Contacts of the helix formed by residues 591 - 607 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ASP* 4.0 19.1 - - - +
235A SER* 4.6 0.2 + - - -
257A ASN* 5.9 0.4 - - - -
259A GLU* 3.4 34.9 + - - +
586A PRO* 4.0 16.6 - - + +
588A LYS* 3.0 41.9 + - + +
590A SER* 1.3 81.4 + - - +
592A TRP* 1.3 64.3 + - - +
593A PRO* 3.4 3.3 - - - -
594A GLU* 3.6 9.3 + - + +
595A TYR* 3.4 19.1 + - - +
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Residues in contact with TRP 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582A ARG* 3.4 38.4 - - + -
585A ALA* 3.7 10.7 - - + +
586A PRO* 2.9 34.4 + - + -
588A LYS 3.3 14.1 - - - -
589A LYS* 2.9 48.9 + - + +
591A LYS* 1.3 76.4 - - - +
593A PRO* 1.3 64.7 - - + +
595A TYR* 3.2 3.6 + - - -
596A PHE* 2.8 55.2 + + + -
626A GLU* 3.6 31.2 - - + -
627A ILE* 4.1 12.3 - - + -
630A TYR* 4.0 9.4 - + - +
166B ARG* 4.8 1.8 - - - -
168B ASN* 4.0 18.6 - - + -
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Residues in contact with PRO 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590A SER 3.6 10.8 - - - +
591A LYS 3.4 4.0 - - - -
592A TRP* 1.3 95.0 - - + +
594A GLU* 1.3 62.8 + - - +
596A PHE* 4.1 3.0 - - + +
597A GLU* 3.2 20.8 + - - +
630A TYR* 4.4 11.0 - - + +
168B ASN* 3.7 28.5 - - + +
171B GLU* 3.8 31.9 - - + +
172B LYS* 6.1 1.8 - - + +
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Residues in contact with GLU 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591A LYS* 3.6 10.9 + - + +
592A TRP 3.3 0.4 - - - -
593A PRO* 1.3 77.9 - - - +
595A TYR* 1.3 65.0 + - - +
597A GLU* 3.2 20.5 - - - +
598A TRP* 3.6 11.7 - - - -
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Residues in contact with TYR 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A VAL* 3.7 12.1 - - + +
580A ALA 3.2 12.0 + - - -
581A PHE 2.7 30.3 + - - -
584A LYS* 3.8 15.1 - - + +
585A ALA* 3.5 17.0 - - + -
586A PRO* 3.5 37.7 - - + -
591A LYS 3.4 3.8 + - - +
592A TRP 3.2 4.4 + - - +
594A GLU* 1.3 79.5 - - - +
596A PHE* 1.3 92.0 + + - +
597A GLU 3.0 1.2 + - - -
598A TRP* 3.1 49.5 + + - +
599A ALA* 3.1 34.1 + - + +
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Residues in contact with PHE 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A PHE* 3.7 55.9 - + - -
582A ARG* 4.6 2.7 - - + -
585A ALA* 4.3 7.0 - - + -
592A TRP* 2.8 56.9 + + + +
593A PRO 4.3 1.3 - - - +
595A TYR* 1.3 87.4 - + - +
597A GLU* 1.3 62.7 + - - +
599A ALA* 3.8 2.9 - - + -
600A ILE* 2.9 33.8 + - + +
627A ILE* 4.1 14.4 - - + -
630A TYR* 3.6 58.1 - + + -
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Residues in contact with GLU 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A PRO 3.2 13.6 + - - +
594A GLU* 3.2 15.7 - - - +
595A TYR 3.0 0.8 + - - -
596A PHE* 1.3 79.7 - - - +
598A TRP* 1.3 59.1 + - + +
600A ILE* 4.1 4.8 - - - +
601A ASN* 2.9 31.4 + - - +
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Residues in contact with TRP 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534A VAL* 4.3 13.0 - - + -
537A MET* 3.4 34.5 - - + -
548A GLU* 3.7 31.2 + - + +
549A ARG* 4.0 23.7 - - + +
552A ALA* 3.8 16.6 - - + -
553A TYR* 3.7 22.2 - + + +
584A LYS* 4.3 9.6 - - + -
594A GLU 3.6 14.1 - - - -
595A TYR* 3.1 49.6 + + - +
597A GLU* 1.3 78.1 - - + +
599A ALA* 1.3 61.1 + - - +
600A ILE 3.3 0.2 - - - -
601A ASN* 3.6 0.9 - - - +
602A ALA* 2.7 36.4 + - + +
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Residues in contact with ALA 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A VAL* 4.2 13.3 - - + +
581A PHE* 4.2 17.5 - - + -
595A TYR* 3.1 44.9 + - + +
596A PHE* 4.0 7.9 - - - +
598A TRP* 1.3 84.9 - - - +
600A ILE* 1.3 64.1 + - - +
602A ALA* 3.2 2.6 + - - +
603A PHE* 2.9 24.1 + - - +
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Residues in contact with ILE 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581A PHE* 4.1 13.2 - - + -
596A PHE* 2.9 38.6 + - + +
597A GLU* 4.1 4.7 - - - +
599A ALA* 1.3 76.6 - - - +
601A ASN* 1.3 66.0 + - - +
603A PHE* 3.4 1.0 + - - +
604A ASN* 3.0 41.6 + - - +
630A TYR* 3.9 16.6 - - + +
633A GLN* 3.6 52.9 - - + +
634A LEU* 3.9 11.4 - - + -
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Residues in contact with ASN 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A PHE* 3.4 36.7 - - + +
553A TYR* 3.3 27.6 + - + +
597A GLU* 2.9 22.7 + - - +
598A TRP 3.3 1.5 + - - +
599A ALA 3.3 0.4 - - - -
600A ILE* 1.3 82.5 - - - +
602A ALA* 1.3 64.4 + - - +
604A ASN* 3.8 4.9 + - - +
605A LEU* 2.9 20.3 + - - +
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Residues in contact with ALA 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A PRO* 3.7 18.8 - - + +
534A VAL* 4.1 12.6 - - + -
552A ALA* 4.1 20.0 - - + +
553A TYR* 3.8 12.7 - - + -
556A ALA* 3.3 13.4 - - - +
598A TRP 2.7 21.7 + - - +
599A ALA 3.2 4.7 + - - +
601A ASN* 1.3 73.6 - - - +
603A PHE* 1.3 63.6 + - - +
605A LEU* 3.3 1.8 + - - -
606A ALA 3.2 17.2 + - - -
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Residues in contact with PHE 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A PRO* 4.3 8.9 - - + +
576A ILE* 3.7 43.7 - - + -
578A GLU* 4.3 27.3 + - + +
581A PHE* 5.5 2.0 - - + -
599A ALA 2.9 15.7 + - - +
602A ALA* 1.3 75.1 - - - +
604A ASN* 1.3 72.8 + - - +
606A ALA* 3.1 5.5 + - - +
607A ALA* 2.8 45.7 + - + +
615A ILE* 4.6 7.0 - - + -
617A ALA* 4.2 20.9 - - + -
619A MET* 5.6 0.9 - - + -
634A LEU* 3.7 39.5 - - + -
635A GLU 4.4 4.0 - - - -
636A PHE* 4.6 7.6 - - + -
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Residues in contact with ASN 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A SER 4.1 2.3 - - - +
382A PHE* 3.5 22.6 + - + +
384A ARG* 5.6 0.9 - - - +
600A ILE* 3.0 30.6 + - - +
601A ASN* 3.9 6.2 + - - +
603A PHE* 1.3 77.8 - - - +
605A LEU* 1.3 60.9 + - - +
607A ALA* 3.5 3.4 - - - +
608A ASN* 2.9 30.3 + - - +
633A GLN 3.1 21.6 + - - -
634A LEU* 3.5 4.4 - - - -
635A GLU* 2.7 42.7 + - + +
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Residues in contact with LEU 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A SER* 3.6 35.0 - - - +
382A PHE* 3.9 24.0 - - + -
553A TYR* 3.7 34.8 - - + +
556A ALA* 3.8 9.0 - - + -
557A LEU* 3.7 30.3 - - + +
560A ASN* 3.4 20.9 + - + +
601A ASN 2.9 17.0 + - - +
602A ALA 3.6 4.7 - - - +
603A PHE 3.2 0.2 - - - -
604A ASN* 1.3 75.8 - - - +
606A ALA* 1.3 63.2 + - - +
608A ASN* 3.4 8.5 - - + +
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Residues in contact with ALA 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A PRO* 4.0 17.5 - - + -
556A ALA* 3.6 21.0 - - - +
559A ILE* 3.8 19.5 - - + -
560A ASN* 3.2 17.6 + - - -
563A VAL* 3.4 19.1 - - - +
576A ILE* 4.3 8.1 - - + -
602A ALA 3.2 8.8 + - - +
603A PHE 3.1 8.3 + - - +
605A LEU* 1.3 81.2 - - - +
607A ALA* 1.3 55.4 + - - +
608A ASN 3.3 0.4 - - - -
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Residues in contact with ALA 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ARG* 3.8 12.9 + - - -
563A VAL* 5.2 0.7 - - - -
576A ILE* 3.9 16.6 - - + -
603A PHE* 2.8 38.9 + - + +
604A ASN* 3.5 5.2 - - - +
606A ALA* 1.3 75.1 - - - +
608A ASN* 1.3 52.9 + - - +
609A ALA* 2.6 24.3 + - - +
615A ILE* 4.0 18.8 - - + +
635A GLU* 4.9 6.1 - - + +
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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
------------------------------------------------------------
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