Contacts of the helix formed by residues 604 - 609 (chain B) in PDB entry 5IJ7
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579B GLU* 3.3 12.6 - - - -
580B CYS 4.6 0.4 - - - +
590B ALA* 4.3 13.0 - - + -
597B LYS 5.8 1.1 - - - -
599B VAL* 4.1 7.6 - - - -
601B CYS* 3.6 31.9 - - - -
602B LYS 3.7 0.4 - - - -
603B ASN* 1.3 79.9 - - - +
605B SER* 1.4 64.2 + - - +
607B GLN* 3.2 32.9 - - + +
608B ARG* 3.3 39.0 + - - +
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Residues in contact with SER 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579B GLU* 3.1 5.0 + - - -
602B LYS* 4.3 14.9 + - - -
603B ASN* 3.9 0.4 - - - -
604B CYS* 1.4 74.1 + - - +
606B ILE* 1.4 55.9 - - - +
609B GLY* 2.8 29.5 + - - -
610B SER* 3.0 25.9 + - - -
612B LYS* 6.0 0.2 - - - -
637B PHE* 3.4 43.8 - - - +
711B PHE* 5.7 1.1 - - - -
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Residues in contact with ILE 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579B GLU* 2.8 20.1 + - - +
605B SER* 1.4 69.9 - - - +
607B GLN* 1.4 61.9 + - - +
609B GLY* 3.1 13.9 + - - -
637B PHE* 3.6 28.3 - - + -
640B GLU* 3.8 15.8 - - + +
700B MET* 3.6 32.3 - - + -
702B VAL* 4.0 13.5 - - + -
707B ARG* 3.5 50.1 + - + +
708B ILE 4.4 0.2 - - - -
709B GLY* 3.9 25.6 - - - +
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Residues in contact with GLN 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579B GLU* 3.1 25.6 + - - +
580B CYS 2.6 22.9 + - - +
582B PRO* 3.4 30.1 - - - +
590B ALA* 4.6 4.6 + - - +
604B CYS* 3.2 28.5 - - + +
606B ILE* 1.4 77.0 - - - +
608B ARG* 1.3 59.4 + - + +
609B GLY 3.9 0.2 + - - -
702B VAL* 3.6 11.9 - - + +
703B ASN* 3.7 11.7 + - - +
707B ARG* 3.6 17.1 + - - +
627T ILE* 3.5 42.9 - - + +
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Residues in contact with ARG 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589B GLY 3.6 3.8 + - - -
590B ALA 2.9 29.3 + - - -
592B ASP 2.8 21.8 + - - -
593B HIS 2.8 27.3 + - - -
594B TRP* 3.6 22.0 + - + +
596B SER 3.0 18.2 + - - +
597B LYS* 3.3 31.8 - - + -
599B VAL* 3.5 10.6 - - - +
604B CYS* 3.3 38.2 + - - +
607B GLN* 1.3 81.1 - - + +
609B GLY* 1.3 62.2 + - - +
610B SER* 3.6 11.9 - - - +
627T ILE* 4.6 7.6 - - + -
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Residues in contact with GLY 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLN* 5.4 3.8 + - - -
597B LYS* 3.2 14.8 + - - -
605B SER 2.8 10.9 + - - -
606B ILE* 3.1 11.2 + - - -
607B GLN 3.4 0.4 - - - -
608B ARG* 1.3 79.7 - - - +
610B SER* 1.4 49.0 + - - -
611B LYS* 2.8 33.1 + - - +
637B PHE* 4.9 2.5 - - - -
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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