Contacts of the helix formed by residues 584 - 604 (chain B) in PDB entry 2YPB
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 584 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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582B ALA 4.0 5.6 + - - +
583B GLN* 1.3 77.7 - - - +
585B LYS* 1.3 67.0 + - - +
586B LEU* 3.4 9.6 + - - +
587B LEU* 3.0 27.8 + - + +
588B ILE* 2.9 27.7 + - - +
24F A 3.5 47.5 + - - +
25F C 3.4 5.4 - - - -
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Residues in contact with LYS 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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199A ARG* 6.3 0.4 - - - +
200A GLN* 6.2 1.6 - - - +
203A VAL* 4.9 13.7 - - + -
559B VAL* 5.4 4.0 - - - +
562B ILE* 5.9 1.3 - - - -
563B ASN* 3.1 24.1 + - - +
566B PHE* 3.3 44.0 - - + -
584B THR* 1.3 72.7 - - - +
586B LEU* 1.3 66.9 + - - +
588B ILE* 4.6 1.1 - - + +
589B LEU* 3.1 23.0 + - - +
25F C 3.0 44.2 + - - +
26F A 2.7 28.9 + - - -
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Residues in contact with LEU 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ARG* 6.0 1.8 - - - +
202A ASN* 3.9 18.4 - - + +
203A VAL* 3.7 42.3 - - + +
206A ALA* 3.9 13.0 - - + -
584B THR* 3.2 7.4 + - - +
585B LYS* 1.3 78.0 - - - +
587B LEU* 1.3 55.2 + - + +
589B LEU* 2.7 31.9 + - - +
590B GLN* 3.1 38.2 + - - +
24F A 5.6 7.2 - - - +
25F C 4.6 1.0 + - - -
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Residues in contact with LEU 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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581B LYS* 3.6 42.2 - - + +
582B ALA 3.7 17.3 - - - +
583B GLN* 4.6 3.6 - - + -
584B THR* 3.0 22.0 + - + +
586B LEU* 1.3 78.9 - - + +
588B ILE* 1.3 57.5 + - - +
590B GLN* 3.2 24.9 + - + +
591B GLN* 2.8 61.9 + - + +
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Residues in contact with ILE 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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566B PHE* 3.5 52.9 - - + +
567B ARG* 5.4 0.4 - - - -
569B LEU* 4.0 28.9 - - + -
570B GLY* 4.1 15.5 - - - +
573B CYS* 4.3 2.6 - - - -
583B GLN* 4.0 26.0 - - + +
584B THR 2.9 24.3 + - - +
585B LYS* 3.6 4.5 - - + +
587B LEU* 1.3 75.2 - - - +
589B LEU* 1.3 53.5 + - + +
591B GLN* 3.1 9.5 + - - +
592B ALA* 2.7 34.3 + - - +
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Residues in contact with LEU 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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203A VAL* 4.1 6.7 - - + +
206A ALA* 3.7 31.2 - - + +
207A PHE* 3.7 44.2 - - + -
210A LEU* 3.5 23.0 - - + +
228A ILE* 6.0 0.7 - - + -
229A LEU* 4.0 23.1 - - + -
566B PHE* 4.0 3.8 - - + -
585B LYS 3.1 20.6 - - - +
586B LEU* 2.7 17.1 + - - +
588B ILE* 1.3 73.5 - - + +
590B GLN* 1.3 61.2 + - - +
592B ALA* 3.2 3.2 + - - +
593B VAL* 3.1 28.0 + - - +
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Residues in contact with GLN 590 (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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206A ALA* 5.0 6.7 - - + -
209A GLU* 6.0 1.3 - - - +
586B LEU* 3.1 40.4 + - + +
587B LEU* 3.4 34.9 - - + +
589B LEU* 1.3 75.5 - - - +
591B GLN* 1.3 62.4 + - - +
593B VAL* 3.4 8.8 + - - +
594B GLN* 3.1 21.8 + - - +
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Residues in contact with GLN 591 (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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573B CYS* 4.1 12.0 - - + +
574B GLN* 4.7 2.0 - - - +
577B LEU* 3.6 24.2 - - + +
579B SER* 3.5 32.3 + - - -
581B LYS* 5.3 4.0 + - - +
583B GLN* 3.1 32.8 + - - +
587B LEU* 2.8 46.9 + - + +
588B ILE* 3.5 5.4 - - - +
590B GLN* 1.3 73.4 - - - +
592B ALA* 1.3 60.7 + - - +
594B GLN* 3.3 6.5 + - - +
595B VAL* 3.0 34.4 + - - +
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Residues in contact with ALA 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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210A LEU* 3.5 27.1 - - + -
232A ALA* 5.6 0.9 - - + -
236A ILE* 4.5 4.8 - - + +
569B LEU* 4.4 16.4 - - + -
573B CYS* 3.8 19.7 - - - -
588B ILE 2.7 20.4 + - - +
589B LEU* 3.2 0.6 + - - -
591B GLN* 1.3 73.9 - - - +
593B VAL* 1.3 61.9 + - - +
595B VAL* 3.7 4.1 + - - +
596B ILE* 3.3 28.3 + - + +
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Residues in contact with VAL 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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206A ALA 5.1 0.9 - - - +
209A GLU* 4.6 14.4 - - + +
210A LEU* 4.0 28.3 - - + +
213A LEU* 3.7 28.5 - - + -
589B LEU 3.1 17.8 + - - +
590B GLN* 3.6 10.8 - - - +
591B GLN 3.2 0.2 - - - -
592B ALA* 1.3 73.7 - - - +
594B GLN* 1.3 66.2 + - - +
595B VAL 2.9 5.3 + - - -
596B ILE* 3.0 12.8 + - - +
597B LEU* 3.0 29.9 + - + +
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Residues in contact with GLN 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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577B LEU* 3.5 37.7 - - + +
590B GLN 3.1 13.2 + - - +
591B GLN* 3.3 7.3 + - - +
593B VAL* 1.3 80.3 - - - +
595B VAL* 1.3 57.8 + - - +
597B LEU* 4.5 5.7 - - - +
598B GLY* 3.1 21.6 + - - -
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Residues in contact with VAL 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ILE* 4.0 35.0 - - + -
573B CYS* 4.3 16.8 - - + +
576B HIS* 4.1 24.9 - - + -
577B LEU* 4.1 20.0 - - + -
591B GLN 3.0 21.2 + - - +
592B ALA* 3.8 7.2 - - - +
593B VAL 2.9 0.8 + - - -
594B GLN* 1.3 75.8 - - - +
596B ILE* 1.3 54.9 + - - +
598B GLY* 2.9 4.3 + - - -
599B LEU* 2.8 45.3 + - + +
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Residues in contact with ILE 596 (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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210A LEU* 5.5 4.0 - - + -
213A LEU* 4.3 28.9 - - + -
214A ILE* 5.2 5.4 - - + -
232A ALA* 4.6 14.4 - - + +
235A TYR* 3.7 29.8 - - + -
236A ILE* 3.7 25.8 - - + -
239A LEU* 4.5 7.6 - - + -
592B ALA 3.3 14.4 - - - +
593B VAL* 3.0 7.0 + - - +
595B VAL* 1.3 77.4 - - - +
597B LEU* 1.3 57.5 + - - +
599B LEU* 3.3 0.9 + - - +
600B GLU* 2.9 59.5 + - + +
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Residues in contact with LEU 597 (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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213A LEU* 4.1 26.0 - - + -
593B VAL* 3.0 33.9 + - + +
594B GLN* 4.5 4.9 - - - +
596B ILE* 1.3 77.3 - - - +
598B GLY* 1.3 60.9 + - - +
600B GLU* 4.0 17.0 - - - +
601B GLN* 3.3 26.3 + - - +
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Residues in contact with GLY 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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594B GLN 3.1 14.8 + - - -
595B VAL 2.9 8.2 + - - -
597B LEU* 1.3 78.0 - - - +
599B LEU* 1.3 60.6 + - - +
601B GLN* 4.1 3.5 - - - +
602B GLN* 3.4 28.5 + - - +
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Residues in contact with LEU 599 (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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236A ILE* 4.0 26.7 - - + +
239A LEU* 3.6 38.1 - - + -
240A ALA* 4.7 3.4 - - - +
243A LEU* 4.0 25.6 - - + -
576B HIS* 4.5 21.3 - - + +
595B VAL* 2.8 27.7 + - + +
596B ILE* 5.0 0.2 - - - -
598B GLY* 1.3 72.1 - - - +
600B GLU* 1.3 56.3 + - - +
602B GLN* 3.0 15.4 + - - +
603B VAL* 2.6 38.6 + - + +
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Residues in contact with GLU 600 (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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213A LEU* 4.5 8.4 - - - +
235A TYR* 2.9 30.7 + - - +
239A LEU* 4.0 16.4 - - + +
596B ILE* 2.9 32.9 + - - +
597B LEU* 4.0 20.5 - - - +
599B LEU* 1.3 72.2 - - - +
601B GLN* 1.3 63.3 + - - +
603B VAL* 3.3 12.2 - - + +
604B ARG* 2.9 49.6 + - - +
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Residues in contact with GLN 601 (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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597B LEU 3.3 18.1 + - - +
598B GLY* 4.1 4.7 - - - +
599B LEU 3.2 0.4 - - - -
600B GLU* 1.3 78.1 - - - +
602B GLN* 1.3 58.5 + - - +
604B ARG* 3.4 4.1 + - - +
605B GLU* 3.1 58.3 + - - +
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Residues in contact with GLN 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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243A LEU* 3.3 34.2 - - + +
598B GLY 3.4 16.1 + - - +
599B LEU* 3.0 28.6 + - - +
601B GLN* 1.3 77.8 - - + +
603B VAL* 1.3 63.7 + - + +
605B GLU* 3.3 17.5 + - - +
606B ARG* 3.2 42.4 + - - +
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Residues in contact with VAL 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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239A LEU* 4.8 14.4 - - + +
242A LEU* 4.5 22.7 - - + -
243A LEU* 3.6 27.4 - - + -
246A GLN* 4.4 12.8 - - - +
599B LEU* 2.6 21.0 + - + +
600B GLU* 3.3 19.5 - - + +
602B GLN* 1.3 74.5 - - - +
604B ARG* 1.3 71.3 + - + +
605B GLU 3.3 0.9 - - - -
606B ARG* 3.5 8.5 + - - +
607B ASN* 2.9 24.8 + - - +
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Residues in contact with ARG 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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235A TYR* 5.0 5.1 + - - -
600B GLU* 2.9 45.3 + - - +
601B GLN* 3.7 4.5 - - - +
603B VAL* 1.3 83.1 - - + +
605B GLU* 1.3 60.1 + - - +
606B ARG 3.3 1.1 - - - -
607B ASN* 4.2 9.6 - - - +
608B LEU* 3.1 26.2 - - - +
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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