Contacts of the helix formed by residues 596 - 603 (chain S) in PDB entry 1I84
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 ALA 596 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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552S ASP* 3.0 21.5 + - - -
595S SER* 1.3 80.2 + - - +
597S TRP* 1.3 61.0 + - - +
598S LEU 3.4 0.7 - - - -
599S THR* 3.0 24.6 + - - +
600S LYS* 3.3 30.7 + - - +
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Residues in contact with TRP 597 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475S ASN 4.3 0.4 - - - -
476S SER* 3.8 10.6 - - - +
477S PHE* 3.2 45.8 - + + +
480S LEU* 3.3 32.5 - - + -
537S VAL* 4.0 8.1 - - + -
541S LEU* 3.4 39.7 - - + +
552S ASP* 2.8 2.6 + - - +
555S PHE* 3.9 6.3 - + - -
581S PHE* 3.1 36.1 - + - -
592S TYR* 4.1 13.9 - - + -
593S ASN 3.0 12.3 + - - -
594S ALA* 2.9 19.3 - - - +
595S SER 2.7 29.9 + - - -
596S ALA* 1.3 72.2 - - - +
598S LEU* 1.3 60.1 + - - +
600S LYS* 3.5 6.0 + - + +
601S ASN* 2.8 33.3 + - - +
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Residues in contact with LEU 598 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541S LEU* 3.4 42.4 - - + +
544S GLU* 3.6 20.6 - - - +
545S CYS* 3.5 25.6 - - + +
550S ALA* 4.1 6.7 - - + +
551S THR* 3.8 14.8 - - - +
552S ASP* 3.1 32.4 + - - +
555S PHE* 4.7 4.0 - - + -
597S TRP* 1.3 76.6 - - - +
599S THR* 1.3 63.4 + - - +
601S ASN* 3.8 4.9 - - - +
602S MET* 3.2 25.1 + - + +
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Residues in contact with THR 599 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425S PHE* 3.2 42.8 - - + -
552S ASP* 4.9 1.7 + - - -
596S ALA* 3.0 25.7 + - - +
598S LEU* 1.3 74.5 - - - +
600S LYS* 1.3 62.3 + - - +
602S MET* 3.0 6.7 + - - +
603S ASP 2.8 24.8 + - - -
604S PRO* 3.5 13.0 - - + +
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Residues in contact with LYS 600 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275S SER* 4.8 9.4 + - - +
432S LYS* 5.4 8.1 - - - +
476S SER* 3.2 26.0 + - - +
477S PHE* 4.8 16.2 - - + -
478S GLU* 3.7 24.3 + - - +
595S SER 5.3 1.0 + - - -
596S ALA* 3.3 29.2 + - - +
597S TRP* 3.9 5.2 - - + +
599S THR* 1.3 78.7 - - - +
601S ASN* 1.3 60.7 + - - +
602S MET 2.9 6.1 + - - -
603S ASP* 3.2 24.9 + - - +
659S VAL* 4.0 8.9 - - - +
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Residues in contact with ASN 601 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477S PHE* 3.9 14.6 - - + -
538S LEU* 4.6 1.8 + - - +
541S LEU* 3.0 39.4 + - + +
542S ASP* 3.2 18.7 + - - +
545S CYS* 4.7 5.4 - - - -
597S TRP 2.8 20.2 + - - +
598S LEU* 3.8 7.4 - - - +
600S LYS* 1.3 75.6 - - - +
602S MET* 1.3 56.9 + - - +
658S THR* 2.6 25.9 + - - -
659S VAL* 3.3 25.3 + - - +
660S GLY 3.5 11.3 + - - +
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Residues in contact with MET 602 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545S CYS* 2.9 44.2 - - - +
546S TRP* 3.1 35.9 - - + -
598S LEU* 3.2 16.5 + - + +
599S THR* 3.0 5.8 + - - +
600S LYS 3.0 1.0 - - - -
601S ASN* 1.3 79.2 - - - +
603S ASP* 1.3 72.9 + - - +
604S PRO* 4.5 14.3 - - + +
632S VAL* 4.7 14.0 - - + +
657S ARG 5.4 3.5 - - - +
658S THR* 6.0 0.7 - - - +
659S VAL* 5.6 0.4 - - - -
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Residues in contact with ASP 603 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274S LYS* 3.9 24.5 + - - -
432S LYS* 5.9 1.0 - - - +
433S ALA* 4.9 10.2 - - - +
436S GLU* 5.7 0.5 - - - +
599S THR 2.8 11.2 + - - -
600S LYS* 3.2 16.8 + - - +
602S MET* 1.3 83.3 - - - +
604S PRO* 1.3 65.4 - - - +
632S VAL* 4.2 8.1 + - - +
659S VAL* 4.7 14.5 - - + +
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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