Contacts of the helix formed by residues 577 - 589 (chain B) in PDB entry 1XYZ
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 SER 577 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575B ASP* 2.7 25.5 + - - -
576B PHE* 1.3 76.8 - - - +
578B LYS* 1.3 70.7 + - - +
580B ASP* 4.0 3.8 - - - +
581B GLN* 3.2 23.2 + - - +
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Residues in contact with LYS 578 (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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710A GLU* 4.1 33.8 + - - +
538B TYR* 3.6 42.2 - - + +
561B GLU* 3.6 34.4 + - + +
575B ASP* 4.6 1.4 + - - -
576B PHE 3.5 0.2 - - - -
577B SER* 1.3 81.1 + - - +
579B GLY* 1.3 66.0 + - - +
581B GLN* 3.1 10.7 + - - +
582B LEU* 3.0 19.8 + - - +
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Residues in contact with GLY 579 (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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558B CYS* 4.5 18.2 - - - -
561B GLU* 5.0 4.4 + - - +
562B MET* 4.6 10.5 - - - -
567B LEU* 6.3 1.1 - - - +
575B ASP 5.6 0.2 + - - -
576B PHE* 3.4 4.4 + - - +
577B SER 3.4 0.4 - - - -
578B LYS* 1.3 79.9 - - - +
580B ASP* 1.3 56.3 + - - +
582B LEU* 3.4 3.3 + - - +
583B LEU* 3.0 26.9 + - - +
593B MET* 4.0 5.2 - - - +
633B TYR* 3.5 18.2 - - - -
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Residues in contact with ASP 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B PHE* 2.9 22.4 + - - +
577B SER* 4.0 3.6 - - - +
579B GLY* 1.3 73.4 - - - +
581B GLN* 1.3 64.9 + - - +
583B LEU* 3.8 8.1 - - - +
584B ALA* 3.1 23.6 + - - +
632B HIS* 2.8 32.3 + - - -
633B TYR* 2.7 31.7 + - - -
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Residues in contact with GLN 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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537B PHE* 4.1 25.1 + - + -
538B TYR* 3.7 33.6 + - - +
540B ASN* 5.8 0.4 + - - -
577B SER 3.2 14.8 + - - +
578B LYS* 3.1 13.9 + - - +
580B ASP* 1.3 74.9 - - - +
582B LEU* 1.3 64.9 + - - +
584B ALA* 3.4 6.4 + - - +
585B PHE* 3.3 20.6 + - - +
588B ARG* 5.1 1.2 + - - -
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Residues in contact with LEU 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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533B VAL* 4.0 30.3 - - + -
537B PHE* 4.0 25.9 - - + -
538B TYR* 3.8 15.9 - - - +
556B VAL* 4.2 16.4 - - + -
557B VAL 4.2 2.9 - - - +
558B CYS* 3.7 35.9 - - - +
578B LYS 3.0 7.5 + - - +
579B GLY 3.9 6.1 - - - +
581B GLN* 1.3 77.0 - - - +
583B LEU* 1.3 61.8 + - - +
585B PHE* 3.2 16.2 + - + +
586B ALA* 2.9 20.4 + - - +
593B MET* 4.0 11.9 - - + -
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Residues in contact with LEU 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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579B GLY 3.0 17.1 + - - +
580B ASP* 3.8 8.7 - - - +
581B GLN 3.3 0.2 - - - -
582B LEU* 1.3 77.4 - - - +
584B ALA* 1.3 57.4 + - - +
586B ALA* 3.2 6.3 + - + -
587B GLU* 2.9 58.3 + - + +
593B MET* 4.0 24.4 - - + -
633B TYR* 3.9 27.1 - - + -
636B LYS* 3.9 41.3 - - + +
637B ILE* 5.4 0.2 - - + -
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Residues in contact with ALA 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 ASP 3.1 16.9 + - - +
581B GLN* 3.8 6.1 - - - +
582B LEU 3.3 0.2 - - - -
583B LEU* 1.3 75.4 - - - +
585B PHE* 1.3 62.2 + - - +
587B GLU* 3.3 11.7 + - - +
588B ARG* 3.1 37.9 + - - +
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Residues in contact with PHE 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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537B PHE* 3.6 29.8 - + + -
546B ASN* 4.8 9.2 - - - -
549B LEU* 3.9 34.8 - - + -
550B GLN* 3.7 34.3 - - + -
556B VAL* 4.9 1.3 - - + -
581B GLN 3.3 10.9 + - - +
582B LEU* 3.2 18.5 + - + +
584B ALA* 1.3 78.7 - - - +
586B ALA* 1.3 66.0 + - + +
588B ARG* 3.3 28.6 + - - +
589B ASN* 3.0 45.5 + - - +
591B MET* 4.1 17.0 - - + -
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Residues in contact with ALA 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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556B VAL* 4.1 21.3 - - + -
582B LEU 2.9 12.9 + - - +
583B LEU* 3.5 18.6 - - + +
585B PHE* 1.3 75.5 - - - +
587B GLU* 1.3 63.4 + - + +
589B ASN 3.2 2.9 + - - -
590B GLY 3.1 4.2 + - - -
591B MET* 2.9 53.1 + - + +
592B GLN 4.8 1.6 - - - +
593B MET* 4.9 4.3 - - + -
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Residues in contact with GLU 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 LEU* 2.9 41.6 + - + +
584B ALA* 3.7 8.9 - - - +
586B ALA* 1.3 78.3 - - + +
588B ARG* 1.3 61.6 + - - +
589B ASN 3.3 0.9 + - - -
590B GLY* 3.5 8.4 + - - -
591B MET 5.0 2.9 - - - +
636B LYS* 3.8 26.6 + - - +
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Residues in contact with ARG 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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581B GLN 5.1 1.0 + - - -
584B ALA* 3.1 21.6 + - - +
585B PHE* 3.3 42.9 + - - +
587B GLU* 1.3 75.1 - - - +
589B ASN* 1.3 77.0 + - - +
590B GLY 3.6 0.7 - - - -
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Residues in contact with ASN 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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519B ARG* 3.0 23.2 + - - -
550B GLN* 3.8 28.9 + - - +
585B PHE* 3.0 48.3 + - - +
586B ALA 3.2 1.2 + - - -
587B GLU 3.1 1.0 - - - -
588B ARG* 1.3 91.8 - - - +
590B GLY* 1.3 63.5 + - - +
591B MET* 3.2 21.8 + - + +
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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