Contacts of the helix formed by residues 591 - 607 (chain B) in PDB entry 1XR2
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 LYS 591 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B ASP* 3.0 31.1 + - - +
256B SER 5.6 0.8 + - - -
257B ASN* 4.7 1.4 - - - +
259B GLU* 2.6 38.1 + - - -
586B PRO* 3.9 17.2 - - + +
588B LYS* 3.0 27.2 + - + +
590B SER* 1.3 82.4 + - - +
592B TRP* 1.3 63.7 + - - +
593B PRO* 3.3 3.9 - - - -
594B GLU* 3.6 8.9 + - + +
595B TYR* 3.4 18.2 + - - +
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Residues in contact with TRP 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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166A ARG* 4.8 1.8 - - - -
168A ASN* 4.0 19.3 - - + -
582B ARG* 3.5 38.4 - - - -
585B ALA* 3.6 8.1 - - + +
586B PRO* 2.9 35.4 + - + -
587B ILE 5.9 0.2 - - - -
588B LYS 3.4 13.2 - - - -
589B LYS* 3.1 54.6 + - + +
591B LYS* 1.3 75.8 - - - +
593B PRO* 1.3 69.5 - - + +
595B TYR* 3.2 3.5 + - - -
596B PHE* 2.8 51.8 + + + +
626B GLU* 3.7 29.8 - - + -
627B ILE* 3.9 9.6 - - + -
630B TYR* 4.1 7.0 - + - +
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Residues in contact with PRO 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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168A ASN* 3.8 29.8 - - + +
171A GLU* 3.4 34.3 - - + +
172A LYS* 5.9 2.0 - - + +
590B SER 3.6 10.5 - - - +
591B LYS 3.3 4.9 - - - -
592B TRP* 1.3 94.8 - - + +
594B GLU* 1.3 61.9 + - - +
596B PHE* 4.1 1.2 - - - +
597B GLU* 3.2 21.0 + - - +
630B TYR* 4.5 11.5 - - + +
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Residues in contact with GLU 594 (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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591B LYS* 3.6 9.2 + - + +
592B TRP 3.3 0.2 - - - -
593B PRO* 1.3 76.7 - - - +
595B TYR* 1.3 69.3 + - - +
597B GLU* 3.2 18.7 + - - +
598B TRP* 3.3 13.3 - - + -
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Residues in contact with TYR 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B VAL* 3.7 8.3 - - - +
580B ALA 3.1 15.2 + - - -
581B PHE* 2.8 31.2 + - - -
584B LYS* 3.4 22.7 - - + +
585B ALA* 3.6 23.8 - - + -
586B PRO* 3.6 24.7 - - + -
591B LYS 3.4 5.9 + - - +
592B TRP 3.2 5.7 + - - +
594B GLU* 1.3 78.4 - - - +
596B PHE* 1.3 94.7 + + - +
597B GLU 3.0 1.9 + - - -
598B TRP* 3.0 56.5 + + - +
599B ALA* 3.1 20.2 + - + +
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Residues in contact with PHE 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B PHE* 3.4 62.1 - + - -
582B ARG* 4.6 2.7 - - - -
585B ALA* 4.2 7.6 - - + -
592B TRP* 2.8 61.5 + + + +
593B PRO 4.4 0.9 - - - +
595B TYR* 1.3 88.6 - + - +
597B GLU* 1.3 61.3 + - - +
598B TRP 3.3 0.2 - - - -
599B ALA* 3.8 2.9 - - - -
600B ILE* 2.9 33.8 + - + +
627B ILE* 4.1 15.5 - - + -
630B TYR* 3.5 46.2 - + + -
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Residues in contact with GLU 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B PRO 3.2 14.6 + - - +
594B GLU* 3.2 15.7 - - - +
595B TYR 3.0 1.2 + - - -
596B PHE* 1.3 79.0 - - - +
598B TRP* 1.3 58.4 + - + +
600B ILE* 3.9 5.3 - - - +
601B ASN* 3.0 31.6 + - - +
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Residues in contact with TRP 598 (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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534B VAL* 4.1 22.7 - - + -
537B MET* 4.7 7.4 - - - -
548B GLU* 3.5 35.6 + - + +
549B ARG* 3.5 37.6 - - + +
552B ALA* 3.8 29.2 - - + -
553B TYR* 3.5 21.8 - - + +
584B LYS* 4.9 7.0 - - + -
594B GLU 3.3 21.7 - - - -
595B TYR* 3.0 42.3 + + - +
597B GLU* 1.3 76.1 - - + +
599B ALA* 1.3 62.8 + - - +
600B ILE 3.2 1.8 - - - -
601B ASN* 3.7 0.7 - - - -
602B ALA* 2.7 35.7 + - - +
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Residues in contact with ALA 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B VAL* 4.0 14.9 - - + +
581B PHE* 4.1 21.7 - - + -
595B TYR* 3.1 45.8 + - + +
596B PHE* 4.1 3.1 - - - -
598B TRP* 1.3 85.1 - - - +
600B ILE* 1.3 63.2 + - - +
602B ALA* 3.7 1.6 - - - +
603B PHE* 3.0 24.4 + - - +
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Residues in contact with ILE 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B PHE* 4.2 12.8 - - + -
596B PHE* 2.9 36.5 + - + +
597B GLU* 3.9 5.4 - - - +
599B ALA* 1.3 74.4 - - - +
601B ASN* 1.3 73.5 + - - +
603B PHE* 3.1 4.0 + - - +
604B ASN* 2.9 41.9 + - - +
630B TYR* 4.0 17.3 - - + +
633B GLN* 3.7 51.6 - - + +
634B LEU* 3.9 9.2 - - + -
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Residues in contact with ASN 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B PHE* 3.2 36.0 - - + +
553B TYR* 3.2 29.4 + - + +
597B GLU* 3.0 20.5 + - - +
598B TRP 3.7 0.4 - - - +
600B ILE* 1.3 87.8 - - - +
602B ALA* 1.3 57.1 + - - +
604B ASN* 3.3 5.4 + - - +
605B LEU 2.8 25.6 + - - -
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Residues in contact with ALA 602 (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 PRO* 3.6 19.3 - - + +
534B VAL* 4.2 5.8 - - + -
552B ALA* 4.0 18.2 - - + +
553B TYR* 3.6 21.5 - - + -
556B ALA* 3.4 11.7 - - - +
598B TRP 2.7 22.5 + - - +
599B ALA 3.7 3.8 - - - +
601B ASN* 1.3 73.1 - - - +
603B PHE* 1.3 64.3 + - - +
605B LEU* 3.2 1.3 + - - -
606B ALA 3.1 17.8 + - - -
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Residues in contact with PHE 603 (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 PRO* 4.1 9.1 - - + +
576B ILE* 4.0 36.6 - - + -
578B GLU* 4.3 28.5 - - + +
581B PHE* 5.5 1.6 - + + -
599B ALA 3.0 14.8 + - - +
600B ILE 3.6 7.0 - - - +
602B ALA* 1.3 75.6 - - - +
604B ASN* 1.3 73.0 + - - +
606B ALA* 3.1 5.5 + - - +
607B ALA* 2.8 45.3 + - + +
615B ILE* 4.6 5.2 - - + -
617B ALA* 4.0 23.1 - - + -
619B MET* 5.8 1.3 - - + -
634B LEU* 3.7 33.7 - - + -
636B PHE* 4.4 15.7 - + + -
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Residues in contact with ASN 604 (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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381B SER 4.1 0.7 - - - +
382B PHE* 3.2 25.6 + - + +
384B ARG* 5.6 0.2 - - - +
600B ILE* 2.9 29.6 + - - +
601B ASN* 3.8 8.1 - - - +
603B PHE* 1.3 79.0 - - - +
605B LEU* 1.3 61.0 + - - +
607B ALA* 3.4 4.1 - - - +
608B ASN* 2.8 30.5 + - - +
633B GLN 3.2 21.0 + - - -
634B LEU* 3.5 5.5 - - - -
635B GLU* 2.7 41.8 + - + +
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Residues in contact with LEU 605 (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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381B SER* 3.3 33.7 - - - +
382B PHE* 3.9 18.5 - - + -
553B TYR* 3.5 31.6 - - + +
556B ALA* 3.6 10.1 - - + -
557B LEU* 3.2 38.8 - - + +
560B ASN* 3.3 21.6 + - + +
601B ASN 2.8 17.7 + - - +
602B ALA* 3.5 5.8 - - - +
603B PHE 3.2 0.2 - - - -
604B ASN* 1.3 77.0 - - - +
606B ALA* 1.3 63.0 + - - +
608B ASN* 3.3 4.4 + - + +
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Residues in contact with ALA 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B PRO* 4.0 18.4 - - + -
556B ALA* 3.6 17.5 - - - +
559B ILE* 3.8 22.4 - - + -
560B ASN* 3.3 15.7 + - - +
563B VAL* 3.4 21.0 - - - +
576B ILE* 4.3 8.5 - - + -
602B ALA 3.1 8.9 + - - +
603B PHE 3.5 7.6 - - - +
605B LEU* 1.3 82.3 - - - +
607B ALA* 1.3 56.6 + - - +
608B ASN 3.4 0.2 - - - -
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Residues in contact with ALA 607 (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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384B ARG* 3.6 15.0 + - - -
563B VAL* 5.4 0.2 - - - -
576B ILE* 3.8 20.2 - - + -
603B PHE* 2.8 36.2 + - + +
604B ASN* 3.4 5.6 - - - +
605B LEU 3.2 0.2 - - - -
606B ALA* 1.3 76.8 - - - +
608B ASN* 1.3 51.9 + - - +
609B ALA* 2.5 23.3 + - - +
615B ILE* 4.0 17.1 - - + +
635B GLU* 4.8 4.9 - - + +
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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
------------------------------------------------------------
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