Contacts of the helix formed by residues 588 - 602 (chain B) in PDB entry 2NUP
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 LEU 588 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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533B LEU* 3.9 48.2 - - + +
536B LEU* 5.0 8.3 - - + +
542B THR* 3.0 37.9 + - + +
544B ILE* 3.7 31.4 - - + -
586B VAL 3.3 3.8 + - - -
587B ASN* 1.3 68.1 - - - +
589B ASN* 1.3 62.0 + - - +
591B SER* 4.9 1.3 - - - -
592B LYS* 2.8 50.5 + - + +
595B VAL* 4.3 10.3 - - + -
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Residues in contact with ASN 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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539B ASN 5.7 0.2 - - - +
540B THR* 3.4 38.9 - - - +
542B THR* 4.6 1.6 + - - -
587B ASN* 3.2 11.5 + - - +
588B LEU* 1.3 83.7 - - - +
590B GLU* 1.3 68.1 + - + +
592B LYS* 3.5 19.8 + - - +
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Residues in contact with GLU 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B GLU* 4.5 12.1 - - - +
587B ASN* 3.0 26.3 + - + +
589B ASN* 1.3 81.6 - - + +
591B SER* 1.3 63.4 + - - +
592B LYS 3.7 0.7 + - - -
593B GLU* 5.3 1.2 + - - +
117C THR* 3.5 27.7 - - - +
121C LYS* 4.0 13.8 + - - -
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Residues in contact with SER 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B LEU* 4.6 3.0 + - - -
586B VAL* 4.1 24.7 - - - +
587B ASN* 2.9 18.9 + - - +
588B LEU 3.5 2.7 - - - -
590B GLU* 1.3 80.4 - - - +
592B LYS* 1.3 64.2 + - - +
593B GLU 3.3 2.7 - - - -
594B LEU* 3.0 38.5 + - - +
595B VAL* 3.1 12.6 + - - +
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Residues in contact with LYS 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B LEU* 4.1 21.7 - - + -
534B ASP* 2.5 48.5 + - - +
588B LEU* 2.8 38.2 + - + +
589B ASN* 3.5 17.5 + - - +
590B GLU 3.5 1.6 + - - +
591B SER* 1.3 72.9 - - - +
593B GLU* 1.3 69.5 + - + +
595B VAL* 3.2 9.2 - - - +
596B GLN* 3.0 40.6 + - - +
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Residues in contact with GLU 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B GLU* 6.1 2.0 - - - +
590B GLU 6.0 0.9 - - - +
591B SER* 3.3 1.0 - - - -
592B LYS* 1.3 82.9 - - + +
594B LEU* 1.3 65.9 + - + +
596B GLN* 3.3 25.0 + - - +
597B ASP* 2.8 26.1 + - - +
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Residues in contact with LEU 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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558B LEU* 3.7 35.2 - - + +
559B GLN 3.4 39.3 - - - +
560B GLU* 3.4 20.6 - - + +
562B LEU 5.1 5.4 - - - +
564B GLN* 6.2 2.7 - - - -
565B PRO* 5.4 8.7 - - + +
591B SER* 3.0 28.0 + - - +
593B GLU* 1.3 83.2 - - + +
595B VAL* 1.3 61.9 + - - +
597B ASP* 3.5 11.9 + - - +
598B LEU* 3.5 17.0 + - - +
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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
----------------------------------------------------------
533B LEU* 3.8 22.7 - - + -
544B ILE* 4.0 11.2 - - + -
546B PHE* 4.2 16.8 - - + -
558B LEU* 3.7 22.7 - - + -
586B VAL* 3.9 18.4 - - + -
588B LEU* 4.3 13.7 - - + -
591B SER* 3.1 13.6 + - - +
592B LYS 3.2 12.3 - - - +
594B LEU* 1.3 73.7 - - - +
596B GLN* 1.3 70.2 + - - +
598B LEU* 3.2 8.5 + - - +
599B LEU* 2.9 28.5 + - + +
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Residues in contact with GLN 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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530B LEU* 3.4 24.2 + - + +
533B LEU* 3.5 22.2 - - + +
592B LYS* 3.0 38.2 + - - +
593B GLU* 3.3 26.2 + - - +
595B VAL* 1.3 79.1 - - - +
597B ASP* 1.3 64.2 + - - +
599B LEU 3.4 0.9 + - - -
600B LYS* 3.2 39.1 + - - +
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Residues in contact with ASP 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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565B PRO* 5.6 7.6 - - + -
593B GLU* 2.8 23.1 + - - +
594B LEU* 3.7 13.4 - - - +
595B VAL 3.2 0.6 - - - -
596B GLN* 1.3 77.8 - - - +
598B LEU* 1.3 52.7 + - - +
600B LYS* 2.9 15.4 + - - +
601B THR* 2.6 44.1 + - - +
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Residues in contact with LEU 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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546B PHE* 4.0 22.9 - - + -
556B TYR* 3.8 30.3 - - + -
558B LEU* 3.9 34.3 - - + -
565B PRO* 4.4 13.2 - - + +
594B LEU 3.5 10.3 + - - +
595B VAL* 3.2 8.9 + - - +
597B ASP* 1.3 79.0 - - - +
599B LEU* 1.3 57.9 + - + +
601B THR* 4.1 4.3 - - - -
602B LEU* 2.8 45.0 + - + +
605B MET* 3.6 24.7 - - + -
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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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510B PHE* 5.2 0.9 - - + -
526B CYS* 3.3 42.5 - - + +
529B LEU* 3.6 36.1 - - + -
530B LEU* 3.4 39.0 - - + +
533B LEU* 4.3 14.4 - - + -
546B PHE* 3.6 35.0 - - + -
595B VAL* 2.9 17.2 + - + +
597B ASP 3.2 0.2 - - - -
598B LEU* 1.3 79.2 - - + +
600B LYS* 1.3 58.1 + - - +
602B LEU* 4.6 3.8 - - + -
603B PRO* 3.3 11.4 - - - +
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Residues in contact with LYS 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B LEU* 3.7 27.4 - - + -
596B GLN* 3.2 27.9 + - - +
597B ASP* 2.9 15.3 + - - +
599B LEU* 1.3 80.0 - - - +
601B THR* 1.3 57.5 + - - +
602B LEU 3.7 0.2 - - - -
603B PRO* 4.1 3.7 - - - +
604B GLN* 3.4 25.2 + - - +
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Residues in contact with THR 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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182A GLY* 4.3 27.3 + - - +
183A ILE* 5.2 1.3 - - + -
565B PRO* 5.6 3.3 - - + +
597B ASP* 2.6 27.1 + - - +
598B LEU* 3.9 5.3 - - - -
600B LYS* 1.3 79.8 - - - +
602B LEU* 1.3 65.5 + - - +
603B PRO 3.4 1.1 - - - -
604B GLN* 3.0 26.6 + - + +
605B MET* 3.3 33.0 + - + +
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Residues in contact with LEU 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B PHE* 4.1 28.5 - - + -
522B LEU* 4.0 6.0 - - + +
526B CYS* 4.1 10.8 - - - -
546B PHE* 4.8 8.3 - - + -
548B THR* 3.6 16.6 - - + -
556B TYR* 3.3 31.4 - - + +
598B LEU* 2.8 40.6 + - + +
599B LEU* 4.6 5.8 - - + -
601B THR* 1.3 71.8 - - - +
603B PRO* 1.3 71.7 - - + +
604B GLN 2.9 1.4 + - - -
605B MET* 3.0 25.8 + - + +
606B PHE* 3.6 18.6 - - + -
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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
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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