Contacts of the helix formed by residues 604 - 609 (chain G) 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 CYS 604 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579G GLU* 3.1 11.7 - - - -
590G ALA* 4.4 11.9 - - + -
599G VAL* 3.8 17.7 - - - -
601G CYS* 3.5 29.4 - - - -
602G LYS* 5.2 0.2 - - - -
603G ASN* 1.3 81.0 - - - +
605G SER* 1.3 64.6 + - - +
607G GLN* 3.5 23.5 - - - +
608G ARG* 3.2 40.2 + - - +
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Residues in contact with SER 605 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579G GLU* 3.1 6.4 + - - -
602G LYS* 4.7 10.6 + - - -
603G ASN* 5.0 0.2 - - - -
604G CYS* 1.3 80.4 + - - +
606G ILE* 1.3 58.0 + - - +
609G GLY* 2.9 24.6 + - - -
610G SER* 2.9 25.7 + - - -
637G PHE* 3.3 43.0 - - - +
711G PHE* 6.1 0.2 - - - -
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Residues in contact with ILE 606 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579G GLU* 3.1 26.3 + - + +
605G SER* 1.3 75.8 - - - +
607G GLN* 1.3 65.0 + - - +
609G GLY* 3.3 10.8 + - - -
637G PHE* 3.6 26.7 - - + -
640G GLU* 3.4 15.8 - - + +
700G MET* 3.9 26.0 - - + -
702G VAL* 4.2 8.5 - - + -
707G ARG* 3.3 60.3 + - + +
709G GLY* 4.5 11.2 - - - -
711G PHE* 4.9 2.2 - - + -
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Residues in contact with GLN 607 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579G GLU* 3.1 15.3 + - - +
580G CYS* 2.6 36.8 + - - +
582G PRO* 4.1 16.5 - - - +
590G ALA* 4.3 5.4 - - - +
604G CYS* 3.5 31.3 - - - +
606G ILE* 1.3 80.1 - - - +
608G ARG* 1.3 70.6 + - - +
702G VAL* 3.8 16.9 - - + +
703G ASN* 4.2 6.2 - - - +
707G ARG* 3.6 17.3 + - - +
627I ILE* 3.6 36.3 - - + +
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Residues in contact with ARG 608 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589G GLY 4.2 3.6 + - - -
590G ALA 2.7 32.1 + - - -
592G ASP 3.4 14.5 + - - +
593G HIS 3.5 20.6 + - - -
594G TRP* 3.3 31.7 + - - +
596G SER 3.7 12.3 + - - -
597G LYS* 3.7 40.5 + - + +
599G VAL* 4.1 16.6 - - - +
604G CYS* 3.2 29.5 + - - +
605G SER 4.2 0.2 - - - +
606G ILE 3.2 0.6 - - - -
607G GLN* 1.3 82.0 + - - +
609G GLY* 1.3 59.9 + - - +
610G SER* 4.0 12.3 - - - +
627I ILE* 3.8 18.2 - - + -
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Residues in contact with GLY 609 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597G LYS* 5.6 1.3 - - - +
605G SER 2.9 7.5 + - - -
606G ILE* 3.3 10.6 + - - -
607G GLN 3.8 0.2 + - - -
608G ARG* 1.3 80.3 - - - +
610G SER* 1.3 56.5 + - - +
611G LYS* 3.2 24.3 + - - +
637G PHE* 5.2 3.4 - - - -
707G ARG* 6.0 0.2 - - - -
586I GLU 5.5 2.3 - - - +
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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