Contacts of the helix formed by residues 596 - 608 (chain f) in PDB entry 5T0J
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 ASP 596 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560f PRO* 5.4 7.0 - - + +
595f LYS* 1.3 105.8 - - - +
597f PRO* 1.3 76.8 - - + +
598f ASN* 3.0 14.6 + - - +
599f ASN* 3.2 10.0 + - - +
600f LEU* 4.3 3.4 + - - +
641f LEU* 5.0 3.8 - - - -
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Residues in contact with PRO 597 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564f TYR* 5.2 4.5 - - + -
596f ASP* 1.3 88.3 - - + +
598f ASN* 1.3 51.0 + - - +
599f ASN 3.1 0.6 + - - -
600f LEU* 3.2 24.2 + - + +
601f PHE* 2.7 38.4 + - + +
641f LEU* 3.8 22.9 - - + -
644f PHE* 6.0 1.3 - - + -
683f VAL* 6.3 4.3 - - + -
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Residues in contact with ASN 598 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558f ALA 5.5 1.6 + - - -
560f PRO* 3.2 44.5 + - + +
563f SER* 5.0 12.5 + - - +
564f TYR* 4.0 23.9 - - + +
594f ALA* 5.4 5.5 - - - +
595f LYS 2.8 25.2 + - - +
596f ASP* 3.1 9.7 - - - +
597f PRO* 1.3 75.0 - - - +
599f ASN* 1.3 62.9 + - - +
601f PHE* 3.8 9.3 - - - +
602f MET* 3.3 21.8 + - - +
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Residues in contact with ASN 599 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589f LEU 3.6 17.0 + - - +
590f ALA* 5.3 3.4 + - - +
592f TYR* 3.5 29.5 + - - +
594f ALA* 2.7 38.9 + - + +
595f LYS 3.8 3.8 - - - +
596f ASP 3.6 8.3 - - - +
597f PRO 3.1 0.8 - - - -
598f ASN* 1.3 86.2 + - - +
600f LEU* 1.3 59.4 + - + +
602f MET* 3.7 6.7 - - - +
603f VAL* 3.4 18.6 - - - +
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Residues in contact with LEU 600 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596f ASP 4.7 2.7 - - - +
597f PRO* 3.3 30.7 - - + +
599f ASN* 1.3 76.6 - - + +
601f PHE* 1.3 63.2 + - + +
602f MET 3.3 0.9 - - - -
603f VAL* 4.0 5.8 - - - +
604f ARG* 2.9 33.8 + - + +
641f LEU* 3.6 42.6 - - + +
642f VAL* 5.1 2.0 - - + +
644f PHE* 3.7 32.3 - - + -
645f LEU* 4.3 22.9 - - + -
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Residues in contact with PHE 601 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564f TYR* 3.2 65.7 - + + -
567f ILE* 3.6 26.5 - - + +
568f PHE* 4.3 11.0 - - + -
597f PRO* 2.7 21.9 + - + +
598f ASN 3.8 4.5 - - - +
599f ASN 3.4 0.2 - - - -
600f LEU* 1.3 76.1 - - + +
602f MET* 1.3 64.8 + - - +
604f ARG* 5.3 0.2 - - - -
605f LEU* 3.1 55.5 + - + +
644f PHE* 6.1 6.5 - + - -
677f GLU* 5.0 9.9 - - - -
680f PRO* 5.5 2.2 - - + -
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Residues in contact with MET 602 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555f SER* 3.7 31.0 - - - +
563f SER* 4.8 9.2 - - - +
566f SER* 4.5 8.7 - - - -
567f ILE* 3.5 39.3 - - + +
585f MET* 4.2 19.7 - - + -
589f LEU* 3.7 42.0 - - + -
592f TYR* 6.2 1.1 - - + -
598f ASN 3.3 9.9 + - - +
599f ASN* 3.7 11.7 - - - +
601f PHE* 1.3 81.4 - - - +
603f VAL* 1.3 67.2 + - + +
606f ALA* 3.3 19.8 + - - +
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Residues in contact with VAL 603 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586f LEU* 4.4 8.1 - - + +
589f LEU* 3.5 43.3 - - + +
590f ALA* 3.7 23.6 - - + +
599f ASN 3.4 18.2 - - - +
600f LEU* 3.6 4.8 + - - +
601f PHE 3.5 0.2 - - - -
602f MET* 1.3 76.6 - - + +
604f ARG* 1.3 71.6 + - - +
606f ALA* 3.1 8.8 + - - +
607f GLN* 3.0 39.0 + - + +
628f LEU* 5.6 2.7 - - + -
632f VAL* 6.2 0.2 - - + -
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Residues in contact with ARG 604 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600f LEU* 2.9 21.8 + - + +
601f PHE* 5.3 0.2 - - - -
603f VAL* 1.3 84.6 - - - +
605f LEU* 1.3 62.8 + - - +
607f GLN* 3.1 39.0 + - - +
608f GLY 3.8 2.4 + - - -
628f LEU* 3.5 22.8 + - - +
629f MET* 4.3 5.8 - - - +
632f VAL* 3.4 32.7 - - - +
644f PHE* 5.8 1.6 - - + -
645f LEU* 3.1 51.4 + - + +
648f ARG* 3.7 22.3 - - + +
649f ASN* 3.3 35.8 - - - +
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Residues in contact with LEU 605 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567f ILE* 3.6 35.4 - - + +
568f PHE* 5.0 2.9 - - + -
571f GLY* 4.0 17.9 - - - -
601f PHE* 3.1 52.0 + - + +
603f VAL 3.3 0.4 - - - -
604f ARG* 1.3 78.0 - - - +
606f ALA* 1.3 59.9 + - - +
608f GLY* 3.2 10.2 + - - -
609f LEU* 3.2 21.4 - - + +
648f ARG* 5.4 5.1 - - - +
652f LEU* 5.9 1.0 - - - +
677f GLU* 5.4 8.3 - - - +
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Residues in contact with ALA 606 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567f ILE* 3.8 15.3 - - + -
582f LEU* 5.4 2.7 - - + +
585f MET* 5.1 8.7 - - + -
586f LEU* 3.9 24.7 - - + +
589f LEU* 5.5 2.0 - - + -
602f MET 3.3 17.7 + - - +
603f VAL* 3.1 7.2 + - - +
605f LEU* 1.3 76.4 - - - +
607f GLN* 1.3 64.0 + - - +
608f GLY 3.2 0.4 - - - -
609f LEU* 3.2 33.8 + - + +
610f THR 4.4 0.5 + - - -
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Residues in contact with GLN 607 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586f LEU* 3.3 38.8 - - - +
603f VAL* 3.0 28.3 + - + +
604f ARG* 3.1 41.3 + - - +
606f ALA* 1.3 78.9 - - - +
608f GLY* 1.3 54.2 + - - +
609f LEU 3.2 0.4 - - - -
610f THR* 3.3 23.9 + - - +
625f ASP* 4.9 13.9 + - - +
628f LEU* 3.4 36.7 - - - +
649f ASN* 4.3 10.7 - - + +
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Residues in contact with GLY 608 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575f SER* 4.0 0.7 - - - -
604f ARG 3.8 2.6 + - - -
605f LEU 3.2 8.5 + - - -
606f ALA 3.2 0.6 - - - -
607f GLN* 1.3 74.5 - - - +
609f LEU* 1.3 59.5 + - - +
610f THR* 3.2 7.2 - - - -
611f HIS* 2.9 24.1 - - - +
612f LEU* 3.8 12.5 - - - +
649f ASN* 5.3 6.5 - - - +
652f LEU* 3.8 26.3 - - - +
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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