Contacts of the helix formed by residues 541 - 558 (chain A) 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 ASP 541 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542A VAL* 1.3 78.1 + - - +
543A LEU* 3.2 17.4 + - - +
544A ARG* 3.3 55.3 + - + +
545A TRP* 3.9 7.1 + - - +
548A ARG* 5.6 0.9 + - - -
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Residues in contact with VAL 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A ALA* 3.6 39.7 - - + +
533A ARG* 4.3 13.2 - - + +
534A ALA* 4.2 28.0 - - + +
537A GLU* 6.4 0.2 - - - -
541A ASP* 1.3 77.6 + - - +
543A LEU* 1.3 67.8 + - + +
544A ARG 3.1 1.8 - - - -
545A TRP* 3.2 11.2 + - + +
546A LEU* 3.1 20.3 + - + +
590A LEU* 4.5 11.9 - - + -
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Residues in contact with LEU 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ASP* 3.2 11.6 + - - +
542A VAL* 1.3 79.6 - - + +
544A ARG* 1.3 75.9 + - - +
546A LEU* 3.2 8.3 + - + +
547A ASP* 2.9 36.2 + - - +
585A ARG* 3.4 58.3 - - + +
590A LEU* 4.1 17.3 - - + -
591A GLN* 3.4 26.5 - - - +
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Residues in contact with ARG 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ASP* 3.3 45.5 + - + +
542A VAL 3.1 0.2 - - - -
543A LEU* 1.3 102.7 - - - +
545A TRP* 1.3 60.7 + - - +
547A ASP* 3.3 10.4 + - - +
548A ARG* 3.1 62.3 + - - +
585A ARG* 4.6 8.7 - - - +
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Residues in contact with TRP 545 (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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37A PRO* 5.9 0.9 - - + -
526A MET* 3.3 47.3 - - + -
529A LEU* 4.0 18.4 - - + -
530A ALA* 4.2 14.1 - - + -
533A ARG* 3.3 40.6 - - - +
541A ASP 3.9 7.7 + - - +
542A VAL* 3.2 14.3 + - + +
544A ARG* 1.3 77.6 - - - +
546A LEU* 1.3 96.8 + - + +
547A ASP 3.4 0.2 + - - -
548A ARG* 3.7 13.5 + - + +
549A GLN* 3.1 44.3 + - + +
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Residues in contact with LEU 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A MET* 4.0 12.1 - - + +
530A ALA* 4.0 12.6 - - + -
542A VAL* 3.1 11.3 + - + +
543A LEU* 3.4 20.6 - - + +
545A TRP* 1.3 110.6 - - + +
547A ASP* 1.3 59.0 + - - +
549A GLN* 3.8 3.7 + - - +
550A LEU* 3.3 23.2 + - - +
581A MET* 4.2 22.9 - - + +
584A LEU* 3.8 27.6 - - + -
585A ARG* 4.7 7.0 - - + +
590A LEU* 3.9 22.4 - - + -
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Residues in contact with ASP 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A LEU* 2.9 19.5 + - - +
544A ARG* 3.8 12.9 + - - +
545A TRP 3.2 0.2 - - - -
546A LEU* 1.3 76.6 - - - +
548A ARG* 1.3 54.3 + - + +
549A GLN 2.9 4.7 - - - -
550A LEU* 2.9 9.2 + - - +
551A ILE* 2.7 47.9 + - + +
581A MET* 5.7 0.7 - - - +
585A ARG* 2.7 42.7 + - - -
752A PHE* 4.3 11.3 - - - -
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Residues in contact with ARG 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A ASP 5.6 1.0 + - - -
544A ARG* 3.1 52.5 + - - +
545A TRP* 4.3 10.9 - - - +
547A ASP* 1.3 77.1 - - + +
549A GLN* 1.3 68.1 + - - +
551A ILE* 4.2 10.7 - - + +
552A ARG* 3.0 40.0 + - - +
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Residues in contact with GLN 549 (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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35A VAL* 3.4 31.9 - - + +
36A VAL* 6.0 1.0 - - + +
526A MET* 4.2 17.3 - - + -
545A TRP* 3.1 49.0 + - + +
546A LEU* 4.1 4.7 - - + +
547A ASP 2.9 0.8 - - - -
548A ARG* 1.3 86.0 - - - +
550A LEU* 1.3 59.3 + - - +
552A ARG* 3.0 35.2 + - - +
553A LEU* 2.9 31.2 + - - +
577A TYR* 5.1 4.3 + - - +
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Residues in contact with LEU 550 (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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546A LEU 3.3 16.3 + - - +
547A ASP* 2.9 14.6 + - - +
549A GLN* 1.3 76.1 - - - +
551A ILE* 1.3 60.7 + - + +
553A LEU* 3.2 1.6 + - + +
554A CYS* 2.8 45.9 + - - -
570A PHE* 5.5 0.7 - - + -
577A TYR* 3.7 33.0 - - + -
578A PRO* 4.2 11.9 - - + -
581A MET* 4.0 17.0 - - + -
752A PHE* 3.5 33.7 - - + -
756A LEU* 3.9 26.0 - - + -
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Residues in contact with ILE 551 (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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547A ASP* 2.7 33.6 + - + +
548A ARG* 4.2 9.4 - - + +
550A LEU* 1.3 73.8 - - + +
552A ARG* 1.3 62.8 + - + +
554A CYS* 3.2 2.9 + - - +
555A GLN* 3.0 48.4 + - + +
756A LEU* 4.0 21.5 - - + -
759A LEU* 3.5 48.0 - - + +
760A ALA 4.7 1.1 - - - +
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Residues in contact with ARG 552 (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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35A VAL* 3.7 14.8 - - + -
548A ARG* 3.0 29.4 + - - +
549A GLN* 3.0 34.7 + - - +
550A LEU 3.2 0.4 - - - -
551A ILE* 1.3 78.7 - - + +
553A LEU* 1.3 63.2 + - - +
555A GLN* 2.9 23.9 + - - +
556A LYS* 2.9 15.2 + - - +
764A ALA 5.7 4.2 + - - +
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Residues in contact with LEU 553 (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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21A TRP* 4.5 5.4 - - + -
35A VAL* 3.7 18.3 - - + +
36A VAL* 4.4 10.5 - - + -
517A PHE* 4.2 5.4 - - + -
549A GLN 2.9 18.1 + - - +
550A LEU* 3.6 4.3 - - + +
552A ARG* 1.3 76.6 - - - +
554A CYS* 1.3 62.5 + - - +
557A PHE* 3.1 53.9 + - + -
570A PHE* 3.8 7.6 - - + -
574A PHE* 3.8 26.2 - - + -
577A TYR* 3.4 47.6 - - + +
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Residues in contact with CYS 554 (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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550A LEU* 2.8 24.9 + - - +
551A ILE* 3.4 11.7 - - - +
552A ARG 3.1 0.2 - - - -
553A LEU* 1.3 78.6 - - - +
555A GLN* 1.3 57.1 + - - +
558A GLY* 3.0 22.0 + - - -
560A TYR* 4.9 0.3 - - - -
568A PHE* 3.1 31.5 - - + -
570A PHE* 3.5 26.7 - - - -
578A PRO* 5.1 0.2 - - - -
756A LEU* 3.6 34.5 - - - -
760A ALA* 4.1 10.5 - - + -
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Residues in contact with GLN 555 (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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551A ILE* 3.0 24.5 + - - +
552A ARG* 2.9 15.6 + - - +
554A CYS* 1.3 78.3 - - - +
556A LYS* 1.3 62.8 + - - +
558A GLY 4.3 1.6 + - - +
560A TYR* 3.1 33.2 + - - +
759A LEU 3.2 10.1 + - - -
760A ALA* 3.0 31.9 + - - +
762A SER 3.7 4.6 + - - -
763A SER 3.2 24.0 + - - -
764A ALA* 3.6 27.7 - - + +
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Residues in contact with LYS 556 (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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30A GLU* 3.7 21.2 + - - +
33A ARG* 2.8 32.8 + - - +
34A MET* 4.8 4.0 - - - +
35A VAL* 3.8 14.1 - - + +
510A ILE* 3.4 32.8 - - + +
552A ARG 2.9 12.9 + - - +
555A GLN* 1.3 78.5 - - - +
557A PHE* 1.3 94.7 + - + +
558A GLY 5.0 0.8 - - - +
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Residues in contact with PHE 557 (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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21A TRP* 3.7 23.3 - + - -
34A MET* 5.9 2.2 - - - -
35A VAL* 3.8 9.4 - - + -
510A ILE* 3.6 23.8 - - + -
513A ILE* 4.7 5.2 - - + -
514A ALA* 3.6 28.9 - - + -
553A LEU* 3.1 40.4 + - + +
556A LYS* 1.3 111.8 - - + +
558A GLY* 1.3 66.2 + - - +
559A GLU* 4.6 5.9 - - - +
570A PHE* 3.7 7.5 - - - -
571A SER* 5.1 7.3 + - - -
574A PHE* 3.7 27.9 - + + -
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Residues in contact with GLY 558 (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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554A CYS 3.0 23.1 + - - -
555A GLN 4.5 1.2 - - - +
556A LYS 3.7 0.9 - - - -
557A PHE* 1.3 84.1 - - - +
559A GLU* 1.3 70.3 + - - +
560A TYR* 3.9 13.6 - - - -
568A PHE* 3.7 2.7 - - - -
569A ARG 3.7 2.0 - - - -
570A PHE* 3.3 21.3 - - - -
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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
------------------------------------------------------------
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