Contacts of the helix formed by residues 602 - 610 (chain C) in PDB entry 5J87
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 THR 602 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B PHE* 3.8 35.3 - - + -
417B LYS* 4.4 0.2 - - - +
431B MET* 3.8 25.6 - - + -
471B PHE* 4.8 5.6 - - + -
562C ARG* 3.8 4.0 - - - +
601C PHE* 1.3 74.6 - - - +
603C ASN* 1.3 56.6 + - - +
604C SER* 2.7 26.3 + - - -
605C GLU* 3.2 21.5 + - - +
606C THR* 2.7 35.5 + - - -
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Residues in contact with ASN 603 (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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556C GLY 4.8 7.9 + - - -
557C SER* 4.9 8.1 + - - +
559C PHE 3.7 10.7 + - - -
561C VAL* 3.4 52.9 + - + +
562C ARG* 2.9 38.9 + - - +
602C THR* 1.3 75.5 - - - +
604C SER* 1.3 63.1 + - - +
606C THR* 3.6 3.5 + - - -
607C ALA* 3.4 9.7 + - - +
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Residues in contact with SER 604 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B PHE* 4.1 19.0 + - - +
602C THR* 2.7 24.3 + - - -
603C ASN* 1.3 78.7 - - - +
605C GLU* 1.3 64.4 + - - +
607C ALA* 3.4 11.4 + - - +
608C GLU* 3.2 24.7 - - - +
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Residues in contact with GLU 605 (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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404B PHE* 3.8 19.2 - - + +
405B LEU 4.8 2.3 + - - -
406B LYS* 5.1 4.7 + - - -
407B GLU* 5.3 1.8 + - - +
417B LYS* 2.7 51.2 + - - +
601C PHE* 3.3 24.3 - - + -
602C THR* 3.2 19.7 + - - +
604C SER* 1.3 76.8 + - - +
606C THR* 1.3 67.6 + - - +
607C ALA 3.0 1.7 + - - -
608C GLU* 3.4 17.9 + - - +
609C HIS* 3.3 22.2 + - - +
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Residues in contact with THR 606 (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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561C VAL* 3.7 19.7 - - + +
562C ARG* 4.0 12.2 + - + -
598C TYR* 3.9 33.3 - - + +
601C PHE* 3.6 19.2 - - - +
602C THR 2.7 24.5 + - - -
603C ASN* 3.6 7.2 - - - -
605C GLU* 1.3 77.9 - - - +
607C ALA* 1.3 58.1 + - - +
609C HIS* 3.4 2.9 + - - +
610C ILE* 3.0 44.8 + - + +
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Residues in contact with ALA 607 (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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561C VAL* 4.2 2.9 - - + -
569C LEU* 3.9 31.0 - - + +
603C ASN 3.4 10.3 + - - +
604C SER* 3.4 11.4 + - - +
605C GLU 3.0 1.0 - - - -
606C THR* 1.3 79.6 - - - +
608C GLU* 1.3 59.0 + - + +
610C ILE* 3.1 25.2 - - - +
611C ALA* 4.4 2.6 + - - +
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Residues in contact with GLU 608 (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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604C SER* 3.2 23.9 - - - +
605C GLU* 3.7 20.0 - - - +
606C THR 3.3 0.2 - - - -
607C ALA* 1.3 75.9 - - + +
609C HIS* 1.3 60.0 + - - +
610C ILE 3.1 2.0 - - - -
611C ALA* 3.1 11.7 + - - +
612C GLN* 3.0 31.7 + - + +
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Residues in contact with HIS 609 (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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601C PHE* 3.8 34.1 - + + -
605C GLU 3.3 14.0 + - - +
606C THR* 4.2 2.5 - - - +
608C GLU* 1.3 76.5 - - - +
610C ILE* 1.3 65.3 + - - +
612C GLN* 3.4 38.8 + - + +
613C GLY 3.2 11.1 + - - -
614C LEU* 3.4 44.8 + - + +
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Residues in contact with ILE 610 (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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561C VAL 5.8 0.7 - - - +
564C SER 5.1 5.2 - - - +
566C PRO* 4.0 31.8 - - + +
569C LEU* 3.6 33.2 - - + -
570C MET* 6.2 2.0 - - + -
581C TRP* 5.3 6.3 - - + -
598C TYR* 4.7 16.4 - - + +
606C THR* 3.0 27.2 + - + +
607C ALA* 3.1 28.9 - - - +
609C HIS* 1.3 77.9 - - - +
611C ALA* 1.3 77.3 + - + +
613C GLY* 3.4 2.8 + - - -
614C LEU 4.4 9.0 - - - +
615C ARG* 3.2 24.2 + - - +
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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