Contacts of the helix formed by residues 602 - 610 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562D ARG* 3.5 5.2 - - - +
600D ARG 4.3 1.3 + - - +
601D PHE* 1.3 73.7 - - - +
603D ASN* 1.3 57.4 + - - +
604D SER* 4.2 4.5 + - - -
605D GLU* 2.8 43.1 + - - +
606D THR* 2.7 32.4 + - - -
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Residues in contact with ASN 603 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556D GLY 4.9 6.9 + - - -
557D SER* 5.4 7.3 - - - +
558D LYS 5.5 0.8 - - - -
559D PHE 4.0 18.4 + - - -
561D VAL* 3.2 30.9 - - + +
562D ARG* 2.6 48.5 + - - +
602D THR* 1.3 73.2 - - - +
604D SER* 1.3 59.2 + - - +
606D THR* 3.4 0.6 + - - +
607D ALA* 3.0 24.4 + - - +
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Residues in contact with SER 604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555D VAL* 4.4 19.5 + - - +
561D VAL* 6.0 0.2 - - - -
602D THR* 3.2 5.0 + - - -
603D ASN* 1.3 79.9 - - - +
605D GLU* 1.3 60.4 + - - +
607D ALA* 3.6 6.8 + - - +
608D GLU* 3.1 32.1 + - - +
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Residues in contact with GLU 605 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600D ARG 4.7 1.4 - - - +
601D PHE* 3.7 28.9 - - + -
602D THR* 2.8 44.4 + - - +
604D SER* 1.3 76.7 - - - +
606D THR* 1.3 58.9 + - - +
608D GLU* 3.0 18.2 + - - +
609D HIS* 2.8 28.8 + - - +
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Residues in contact with THR 606 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561D VAL* 4.2 11.2 - - + -
562D ARG* 3.2 27.6 + - + -
598D TYR* 3.4 38.0 - - + +
601D PHE* 3.5 12.5 - - - +
602D THR 2.7 13.1 + - - -
603D ASN 3.8 4.7 - - - -
605D GLU* 1.3 72.3 - - - +
607D ALA* 1.3 59.1 + - - +
609D HIS* 2.8 9.3 + - + +
610D ILE* 2.8 50.4 + - + +
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Residues in contact with ALA 607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555D VAL* 6.4 2.2 - - + -
561D VAL* 3.8 9.6 - - + -
569D LEU* 3.6 40.1 - - + +
570D MET* 5.6 0.5 - - - +
603D ASN 3.0 18.0 + - - +
604D SER* 3.8 8.1 - - - +
605D GLU 3.2 0.2 - - - -
606D THR* 1.3 78.0 - - - +
608D GLU* 1.3 61.6 + - + +
611D ALA* 3.5 15.9 + - - +
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Residues in contact with GLU 608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604D SER* 3.1 23.0 + - - +
605D GLU* 3.0 16.6 + - - +
607D ALA* 1.3 78.4 - - + +
609D HIS* 1.3 63.3 + - - +
611D ALA* 3.0 19.9 + - - +
612D GLN* 3.3 18.3 + - - +
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Residues in contact with HIS 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620C HIS* 5.8 0.6 - - - -
598D TYR* 3.9 20.5 - + - -
601D PHE* 3.5 39.9 - + + -
605D GLU 2.8 15.2 + - - +
606D THR* 2.8 7.7 + - - +
608D GLU* 1.3 69.0 - - - +
610D ILE* 1.3 63.1 + - + +
612D GLN* 2.8 33.6 + - - +
613D GLY 3.6 3.6 + - - -
614D LEU* 3.2 49.7 + - + +
615D ARG 3.7 14.2 + - - -
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Residues in contact with ILE 610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561D VAL 3.9 9.6 - - - +
562D ARG* 5.4 0.4 - - - -
564D SER 3.3 18.6 - - - +
565D PRO 5.3 0.7 - - - -
566D PRO* 4.3 13.1 - - + +
569D LEU* 3.1 34.1 - - + -
581D TRP* 4.5 15.5 - - + +
598D TYR* 3.6 35.7 - - + +
606D THR* 2.8 29.4 + - + +
607D ALA 4.2 0.4 - - - +
609D HIS* 1.3 79.2 - - + +
611D ALA* 1.3 59.2 + - - +
612D GLN 3.1 3.0 + - - -
613D GLY* 3.4 9.6 + - - -
614D LEU 3.6 20.2 - - - +
615D ARG* 3.7 12.1 + - - -
636D GLU* 5.3 0.9 - - - +
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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