Contacts of the helix formed by residues 571 - 584 (chain J) in PDB entry 6K71
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 CYS 571 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569J ILE 5.5 0.2 - - - +
570J SER* 1.3 75.0 - - - +
572J ASP* 1.3 68.1 + - - +
573J ASN* 3.2 3.8 - - - -
574J LEU* 3.0 30.1 + - + +
575J VAL 3.5 3.6 + - - -
627J ALA 4.2 20.2 - - - +
628J TRP* 4.4 5.2 - - + -
630J PRO* 5.0 9.2 - - - -
631J VAL* 3.7 31.2 - - + +
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Residues in contact with ASP 572 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570J SER* 3.2 22.0 + - - -
571J CYS* 1.3 77.0 - - - +
573J ASN* 1.3 72.2 + - - +
575J VAL* 3.2 16.2 - - + +
576J LEU* 3.0 27.1 + - - +
631J VAL* 5.4 0.9 - - - -
178P GLU* 4.6 18.3 - - + +
179P ILE* 5.2 8.9 - - - +
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Residues in contact with ASN 573 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569J ILE* 3.8 15.6 - - - +
570J SER* 2.9 44.2 + - - +
571J CYS 3.2 4.2 - - - -
572J ASP* 1.3 77.9 + - - +
574J LEU* 1.3 66.8 + - - +
576J LEU* 3.3 17.4 - - + +
577J GLU* 3.0 45.9 + - - +
179P ILE* 6.0 2.9 - - + -
376P PHE* 4.0 26.8 - - + -
377P LEU 5.5 1.1 + - - +
456P TRP* 6.0 3.6 - - + -
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Residues in contact with LEU 574 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560J THR* 3.9 25.5 - - + +
561J LEU* 4.5 31.0 - - + +
563J ARG 5.7 0.4 - - - -
564J GLY* 4.7 9.6 - - - +
565J LYS* 6.1 3.6 - - - -
569J ILE* 4.0 13.7 - - + -
570J SER 3.6 13.5 - - - +
571J CYS* 3.0 12.5 + - + +
573J ASN* 1.3 108.6 + - - +
575J VAL* 1.3 57.7 + - - +
577J GLU* 3.3 14.9 + - - +
578J ILE* 2.9 29.4 + - - +
631J VAL* 5.5 4.7 - - + -
379P ARG* 6.4 0.9 - - + -
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Residues in contact with VAL 575 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571J CYS 3.5 1.8 + - - +
572J ASP* 3.2 24.9 + - + +
574J LEU* 1.3 76.9 - - - +
576J LEU* 1.3 62.0 + - - +
578J ILE* 3.3 12.3 - - + +
579J ASN* 2.8 50.5 + - - +
631J VAL* 3.8 32.5 - - + +
634J ASN* 5.7 7.9 - - + +
635J TYR* 4.3 18.2 - - + -
178P GLU* 4.8 8.3 - - + +
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Residues in contact with LEU 576 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572J ASP* 3.0 10.1 + - - +
573J ASN* 3.3 33.0 - - + +
575J VAL* 1.3 78.9 - - - +
577J GLU* 1.3 69.0 + - + +
579J ASN* 3.4 4.4 + - - +
580J SER* 2.8 29.6 + - - -
175P ALA* 4.4 17.7 - - + +
176P ALA* 5.9 1.8 - - - -
177P ILE* 5.7 0.2 - - + -
178P GLU* 3.2 47.8 - - + +
179P ILE* 5.0 15.3 - - + +
378P LEU* 5.6 0.2 - - + -
382P LEU* 4.6 11.0 - - + -
456P TRP* 5.2 16.2 - - + -
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Residues in contact with GLU 577 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560J THR* 3.7 22.3 + - + +
573J ASN* 3.0 31.6 + - - +
574J LEU* 3.8 12.2 - - + +
576J LEU* 1.3 86.1 - - + +
578J ILE* 1.3 57.1 + - - +
580J SER* 3.3 6.5 + - - -
581J LEU* 2.9 40.4 + - + +
377P LEU 4.6 2.6 - - - +
378P LEU* 3.4 29.1 - - + +
379P ARG* 3.3 33.3 + - - +
380P ARG* 5.8 0.4 - - + +
382P LEU* 5.3 1.6 - - + -
456P TRP* 5.6 1.0 - - - -
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Residues in contact with ILE 578 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553J PHE* 5.2 4.0 - - + -
557J VAL* 3.7 41.7 - - + -
560J THR* 5.6 5.3 - - + +
561J LEU* 4.6 13.5 - - + -
574J LEU 2.9 17.3 + - - +
575J VAL* 3.3 24.0 - - + +
577J GLU* 1.3 77.2 - - - +
579J ASN* 1.3 61.6 + - - +
581J LEU* 3.3 5.6 + - - -
582J LYS* 2.6 33.7 + - - +
592J VAL* 5.9 0.7 - - + -
596J LEU* 3.9 34.8 - - + -
635J TYR* 5.7 0.7 - - + -
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Residues in contact with ASN 579 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575J VAL* 2.8 44.2 + - - +
576J LEU* 3.9 5.2 - - - +
578J ILE* 1.3 76.3 - - - +
580J SER* 1.3 64.9 + - - +
582J LYS* 3.3 22.3 + - - +
583J TYR* 3.4 10.6 + - - +
592J VAL* 6.0 0.5 - - - +
635J TYR* 3.4 27.7 + - - -
171P SER* 5.7 0.2 - - - -
177P ILE* 6.0 3.7 - - + +
178P GLU* 4.9 4.6 + - - +
213P GLY* 5.0 9.3 + - - -
214P THR* 3.8 32.6 + - + +
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Residues in contact with SER 580 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576J LEU 2.8 19.1 + - - -
577J GLU* 3.4 9.9 - - - -
579J ASN* 1.3 76.6 - - - +
581J LEU* 1.3 61.4 + - - +
583J TYR* 3.1 23.1 + - - +
584J ALA* 4.0 6.6 + - - +
171P SER* 5.0 6.9 + - - -
175P ALA* 4.9 8.7 - - - +
382P LEU* 3.9 13.9 - - - +
383P GLY* 3.2 36.9 + - - +
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Residues in contact with LEU 581 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553J PHE* 3.3 6.7 - - - -
556J GLU* 3.6 26.9 - - + +
557J VAL* 5.3 9.0 - - + +
560J THR* 4.8 16.6 - - + +
577J GLU* 2.9 26.7 + - + +
578J ILE* 3.4 6.3 - - - +
580J SER* 1.3 77.7 - - - +
582J LYS* 1.3 64.6 + - - +
583J TYR 3.2 0.9 - - - -
584J ALA* 5.0 0.4 - - - +
380P ARG* 3.4 45.1 - - + +
383P GLY 5.6 6.3 - - - +
384P VAL 5.2 0.7 - - - +
385P ARG* 2.4 47.9 + - + +
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Residues in contact with LYS 582 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553J PHE* 3.6 8.7 - - - -
578J ILE 2.6 20.7 + - - +
579J ASN* 3.3 18.2 - - - +
580J SER 3.2 0.6 - - - -
581J LEU* 1.3 74.3 - - - +
583J TYR* 1.3 73.3 + - + +
586J ASN* 5.4 3.4 - - - +
587J ILE* 3.3 49.9 + - - +
588J SER* 4.9 1.9 - - - +
589J LEU* 4.5 20.6 - - - +
592J VAL* 3.7 31.4 - - + -
635J TYR* 5.2 1.6 - - - +
209P ALA 3.4 23.6 + - - -
210P PHE* 5.1 2.0 - - - +
212P GLN* 4.4 7.5 + - - +
214P THR* 5.1 13.1 + - + +
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Residues in contact with TYR 583 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579J ASN 3.8 8.5 - - - +
580J SER* 3.1 12.9 + - - +
582J LYS* 1.3 90.0 - - + +
584J ALA* 1.3 56.7 + - + +
585J TYR 2.8 4.1 + - - -
586J ASN* 2.6 53.0 + - - +
167P GLN* 3.2 20.9 + - - +
168P PRO* 3.4 21.9 - - - +
170P THR* 2.4 26.0 + - - -
171P SER* 3.3 43.5 - - - -
172P GLU 4.2 2.5 - - - -
210P PHE* 3.2 44.9 - + + -
214P THR* 5.2 7.2 - - + -
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Residues in contact with ALA 584 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580J SER 4.0 5.7 + - - +
581J LEU* 5.4 0.7 - - - -
583J TYR* 1.3 79.1 - - - +
585J TYR* 1.3 57.1 + - - +
168P PRO* 5.1 17.3 - - + +
383P GLY 4.1 13.9 - - - +
385P ARG* 3.4 55.0 - - + +
387P GLU* 3.8 12.0 - - - +
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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