Contacts of the helix formed by residues 583 - 601 (chain C) in PDB entry 5NC5
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 THR 583 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B GLY 4.8 0.7 - - - +
224B PRO* 6.1 2.2 - - + -
228B GLN* 3.2 28.5 + - + +
229B GLN 3.7 5.7 + - - +
230B LEU 3.7 41.1 - - - +
231B ASN* 3.9 2.2 - - + -
582C ALA* 1.3 76.3 - - - +
584C GLN* 1.3 66.1 + - - +
585C GLU* 3.8 4.8 + - - +
586C ARG* 3.0 24.7 + - - +
587C THR* 3.0 22.9 + - - -
622C GLN* 3.5 17.5 - - - +
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Residues in contact with GLN 584 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B THR* 3.6 19.1 - - - +
224B PRO* 3.6 25.0 - - + +
275C TYR 3.3 15.4 + - - +
276C ASP 3.5 13.7 - - - +
278C ILE* 3.2 29.6 - - + +
583C THR* 1.3 74.1 - - - +
585C GLU* 1.3 64.2 + - - +
587C THR 3.1 1.0 + - - -
588C GLN* 2.8 22.0 + - + +
613C ASN* 3.1 26.7 + - - +
622C GLN* 3.3 33.4 + - + +
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Residues in contact with GLU 585 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B PRO* 5.9 5.1 - - + +
225B VAL 4.6 0.2 - - - +
226B LYS* 3.7 28.2 - - - +
227B GLY* 2.7 38.5 + - - -
228B GLN 3.8 9.2 + - - +
583C THR* 3.1 10.7 + - - +
584C GLN* 1.3 82.0 - - - +
586C ARG* 1.3 60.2 + - + +
588C GLN* 3.3 7.2 + - + +
589C LYS* 3.2 19.8 + - - +
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Residues in contact with ARG 586 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B GLN 5.7 0.4 - - - +
229B GLN* 4.9 7.8 + - - +
578C LEU* 3.5 13.3 - - + +
579C PRO* 3.7 21.8 - - - +
580C ALA 5.4 1.0 + - - -
582C ALA* 3.4 29.7 - - - +
583C THR* 3.0 24.5 + - - +
585C GLU* 1.3 76.1 - - + +
587C THR* 1.3 66.6 + - - +
589C LYS* 3.0 19.8 + - - +
590C VAL* 3.4 14.6 + - - +
659C LYS 5.5 0.6 + - - -
660C ASP* 3.9 26.9 + - - +
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Residues in contact with THR 587 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576C VAL* 4.6 2.9 - - + -
578C LEU* 3.2 29.1 - - + +
583C THR 3.0 6.7 + - - -
584C GLN 3.1 6.2 + - - -
586C ARG* 1.3 75.8 - - - +
588C GLN* 1.3 62.5 + - - +
590C VAL* 3.2 4.2 + - - +
591C LEU* 3.0 31.3 + - + +
613C ASN* 3.8 9.6 - - - +
622C GLN 2.5 24.5 + - - -
623C ASN* 3.4 4.7 - - - -
624C THR 3.6 31.0 - - - +
625C GLY 4.3 1.1 - - - +
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Residues in contact with GLN 588 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C ILE* 4.8 11.6 - - - +
280C GLU* 3.9 26.9 + - - +
584C GLN* 2.8 17.3 + - + +
585C GLU* 3.7 7.6 - - + +
586C ARG 3.1 0.2 - - - -
587C THR* 1.3 77.9 - - - +
589C LYS* 1.3 63.3 + - - +
591C LEU* 3.3 13.7 + - - +
592C ASN* 2.8 50.8 + - - +
611C ALA* 5.7 3.2 - - - +
613C ASN* 3.4 28.1 + - - +
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Residues in contact with LYS 589 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585C GLU 3.2 10.6 + - - +
586C ARG* 3.0 14.1 + - - +
588C GLN* 1.3 76.6 - - - +
590C VAL* 1.3 60.0 + - + +
592C ASN* 3.3 12.4 + - - +
593C GLU* 2.8 57.2 + - + +
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Residues in contact with VAL 590 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576C VAL* 3.8 23.6 - - + -
578C LEU* 4.0 17.7 - - + -
586C ARG 3.5 13.7 - - - +
587C THR 3.2 5.5 + - - +
589C LYS* 1.3 74.6 - - + +
591C LEU* 1.3 66.6 + - - +
592C ASN 3.1 1.6 - - - -
593C GLU* 2.9 10.3 + - - +
594C VAL* 2.8 26.9 + - + +
658C ILE* 4.1 16.6 - - + -
659C LYS 5.6 1.6 - - - +
660C ASP 5.5 0.4 - - - +
661C ALA* 3.9 22.7 - - + -
663C VAL* 4.0 12.1 - - + -
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Residues in contact with LEU 591 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576C VAL* 4.3 21.5 - - + -
587C THR* 3.0 29.5 + - + +
588C GLN* 3.9 15.9 - - - +
590C VAL* 1.3 77.3 - - - +
592C ASN* 1.3 54.8 + - - +
594C VAL* 3.6 6.7 - - + +
595C THR* 2.7 40.7 + - - -
611C ALA* 4.1 22.9 - - + -
612C VAL 3.6 5.6 - - - +
613C ASN* 3.5 40.4 - - + +
625C GLY* 4.4 1.8 - - - -
626C ILE 4.3 19.5 - - - +
627C ALA* 4.5 6.7 - - + +
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Residues in contact with ASN 592 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C GLU* 4.3 7.4 - - - +
588C GLN* 2.8 48.1 + - - +
589C LYS* 3.4 10.1 - - - +
591C LEU* 1.3 79.1 - - - +
593C GLU* 1.3 57.1 + - + +
595C THR* 4.0 6.0 + - - -
596C HIS* 3.0 28.9 + - - +
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Residues in contact with GLU 593 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589C LYS* 2.8 46.7 + - + +
590C VAL* 2.9 11.5 + - - +
592C ASN* 1.3 72.6 - - - +
594C VAL* 1.3 60.9 + - - +
596C HIS* 3.3 7.2 + - - +
597C TYR* 3.0 28.1 + - - +
655C PHE* 4.6 2.0 - - - -
658C ILE* 3.8 40.3 - - + +
659C LYS 5.5 0.7 + - - -
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Residues in contact with VAL 594 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574C THR* 4.2 5.4 - - + -
576C VAL* 4.2 12.6 - - + -
590C VAL 2.8 22.0 + - - +
591C LEU* 3.6 6.5 - - + +
593C GLU* 1.3 72.6 - - - +
595C THR* 1.3 66.9 + - - +
597C TYR* 3.2 10.6 + - - +
598C TYR* 3.1 44.7 + - + -
627C ALA* 4.2 19.1 - - + -
655C PHE* 3.9 18.6 - - + -
658C ILE* 4.4 7.4 - - + -
663C VAL* 3.9 26.9 - - + -
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Residues in contact with THR 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C GLY* 4.7 15.3 - - - +
591C LEU* 2.7 24.1 + - - +
592C ASN* 4.0 7.1 + - - -
594C VAL* 1.3 76.3 - - - +
596C HIS* 1.3 57.4 + - - +
598C TYR* 3.2 7.8 + - - +
599C LEU* 2.9 51.0 + - + +
609C VAL* 4.1 18.4 - - + +
611C ALA* 3.9 21.2 - - + +
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Residues in contact with HIS 596 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592C ASN 3.0 20.8 + - - +
593C GLU* 3.4 8.4 + - - +
595C THR* 1.3 75.0 - - - +
597C TYR* 1.3 68.8 + - - +
599C LEU* 3.1 5.8 + - - -
600C THR* 3.0 60.1 + - + +
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Residues in contact with TYR 597 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593C GLU 3.0 10.7 + - - +
594C VAL 3.2 1.5 + - - +
596C HIS* 1.3 81.3 + - - +
598C TYR* 1.3 72.4 + + - +
600C THR* 4.2 2.7 - - - -
601C LYS* 3.1 50.0 + - + +
602C GLU* 3.3 43.6 + - + -
647C ILE 4.3 0.2 + - - -
650C ARG* 3.6 9.6 + - - +
651C ALA* 3.5 37.5 + - + -
654C ALA* 3.8 24.5 - - + -
655C PHE* 3.6 34.3 - + + -
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Residues in contact with TYR 598 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572C PHE* 3.7 21.3 - + - -
574C THR* 2.6 27.3 + - - -
594C VAL* 3.1 43.2 + - + -
595C THR* 3.2 4.3 + - - +
596C HIS 3.2 0.4 - - - -
597C TYR* 1.3 99.0 - + - +
599C LEU* 1.3 60.3 + - - +
602C GLU* 3.5 26.8 - - + +
603C LYS* 3.7 1.0 + - - -
606C VAL* 3.7 29.1 - - + +
609C VAL* 3.8 25.6 - - + -
627C ALA* 4.9 1.1 - - + -
629C VAL* 4.1 11.9 - - + -
647C ILE* 5.2 2.2 - - + -
651C ALA* 3.9 4.9 - - + +
655C PHE* 3.3 20.5 - + - -
665C ALA* 3.4 11.3 - - - +
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Residues in contact with LEU 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282C ASN* 4.0 39.9 - - + +
283C GLY* 5.6 0.4 - - - -
595C THR* 2.9 40.5 + - + +
596C HIS* 3.1 4.5 + - - +
598C TYR* 1.3 79.8 - - - +
600C THR* 1.3 62.7 + - + +
603C LYS* 3.4 22.3 + - - +
606C VAL* 5.0 7.0 - - + +
607C GLU 5.5 3.1 - - - +
609C VAL* 4.3 10.3 - - + -
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Residues in contact with THR 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596C HIS* 3.0 56.0 + - + +
597C TYR* 4.0 1.0 + - - -
598C TYR 3.4 0.4 - - - -
599C LEU* 1.3 82.8 - - + +
601C LYS* 1.3 75.9 + - - +
602C GLU 3.4 1.1 - - - -
603C LYS* 3.0 37.9 + - - +
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Residues in contact with LYS 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597C TYR* 3.1 41.3 + - + +
600C THR* 1.3 85.2 + - - +
602C GLU* 1.4 63.8 - - - +
603C LYS 3.6 0.6 + - - -
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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