Contacts of the helix formed by residues 579 - 593 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577F ILE* 3.0 29.7 + - - +
578F ILE* 1.3 81.8 - - - +
580F GLU* 1.3 67.2 + - - +
581F ASN* 2.9 21.3 + - - +
582F HIS* 2.9 41.5 + - - +
583F ILE* 3.7 11.4 + - - +
620F LEU* 4.2 8.8 - - - +
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Residues in contact with GLU 580 (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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579F GLN* 1.3 74.7 - - - +
581F ASN* 1.3 59.2 + - - +
583F ILE* 3.2 11.1 - - + +
584F LYS* 2.9 31.6 + - - +
620F LEU* 3.8 24.3 - - + +
624F ASN* 5.8 1.3 - - - +
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Residues in contact with ASN 581 (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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545F ASP* 5.5 6.1 - - - +
548F VAL* 5.7 2.1 - - - +
579F GLN* 2.9 32.5 + - - +
580F GLU* 1.3 75.6 - - - +
582F HIS* 1.3 82.7 + - - -
584F LYS* 3.3 6.7 + - - +
585F SER* 2.9 29.8 + - - -
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Residues in contact with HIS 582 (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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544F LEU* 3.5 39.7 - - + +
545F ASP* 4.6 4.9 - - + -
548F VAL* 4.1 35.1 - - + +
577F ILE* 4.5 1.8 + - - +
578F ILE* 3.5 28.9 - - + -
579F GLN* 2.9 33.6 + - - +
580F GLU 3.3 0.4 - - - -
581F ASN* 1.3 100.0 + - - +
583F ILE* 1.3 58.0 + - - +
585F SER* 3.3 4.0 + - - -
586F ILE* 2.9 33.6 + - + +
606F LEU* 6.1 4.3 - - + -
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Residues in contact with ILE 583 (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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578F ILE* 6.6 0.2 - - + -
579F GLN 3.7 4.6 + - - +
580F GLU* 3.2 27.4 - - + +
582F HIS* 1.3 75.6 - - - +
584F LYS* 1.3 60.5 + - - +
586F ILE* 3.2 9.4 + - + +
587F ILE* 2.9 48.5 + - + +
603F LEU* 5.0 11.7 - - + -
606F LEU* 5.6 12.0 - - + +
617F ASN* 4.4 3.8 - - + +
620F LEU* 3.7 22.2 - - + +
621F ILE* 3.5 41.3 - - + +
624F ASN* 4.6 12.3 - - + +
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Residues in contact with LYS 584 (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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580F GLU 2.9 20.1 + - - +
581F ASN* 3.5 8.5 - - - +
583F ILE* 1.3 78.0 - - - +
585F SER* 1.3 56.5 + - - +
587F ILE* 3.3 7.3 + - - +
588F SER* 2.9 28.5 + - - -
624F ASN* 6.1 3.6 - - - -
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Residues in contact with SER 585 (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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548F VAL* 3.8 35.0 + - - +
551F LEU* 4.4 8.5 - - - +
552F ASP* 5.2 5.7 + - - +
581F ASN 2.9 16.9 + - - -
582F HIS 3.7 4.3 - - - -
584F LYS* 1.3 76.9 - - - +
586F ILE* 1.3 58.2 + - - +
588F SER* 3.3 8.1 + - - -
589F LEU* 2.9 28.9 + - - +
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Residues in contact with ILE 586 (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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548F VAL* 5.5 2.2 - - + -
551F LEU* 3.9 16.4 - - + -
561F LEU* 5.7 2.9 - - + -
564F LEU* 3.6 30.3 - - + -
582F HIS* 2.9 21.2 + - + +
583F ILE* 3.2 13.2 + - + +
585F SER* 1.3 76.6 - - - +
587F ILE* 1.3 65.0 + - + +
589F LEU* 3.2 10.9 + - + +
590F LEU* 2.9 26.8 + - + +
599F VAL* 4.2 11.5 - - + +
602F VAL* 5.0 9.0 - - + -
603F LEU* 3.6 34.3 - - + -
606F LEU* 6.0 6.1 - - + -
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Residues in contact with ILE 587 (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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583F ILE* 2.9 30.6 + - + +
584F LYS* 3.9 5.8 - - - +
586F ILE* 1.3 86.1 - - + +
588F SER* 1.3 57.2 + - - +
590F LEU* 3.7 13.7 - - + -
591F ASP* 2.9 29.4 + - + +
603F LEU* 5.2 7.0 - - + -
621F ILE* 6.4 0.7 - - - -
624F ASN* 4.1 29.2 - - + +
625F LEU* 5.0 18.4 - - + -
631F LEU* 4.0 24.7 - - + -
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Residues in contact with SER 588 (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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552F ASP* 6.2 0.3 - - - +
584F LYS 2.9 17.4 + - - -
585F SER* 3.5 9.9 - - - -
587F ILE* 1.3 78.1 - - - +
589F LEU* 1.3 56.5 + - - +
591F ASP* 3.3 3.5 + - - +
592F LYS* 2.9 33.3 + - - +
1582F SER* 3.6 31.3 + - - -
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Residues in contact with LEU 589 (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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551F LEU* 3.6 49.6 - - + +
552F ASP* 5.4 2.0 - - - -
557F SER* 4.5 5.6 - - - +
561F LEU* 4.4 21.8 - - + -
585F SER 2.9 14.0 + - - +
586F ILE* 3.5 13.0 - - + +
588F SER* 1.3 76.8 + - - +
590F LEU* 1.3 57.8 + - - +
593F HIS* 2.9 75.7 + - + +
594F GLY 4.3 0.2 - - - +
596F ASN* 5.2 2.2 + - - +
599F VAL* 4.6 11.9 - - + -
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Residues in contact with LEU 590 (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 ILE 2.9 16.7 + - - +
587F ILE* 3.7 15.9 - - + +
589F LEU* 1.3 76.7 - - - +
591F ASP* 1.3 59.6 + - - +
594F GLY 3.0 29.9 - - - +
595F ARG* 5.3 11.8 - - + +
596F ASN* 5.5 2.0 - - - +
599F VAL* 3.8 34.5 - - + -
600F LEU* 5.0 13.9 - - + -
603F LEU* 5.3 5.4 - - + -
625F LEU* 6.3 3.1 - - + -
631F LEU* 4.2 35.5 - - + +
632F LEU* 5.0 10.5 - - + -
1594F ARG* 5.4 0.9 + - - -
1662F PHE* 5.6 4.9 - - + -
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Residues in contact with ASP 591 (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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587F ILE* 2.9 17.4 + - + +
588F SER* 3.8 5.6 - - - +
590F LEU* 1.3 78.7 - - - +
592F LYS* 1.3 63.7 + - - +
594F GLY 3.8 0.5 + - - -
631F LEU* 3.4 35.1 - - + +
1293F LEU* 5.4 4.2 - - - +
1580F PHE* 5.3 7.6 - - + +
1581F LEU* 4.4 24.1 + - - +
1582F SER* 5.1 6.3 + - - -
1594F ARG* 3.6 29.4 + - - +
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Residues in contact with LYS 592 (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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588F SER* 2.9 19.5 + - - +
589F LEU* 5.0 0.2 - - - -
591F ASP* 1.3 74.3 - - - +
593F HIS* 1.3 71.5 + - + +
594F GLY 3.1 8.2 + - - -
1582F SER* 5.6 4.7 - - - +
1592F PRO* 3.7 23.4 - - + +
1593F PRO* 4.0 1.8 - - + +
1594F ARG* 3.3 27.4 + - - +
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Residues in contact with HIS 593 (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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552F ASP* 4.5 9.4 - - - -
553F ARG 3.8 7.5 + - - -
554F LEU* 3.5 35.6 - - + +
557F SER* 3.7 23.0 - - - -
589F LEU* 2.9 40.7 + - + +
592F LYS* 1.3 86.3 - - + +
594F GLY* 1.3 62.4 + - - +
595F ARG 4.8 0.5 - - - +
596F ASN* 3.4 15.4 + - - +
1593F PRO* 4.4 22.6 - - + +
1594F 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