Contacts of the helix formed by residues 579 - 593 (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 GLN 579 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577D ILE* 3.0 28.4 + - - +
578D ILE* 1.3 80.5 - - - +
580D GLU* 1.3 66.9 + - - +
581D ASN* 2.9 22.1 + - - +
582D HIS* 2.9 41.7 + - - +
583D ILE* 3.7 10.9 + - - +
620D LEU* 4.2 8.7 - - - +
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Residues in contact with GLU 580 (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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579D GLN* 1.3 75.6 - - - +
581D ASN* 1.3 59.2 + - - +
582D HIS 3.3 0.2 - - - -
583D ILE* 3.2 11.8 - - + +
584D LYS* 2.9 30.7 + - - +
620D LEU* 3.8 23.5 - - + +
624D ASN* 5.8 1.1 - - - +
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Residues in contact with ASN 581 (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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545D ASP* 5.5 5.7 - - - +
548D VAL* 5.7 2.1 - - - +
579D GLN* 2.9 32.2 + - - +
580D GLU* 1.3 74.2 - - - +
582D HIS* 1.3 82.4 + - - -
584D LYS* 3.3 6.7 + - - +
585D SER* 2.9 30.0 + - - -
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Residues in contact with HIS 582 (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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544D LEU* 3.5 40.4 - - + +
545D ASP* 4.6 4.3 - - + -
548D VAL* 4.1 34.7 - - + +
577D ILE* 4.5 2.0 + - - +
578D ILE* 3.5 28.6 - - + -
579D GLN* 2.9 33.6 + - - +
580D GLU 3.3 0.4 - - - -
581D ASN* 1.3 99.6 + - - +
583D ILE* 1.3 57.8 + - - +
585D SER* 3.3 3.9 + - - -
586D ILE* 2.9 33.8 + - + +
606D LEU* 6.1 4.3 - - + -
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Residues in contact with ILE 583 (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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578D ILE* 6.6 0.4 - - + -
579D GLN 3.7 5.0 + - - +
580D GLU* 3.2 27.4 - - + +
582D HIS* 1.3 76.3 - - - +
584D LYS* 1.3 59.0 + - - +
586D ILE* 3.2 9.7 + - + +
587D ILE* 2.9 50.8 + - + +
603D LEU* 5.0 10.5 - - + -
606D LEU* 5.6 12.5 - - + +
617D ASN* 4.4 4.5 - - + +
620D LEU* 3.7 21.5 - - + +
621D ILE* 3.5 41.1 - - + +
624D ASN* 4.6 11.7 - - + +
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Residues in contact with LYS 584 (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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580D GLU 2.9 19.9 + - - +
581D ASN* 3.5 8.5 - - - +
583D ILE* 1.3 78.7 - - + +
585D SER* 1.3 57.5 + - - +
587D ILE* 3.3 6.9 + - - +
588D SER* 2.9 28.3 + - - -
624D ASN* 6.1 4.0 - - - -
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Residues in contact with SER 585 (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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548D VAL* 3.8 35.1 + - - +
551D LEU* 4.4 8.0 - - - +
552D ASP* 5.2 7.1 - - - +
581D ASN 2.9 17.3 + - - -
582D HIS 3.7 4.5 - - - -
584D LYS* 1.3 75.1 - - - +
586D ILE* 1.3 57.6 + - - +
588D SER* 3.5 7.6 - - - -
589D LEU* 2.9 28.6 + - - +
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Residues in contact with ILE 586 (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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548D VAL* 5.5 2.2 - - + -
551D LEU* 3.9 15.3 - - + -
561D LEU* 5.7 2.5 - - + -
564D LEU* 3.6 30.7 - - + -
582D HIS* 2.9 20.6 + - + +
583D ILE* 3.2 13.0 + - + +
585D SER* 1.3 76.9 - - - +
587D ILE* 1.3 65.7 + - + +
589D LEU* 3.2 10.4 + - + +
590D LEU* 2.9 26.6 + - + +
599D VAL* 4.2 12.0 - - + +
602D VAL* 5.0 9.0 - - + -
603D LEU* 3.6 33.9 - - + -
606D LEU* 6.0 6.3 - - + -
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Residues in contact with ILE 587 (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* 2.9 31.2 + - + +
584D LYS* 3.9 6.1 - - - +
586D ILE* 1.3 86.7 - - + +
588D SER* 1.3 56.7 + - - +
590D LEU* 3.3 14.1 + - + +
591D ASP* 2.9 29.3 + - + +
603D LEU* 5.2 6.5 - - + -
621D ILE* 6.4 0.7 - - - -
624D ASN* 4.1 28.5 - - + +
625D LEU* 5.0 18.8 - - + -
631D LEU* 4.0 24.5 - - + -
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Residues in contact with SER 588 (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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552D ASP* 6.2 0.3 - - - +
584D LYS 2.9 18.5 + - - -
585D SER* 3.5 9.2 - - - -
586D ILE 3.2 0.2 - - - -
587D ILE* 1.3 76.8 - - - +
589D LEU* 1.3 57.5 + - - +
591D ASP* 3.3 3.2 + - - +
592D LYS* 2.9 32.6 + - - +
1582D SER* 3.6 32.0 + - - -
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Residues in contact with LEU 589 (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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551D LEU* 3.6 48.9 - - + +
552D ASP* 5.4 2.7 - - - -
557D SER* 4.5 5.8 - - - +
561D LEU* 4.4 22.2 - - + -
585D SER 2.9 13.8 + - - +
586D ILE* 3.5 13.7 - - + +
588D SER* 1.3 76.2 + - - +
590D LEU* 1.3 58.4 + - - +
592D LYS* 5.0 0.2 - - - -
593D HIS* 2.9 76.0 + - + +
596D ASN* 5.2 1.9 + - - +
599D VAL* 4.6 12.3 - - + -
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Residues in contact with LEU 590 (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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586D ILE 2.9 16.2 + - - +
587D ILE* 3.3 15.5 + - + +
589D LEU* 1.3 77.1 - - - +
591D ASP* 1.3 60.4 + - - +
594D GLY* 3.0 29.8 - - - +
595D ARG* 5.3 10.5 - - + +
596D ASN* 5.5 2.2 - - - +
599D VAL* 3.8 33.4 - - + -
600D LEU* 5.0 14.4 - - + -
603D LEU* 5.3 5.8 - - + -
625D LEU* 6.3 2.9 - - + -
631D LEU* 4.2 35.5 - - + +
632D LEU* 5.0 10.3 - - + -
1594D ARG* 5.4 1.2 + - - -
1662D PHE* 5.6 4.9 - - + -
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Residues in contact with ASP 591 (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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587D ILE* 2.9 17.7 + - + +
588D SER* 3.8 5.8 - - - +
590D LEU* 1.3 78.8 - - - +
592D LYS* 1.3 64.5 + - - +
594D GLY 3.8 0.2 + - - -
631D LEU* 3.4 35.4 - - + +
1293D LEU* 5.4 4.3 - - - +
1580D PHE* 5.3 7.4 - - + +
1581D LEU* 4.4 24.3 + - - +
1582D SER* 5.1 6.1 + - - -
1594D ARG* 3.6 28.5 + - - +
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Residues in contact with LYS 592 (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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588D SER* 2.9 19.7 + - - +
591D ASP* 1.3 74.5 - - - +
593D HIS* 1.3 70.5 + - + +
594D GLY 3.1 8.3 + - - -
1582D SER* 5.6 5.2 - - - +
1592D PRO* 3.7 22.8 - - + +
1593D PRO* 4.0 2.1 - - + +
1594D ARG* 3.3 27.6 + - - +
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Residues in contact with HIS 593 (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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552D ASP 4.5 9.4 - - - -
553D ARG 3.8 7.4 + - - -
554D LEU* 3.5 35.1 - - + +
557D SER* 3.7 23.1 - - - -
589D LEU* 2.9 38.8 + - + +
592D LYS* 1.3 86.6 - - + +
594D GLY* 1.3 62.2 + - - +
595D ARG 4.8 0.3 - - - +
596D ASN* 3.4 16.2 + - - +
1593D PRO* 4.4 23.3 - - + +
1594D ARG* 5.0 3.4 - - - -
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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