Contacts of the helix formed by residues 596 - 608 (chain D) in PDB entry 6X34
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 ASN 596 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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561D LEU* 4.7 8.8 - - + +
589D LEU* 5.2 2.6 + - - +
590D LEU* 5.5 3.3 - - - +
593D HIS* 3.4 21.7 + - - +
594D GLY 2.8 27.9 + - - -
595D ARG* 1.3 76.6 - - - +
597D HIS* 1.3 64.7 + - - +
598D LYS* 3.3 5.4 + - + +
599D VAL* 3.5 29.7 + - + +
600D LEU* 3.3 19.7 - - - +
1662D PHE* 4.5 4.8 - - - -
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Residues in contact with HIS 597 (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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596D ASN* 1.3 72.3 - - - +
598D LYS* 1.3 73.6 + - - +
599D VAL 3.4 0.2 - - - -
600D LEU* 4.1 8.8 + - - -
601D ASP* 4.1 5.4 + - - +
1661D GLN* 3.5 26.2 - - + +
1662D PHE* 5.0 6.2 - - + +
1665D HIS* 2.8 46.3 + - + +
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Residues in contact with LYS 598 (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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558D SER* 6.0 2.2 - - - +
561D LEU* 3.7 23.1 - - + -
562D GLU* 6.5 0.2 - - - -
565D TYR* 4.8 4.0 - - + +
596D ASN* 3.2 3.0 - - + -
597D HIS* 1.3 105.9 - - - +
599D VAL* 1.3 63.2 + - - +
600D LEU 3.4 0.9 - - - -
601D ASP* 3.6 8.9 + - + +
602D VAL* 3.3 23.7 + - - +
1661D GLN* 4.1 10.8 + - - +
1665D HIS* 5.8 1.3 - - + -
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Residues in contact with VAL 599 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561D LEU* 3.7 33.4 - - + -
586D ILE* 4.2 14.4 - - + +
589D LEU* 4.6 12.6 - - + -
590D LEU* 3.8 33.7 - - + -
596D ASN* 3.5 27.8 + - + +
597D HIS 3.4 0.6 - - - -
598D LYS* 1.3 76.1 - - - +
600D LEU* 1.3 60.7 + - - +
602D VAL* 3.0 6.1 + - + +
603D LEU* 2.9 45.1 + - + +
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Residues in contact with LEU 600 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590D LEU* 5.0 10.8 - - + -
596D ASN 3.3 21.3 - - - +
597D HIS* 4.1 4.2 + - - +
598D LYS 3.4 0.2 - - - -
599D VAL* 1.3 80.2 - - + +
601D ASP* 1.3 57.3 + - - +
603D LEU* 3.3 9.9 + - + +
604D CYS* 2.9 29.0 + - - +
632D LEU* 4.7 9.2 - - + -
1662D PHE* 3.7 22.9 - - + +
1665D HIS* 3.5 25.4 - - + +
1666D THR* 3.5 41.7 - - - +
1669D LEU* 4.3 20.5 - - + +
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Residues in contact with ASP 601 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565D TYR* 3.6 27.5 - - + +
597D HIS 4.1 7.5 + - - +
598D LYS* 3.6 14.6 + - + +
599D VAL 3.2 0.4 - - - -
600D LEU* 1.3 78.7 - - - +
602D VAL* 1.3 56.2 + - - +
604D CYS* 3.3 7.2 + - - +
605D SER* 2.9 29.8 + - - -
1665D HIS* 5.3 4.3 + - + -
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Residues in contact with VAL 602 (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 LEU* 4.0 18.2 - - + -
564D LEU* 4.3 17.9 - - + +
565D TYR* 3.6 31.0 - - + +
568D LEU* 4.0 23.8 - - + -
586D ILE* 5.0 9.9 - - + -
598D LYS 3.3 16.8 - - - +
599D VAL* 3.0 10.0 + - + +
601D ASP* 1.3 77.6 - - - +
603D LEU* 1.3 60.8 + - + +
605D SER* 3.0 8.9 + - - +
606D LEU* 2.9 29.9 + - + +
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Residues in contact with LEU 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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583D ILE* 5.0 13.0 - - + -
586D ILE* 3.6 30.7 - - + -
587D ILE* 5.2 7.4 - - + -
590D LEU* 5.3 5.2 - - + -
599D VAL* 2.9 32.4 + - + +
600D LEU* 3.3 9.8 + - + +
602D VAL* 1.3 80.2 - - + +
604D CYS* 1.3 57.0 + - - +
606D LEU* 3.3 13.9 + - + +
607D CYS* 2.9 29.1 + - - +
621D ILE* 4.9 16.8 - - + -
625D LEU* 5.4 6.7 - - + -
1669D LEU* 3.8 26.1 - - + +
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Residues in contact with CYS 604 (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 LEU 2.9 16.5 + - - +
601D ASP* 3.7 7.6 - - - +
603D LEU* 1.3 75.9 - - - +
605D SER* 1.3 63.6 + - - +
607D CYS* 3.3 17.1 + - - +
608D VAL* 3.7 14.1 + - - +
1668D ARG* 4.8 19.3 - - + -
1669D LEU* 4.0 15.8 - - + +
1672D ALA* 4.1 20.8 - - + +
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Residues in contact with SER 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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565D TYR* 4.9 11.1 + - - -
568D LEU* 3.7 35.6 - - - +
569D ILE* 4.9 15.3 - - - -
575D LEU* 4.0 5.2 - - - +
601D ASP 2.9 14.9 + - - -
602D VAL* 3.0 14.0 + - - +
604D CYS* 1.3 78.3 - - - +
606D LEU* 1.3 61.7 + - - +
608D VAL* 3.0 22.4 - - - +
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Residues in contact with LEU 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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568D LEU* 3.7 31.2 - - + -
575D LEU* 3.2 30.1 - - + +
578D ILE* 3.8 43.5 - - + -
582D HIS* 6.1 3.8 - - + -
583D ILE* 5.6 14.6 - - + +
586D ILE* 6.0 6.1 - - + -
602D VAL* 2.9 16.1 + - + +
603D LEU* 3.3 14.6 + - + +
605D SER* 1.3 79.7 + - - +
607D CYS* 1.3 64.7 + - - +
608D VAL 3.6 0.2 - - - -
617D ASN* 4.0 13.9 - - + +
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Residues in contact with CYS 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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603D LEU 2.9 15.8 + - - +
604D CYS* 3.5 11.7 - - - +
605D SER 3.2 1.0 - - - -
606D LEU* 1.3 80.1 - - - +
608D VAL* 1.3 61.1 + - + +
614D VAL* 3.5 22.3 + - - +
617D ASN* 5.2 3.6 - - - -
618D GLN* 3.4 36.6 + - - +
1669D LEU* 5.4 4.3 - - + -
1672D ALA* 3.4 28.9 - - + -
1673D VAL* 3.6 17.5 - - - -
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Residues in contact with VAL 608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575D LEU* 4.4 1.9 - - - +
604D CYS* 3.7 14.3 + - - +
605D SER* 3.0 18.9 - - - +
607D CYS* 1.3 82.1 - - + +
609D CYS* 1.3 77.1 + - - +
611D GLY* 4.9 0.9 - - - +
612D VAL 3.3 12.3 - - - +
613D ALA* 4.5 4.3 - - + +
618D GLN* 5.3 2.2 - - - +
1672D ALA* 5.4 11.0 - - + +
1676D LEU* 4.1 32.5 - - + -
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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