Contacts of the helix formed by residues 579 - 593 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577B ILE* 3.0 29.2 + - - +
578B ILE* 1.3 80.1 - - - +
580B GLU* 1.3 66.3 + - - +
581B ASN* 2.9 20.1 + - - +
582B HIS* 2.9 41.7 + - - +
583B ILE* 3.7 10.9 + - - +
620B LEU* 4.2 9.5 - - - +
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Residues in contact with GLU 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579B GLN* 1.3 74.9 - - - +
581B ASN* 1.3 59.3 + - - +
583B ILE* 3.2 12.0 - - + +
584B LYS* 2.9 30.8 + - - +
620B LEU* 3.8 23.5 - - + +
624B ASN* 5.8 0.7 - - - +
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Residues in contact with ASN 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545B ASP* 5.5 5.7 - - - +
548B VAL* 5.7 2.7 - - - +
579B GLN* 2.9 31.7 + - - +
580B GLU* 1.3 75.3 - - - +
582B HIS* 1.3 83.3 + - - -
584B LYS* 3.5 7.2 - - - +
585B SER* 2.9 29.8 + - - -
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Residues in contact with HIS 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544B LEU* 3.5 39.7 - - + +
545B ASP* 4.6 4.9 - - + -
548B VAL* 4.1 33.5 - - + +
577B ILE* 4.5 1.8 + - - +
578B ILE* 3.5 28.2 - - + -
579B GLN* 2.9 33.0 + - - +
580B GLU 3.3 0.6 - - - -
581B ASN* 1.3 98.8 + - - +
583B ILE* 1.3 58.3 + - - +
585B SER* 3.3 4.3 + - - -
586B ILE* 2.9 33.8 + - + +
606B LEU* 6.1 4.3 - - + -
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Residues in contact with ILE 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578B ILE* 6.6 0.2 - - + -
579B GLN 3.7 5.0 + - - +
580B GLU* 3.2 27.4 - - + +
582B HIS* 1.3 75.8 - - - +
584B LYS* 1.3 60.6 + - + +
586B ILE* 3.2 9.2 + - + +
587B ILE* 2.9 49.3 + - + +
603B LEU* 5.0 11.2 - - + -
606B LEU* 5.6 13.0 - - + +
617B ASN* 4.4 4.0 - - + +
620B LEU* 3.7 21.5 - - + +
621B ILE* 3.5 40.8 - - + +
624B ASN* 4.6 11.9 - - + +
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Residues in contact with LYS 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580B GLU 2.9 20.9 + - - +
581B ASN* 3.5 7.9 - - - +
583B ILE* 1.3 79.3 - - - +
585B SER* 1.3 57.5 + - - +
587B ILE* 3.3 6.7 + - - +
588B SER* 2.9 28.1 + - - -
624B ASN* 6.1 3.8 - - - -
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Residues in contact with SER 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548B VAL* 3.8 35.3 + - - +
551B LEU* 4.4 8.5 - - - +
552B ASP* 5.2 6.1 - - - +
581B ASN 2.9 16.5 + - - -
582B HIS 3.3 4.7 + - - -
584B LYS* 1.3 76.5 - - - +
586B ILE* 1.3 58.6 + - - +
588B SER* 3.5 8.1 - - - -
589B LEU* 2.9 28.9 + - - +
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Residues in contact with ILE 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548B VAL* 5.5 2.7 - - + -
551B LEU* 3.9 16.6 - - + -
561B LEU* 5.7 2.7 - - + -
564B LEU* 3.6 29.4 - - + -
582B HIS* 2.9 20.7 + - + +
583B ILE* 3.2 13.2 + - + +
585B SER* 1.3 76.2 - - - +
587B ILE* 1.3 63.9 + - + +
589B LEU* 3.2 10.9 + - + +
590B LEU* 2.9 27.2 + - + +
599B VAL* 4.2 11.5 - - + +
602B VAL* 5.0 9.9 - - + -
603B LEU* 3.6 33.2 - - + -
606B LEU* 6.0 5.8 - - + -
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Residues in contact with ILE 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583B ILE* 2.9 31.2 + - + +
584B LYS* 3.9 5.6 - - - +
586B ILE* 1.3 85.2 - - + +
588B SER* 1.3 58.0 + - - +
590B LEU* 3.3 15.1 + - + +
591B ASP* 2.9 29.0 + - + +
603B LEU* 5.2 6.5 - - + -
621B ILE* 6.4 0.7 - - - -
624B ASN* 4.1 28.7 - - + +
625B LEU* 5.0 17.9 - - + -
631B LEU* 4.0 24.9 - - + +
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Residues in contact with SER 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552B ASP* 6.2 0.2 - - - +
584B LYS 2.9 18.2 + - - -
585B SER* 3.5 10.0 + - - -
586B ILE 3.2 0.2 - - - -
587B ILE* 1.3 76.6 - - - +
589B LEU* 1.3 57.2 + - - +
591B ASP* 3.3 3.6 + - - +
592B LYS* 2.9 33.3 + - - +
1582B SER* 3.6 31.7 + - - -
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Residues in contact with LEU 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551B LEU* 3.6 48.5 - - + +
552B ASP* 5.4 2.7 - - - -
557B SER* 4.5 5.2 - - - +
561B LEU* 4.4 22.9 - - + -
585B SER 2.9 14.4 + - - +
586B ILE* 3.5 12.8 - - + +
588B SER* 1.3 77.6 + - - +
590B LEU* 1.3 57.2 + - - +
592B LYS* 5.0 0.2 - - - -
593B HIS* 2.9 77.7 + - + +
596B ASN* 5.2 1.7 + - - +
599B VAL* 4.6 12.1 - - + -
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Residues in contact with LEU 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586B ILE* 2.9 16.3 + - + +
587B ILE* 3.3 15.5 + - + +
589B LEU* 1.3 76.5 - - - +
591B ASP* 1.3 59.6 + - - +
594B GLY 3.0 30.6 - - - +
595B ARG* 5.3 10.9 - - + +
596B ASN* 5.5 2.0 - - - +
599B VAL* 3.8 34.7 - - + +
600B LEU* 5.0 14.4 - - + -
603B LEU* 5.3 5.4 - - + -
625B LEU* 6.3 2.9 - - + -
631B LEU* 4.2 35.6 - - + +
632B LEU* 5.0 9.2 - - + -
1594B ARG* 5.4 1.4 + - - -
1662B PHE* 5.6 5.2 - - + -
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Residues in contact with ASP 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B ILE* 2.9 18.3 + - + +
588B SER* 3.8 5.8 - - - +
590B LEU* 1.3 78.2 - - - +
592B LYS* 1.3 64.7 + - + +
594B GLY 3.8 0.2 + - - -
631B LEU* 3.4 36.2 - - + +
1293B LEU* 5.4 4.0 - - - +
1580B PHE* 5.3 8.2 - - + +
1581B LEU* 4.4 24.2 + - - +
1582B SER* 5.1 6.2 + - - -
1594B ARG* 3.6 29.7 + - - +
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Residues in contact with LYS 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588B SER* 2.9 19.1 + - - +
589B LEU* 5.0 0.2 - - - -
591B ASP* 1.3 74.9 - - + +
593B HIS* 1.3 71.8 + - + +
594B GLY 3.1 8.3 + - - -
1582B SER* 5.6 5.2 - - - +
1592B PRO* 3.7 23.7 - - + +
1593B PRO* 4.0 1.9 - - + +
1594B ARG* 3.3 26.9 + - - +
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Residues in contact with HIS 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552B ASP* 4.5 9.4 - - - -
553B ARG 3.8 7.7 + - - -
554B LEU* 3.5 34.6 - - + +
557B SER* 3.7 22.8 - - - -
589B LEU* 2.9 39.7 + - + +
592B LYS* 1.3 85.5 - - + +
594B GLY* 1.3 62.5 + - - +
595B ARG 4.8 0.3 - - - +
596B ASN* 3.4 16.8 + - - +
1593B PRO* 4.4 22.6 - - + +
1594B ARG* 5.0 3.1 - - - -
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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