
598C THR* 1.3 73.8 + - - +
600C ILE* 1.3 60.6 + - + +
602C GLU* 4.0 14.6 - - + +
603C PHE* 3.4 19.1 - - + -
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Residues in contact with ILE 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A LEU* 4.6 7.9 - - + -
292A TYR* 4.1 24.0 - - + +
293A ASP* 4.6 11.0 - - + -
596C THR* 2.7 33.6 + - + +
597C ILE 3.9 0.4 - - - +
599C GLN* 1.3 71.1 - - + +
601C GLU* 1.3 68.4 + - - +
602C GLU 3.1 1.3 - - - -
603C PHE* 3.0 27.2 + - + +
606C VAL* 6.0 0.2 - - + -
611C LYS* 3.5 45.9 - - + +
614C MET* 4.4 19.1 - - + -
615C LYS* 3.6 23.3 - - + +
618C ASN* 5.0 1.6 - - - +
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Residues in contact with GLU 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597C ILE* 3.3 15.9 + - + +
598C THR* 3.7 7.0 - - - +
600C ILE* 1.3 78.4 - - - +
602C GLU* 1.3 57.4 + - + +
603C PHE 3.0 0.9 + - - -
608C GLU 5.0 4.9 - - - +
611C LYS* 2.8 42.6 + - + +
615C LYS* 3.5 26.5 + - - +
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Residues in contact with GLU 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU* 5.3 4.2 - - - +
346B SER* 4.5 19.9 - - - -
598C THR* 3.0 23.5 + - - +
599C GLN* 4.0 12.3 - - + +
600C ILE 3.1 0.6 + - - -
601C GLU* 1.3 75.0 - - + +
603C PHE* 1.3 56.1 + - - +
604C SER* 3.0 10.1 + - - -
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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