Contacts of the strand formed by residues 800 - 811 (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 800 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B LEU* 3.4 31.6 - - + -
376B ILE* 4.2 20.4 - - + -
453B ASN 5.2 1.9 - - - +
754B THR* 4.7 1.9 - - - +
798B THR* 3.4 20.1 - - + +
799B GLN* 1.3 94.4 - - + +
801B VAL* 1.3 69.9 + - - +
824B CYS* 4.2 18.8 - - - -
825B LEU 3.3 9.9 - - - +
826B PRO* 3.7 3.6 - - + -
827B VAL* 4.1 0.6 - - - +
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Residues in contact with VAL 801 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ILE* 3.7 33.0 - - + -
453B ASN 5.1 1.1 - - - -
754B THR* 3.5 21.1 - - + +
757B LEU* 3.8 24.0 - - + -
795B LEU* 4.4 11.7 - - + -
798B THR* 4.3 7.9 - - - +
800B LEU* 1.3 81.7 - - - +
802B SER* 1.3 65.4 + - - +
803B PHE* 4.1 4.7 - - + -
823B LEU 3.8 0.3 - - - +
824B CYS* 3.4 0.9 - - - -
825B LEU* 2.9 33.9 + - - +
827B VAL* 3.8 16.4 - - + -
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Residues in contact with SER 802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B PHE* 4.1 0.2 - - - +
453B ASN* 2.7 34.9 + - - +
454B LEU* 3.5 12.4 - - - +
753B CYS* 3.2 22.9 - - - -
754B THR* 2.8 15.6 + - - -
801B VAL* 1.3 77.5 + - - +
803B PHE* 1.3 67.9 + - - +
822B THR* 4.4 6.3 - - - -
823B LEU 2.9 12.8 + - - -
824B CYS* 3.6 17.0 - - - +
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Residues in contact with PHE 803 (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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386B PHE* 3.5 25.1 - - + -
393B ILE* 4.1 11.4 - - + -
409B LEU* 3.8 17.9 - - + -
454B LEU* 5.2 0.2 - - - -
751B ILE* 5.5 0.2 - - + -
752B ARG 3.3 6.3 - - - +
753B CYS* 3.0 27.6 - - + -
757B LEU* 3.3 35.7 - - + -
789B MET* 3.7 17.0 - - + -
801B VAL* 4.1 11.9 - - + -
802B SER* 1.3 78.0 - - - +
804B GLN* 1.3 61.0 + - - +
822B THR* 3.1 5.2 - - - +
823B LEU* 2.6 62.6 + - + +
825B LEU* 3.6 27.4 - - + -
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Residues in contact with GLN 804 (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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386B PHE* 4.5 1.1 - - - -
436B THR* 3.5 14.4 - - + +
437B TYR* 2.9 62.6 + - - +
439B ASN* 4.2 3.4 - - - +
454B LEU* 4.5 13.0 - - + +
750B ARG 3.8 1.0 - - - +
751B ILE* 3.6 1.6 - - - -
752B ARG* 2.8 50.3 + - + +
803B PHE* 1.3 75.2 - - - +
805B SER* 1.3 60.5 + - - +
806B ALA* 4.2 0.3 + - - +
820B VAL* 3.4 20.0 - - + +
821B HIS 3.2 13.7 - - - +
822B THR* 3.6 17.6 + - + +
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Residues in contact with SER 805 (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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386B PHE* 4.1 11.0 - - - -
411B LEU* 4.0 14.4 - - - +
413B PRO* 4.5 4.0 - - - +
749B MET* 4.4 5.8 - - - -
750B ARG 3.3 5.6 - - - -
751B ILE* 3.7 25.8 - - - +
804B GLN* 1.3 74.8 - - - +
806B ALA* 1.3 59.9 + - - +
819B ARG 3.8 0.6 - - - +
820B VAL* 3.4 7.1 - - - +
821B HIS* 3.1 48.3 + - - +
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Residues in contact with ALA 806 (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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437B TYR* 3.7 32.1 - - + +
748B VAL 3.6 1.6 - - - +
749B MET* 3.0 28.1 - - - +
750B ARG* 3.0 15.2 + - + +
752B ARG* 4.5 10.5 - - - +
804B GLN* 5.2 0.9 - - - +
805B SER* 1.3 75.0 - - - +
807B LEU* 1.3 61.1 + - - +
808B LEU* 3.9 1.0 + - + +
818B ILE* 4.3 4.7 - - + -
819B ARG 3.4 4.3 - - - -
820B VAL* 4.0 5.6 - - + -
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Residues in contact with LEU 807 (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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413B PRO* 4.4 17.9 - - + +
414B PHE* 4.9 8.7 - - + -
747B ALA* 3.7 26.0 - - + -
748B VAL 3.7 5.4 - - - +
749B MET* 3.8 25.1 - - + -
776B LEU* 4.0 10.1 - - + -
779B VAL* 3.7 29.2 - - + -
806B ALA* 1.3 72.9 - - - +
808B LEU* 1.3 63.1 + - - +
809B TYR* 3.7 13.5 - - + -
817B ARG 3.3 2.4 - - - +
818B ILE* 3.0 7.6 - - - -
819B ARG* 2.7 49.6 + - + +
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Residues in contact with LEU 808 (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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492B ALA* 4.0 12.1 - - + -
496B TYR* 3.4 38.8 - - + +
498B LEU* 6.3 1.1 - - + -
746B GLU 4.2 0.3 - - - +
747B ALA* 2.7 26.3 - - - +
748B VAL* 2.8 37.4 + - + +
806B ALA* 3.9 1.6 + - + -
807B LEU* 1.3 69.6 - - - +
809B TYR* 1.3 60.7 + - - +
816B ARG* 3.7 21.5 + - - +
817B ARG 3.4 5.6 - - - +
818B ILE* 3.7 28.0 - - + +
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Residues in contact with TYR 809 (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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414B PHE* 3.7 30.7 - + - -
489B GLU* 2.7 33.8 + - - -
743B ILE 4.8 1.1 - - - -
744B GLY* 3.4 23.1 - - - -
745B PHE 3.8 2.9 - - - +
747B ALA* 3.1 25.6 - - + -
779B VAL* 4.3 7.2 - - + -
807B LEU* 3.7 19.5 - - + -
808B LEU* 1.3 72.6 - - - +
810B THR* 1.3 63.5 + - - +
811B SER* 4.2 18.3 - - - -
816B ARG* 3.1 15.0 - - - +
817B ARG* 2.9 64.3 + - + +
818B ILE 4.5 0.4 - - - -
819B ARG* 4.3 6.3 + - + -
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Residues in contact with THR 810 (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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501B PRO* 3.5 31.8 - - + +
502B GLN 3.8 14.6 - - - +
744B GLY* 3.3 5.2 - - - -
745B PHE* 2.6 44.8 + - + +
746B GLU* 2.7 16.7 + - - +
809B TYR* 1.3 75.1 - - - +
811B SER* 1.3 73.3 + - - +
814B GLY* 4.2 3.6 - - - -
815B GLU 3.8 5.6 - - - +
816B ARG* 2.7 30.0 + - - +
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Residues in contact with SER 811 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B GLN 4.8 1.9 - - - +
504B PRO* 5.7 0.7 - - - +
743B ILE 4.4 2.2 - - - -
745B PHE* 4.4 4.5 - - - -
809B TYR* 4.1 17.6 - - - -
810B THR* 1.3 85.1 - - - +
812B SER* 1.3 60.9 + - - +
813B LYS* 2.9 15.3 + - - +
814B GLY* 3.0 15.4 + - - -
815B GLU* 3.0 38.4 + - - +
817B ARG* 5.0 10.0 + - - -
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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