Contacts of the helix formed by residues 748 - 761 (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 SER 748 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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582A PHE* 3.7 5.8 - - - -
723A ASN* 4.4 26.0 - - - -
747A VAL* 1.3 90.0 - - - +
749A LEU* 1.3 60.1 + - - +
750A GLN* 3.7 19.3 + - - +
751A VAL* 3.1 22.5 + - - +
752A PHE* 2.8 25.1 + - - +
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Residues in contact with LEU 749 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579A GLN* 3.6 37.5 - - + +
582A PHE* 3.3 50.8 - - + -
583A HIS* 5.7 0.7 - - - +
723A ASN 4.0 7.2 + - - +
748A SER* 1.3 72.9 - - - +
750A GLN* 1.3 59.8 + - - +
752A PHE* 3.1 9.4 + - + -
753A MET* 2.7 62.0 + - + +
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Residues in contact with GLN 750 (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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638A ASP* 4.5 18.4 + - - +
723A ASN* 4.4 5.2 - - - +
748A SER* 3.2 15.0 + - - +
749A LEU* 1.3 89.6 + - + +
751A VAL* 1.3 65.0 + - + +
753A MET* 3.3 6.6 + - - +
754A ASP* 3.1 28.8 + - - +
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Residues in contact with VAL 751 (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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746A ASP* 5.0 9.9 - - + +
747A VAL* 4.5 19.5 - - + +
748A SER* 3.1 26.4 + - - +
750A GLN* 1.3 75.2 - - + +
752A PHE* 1.3 68.1 + - - +
754A ASP* 3.2 7.3 + - + +
755A HIS* 3.0 25.1 + - + +
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Residues in contact with PHE 752 (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* 4.3 4.7 - - - -
550A LEU* 3.5 28.9 - - + -
578A PRO 3.8 22.0 - - - -
582A PHE* 3.7 24.9 - + + -
585A ARG* 3.6 46.9 - - - -
746A ASP* 4.4 17.5 - - + +
747A VAL 5.4 1.1 - - - +
748A SER 2.8 13.4 + - - +
749A LEU* 3.3 25.4 - - + +
751A VAL* 1.3 78.1 - - - +
753A MET* 1.3 68.1 + - - +
755A HIS* 3.4 5.6 + - + +
756A LEU* 3.0 25.9 + - + +
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Residues in contact with MET 753 (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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568A PHE* 5.9 5.8 - - + -
575A SER 5.5 1.8 - - - +
578A PRO* 3.8 36.3 - - + -
579A GLN 5.0 0.4 - - - -
749A LEU* 2.7 47.9 + - + +
750A GLN* 3.6 7.9 - - - +
751A VAL 3.2 0.2 - - - -
752A PHE* 1.3 78.2 - - - +
754A ASP* 1.3 65.1 + - - +
756A LEU* 3.1 15.5 + - + +
757A LYS* 2.9 48.8 + - + +
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Residues in contact with ASP 754 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565A PRO* 5.3 4.7 - - - +
750A GLN* 3.1 19.0 + - - +
751A VAL* 3.2 7.6 + - + +
753A MET* 1.3 75.5 - - - +
755A HIS* 1.3 57.9 + - - +
757A LYS* 3.0 18.0 + - - +
758A LYS* 2.9 50.6 + - - +
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Residues in contact with HIS 755 (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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746A ASP* 3.2 25.2 + - - +
751A VAL* 3.0 17.7 + - + +
752A PHE* 3.8 6.3 - - + +
754A ASP* 1.3 77.3 - - - +
756A LEU* 1.3 61.1 + - - +
758A LYS* 3.4 14.5 + - + +
759A LEU* 3.2 46.7 + - + +
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Residues in contact with LEU 756 (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* 3.9 34.1 - - + -
551A ILE* 4.0 22.4 - - + -
554A CYS* 3.6 35.7 - - + -
568A PHE* 5.6 3.4 - - + -
578A PRO* 4.3 16.8 - - + -
752A PHE* 3.0 19.1 + - + +
753A MET* 3.1 20.4 + - + +
755A HIS* 1.3 78.0 - - - +
757A LYS* 1.3 53.1 + - + +
759A LEU* 3.4 4.5 + - - -
760A ALA* 2.8 34.9 + - + +
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Residues in contact with LYS 757 (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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565A PRO* 3.9 32.0 + - + +
566A SER* 5.3 5.6 + - - +
568A PHE* 4.3 31.0 + - + -
753A MET* 2.9 43.5 + - + +
754A ASP* 3.4 15.9 - - - +
756A LEU* 1.3 75.7 - - + +
758A LYS* 1.3 65.9 + - - +
760A ALA* 3.5 7.5 - - - +
761A VAL* 3.0 31.3 + - - +
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Residues in contact with LYS 758 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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565A PRO* 3.9 24.7 - - + -
754A ASP* 2.9 35.8 + - - +
755A HIS* 3.7 17.3 - - + +
756A LEU 3.4 0.2 - - - -
757A LYS* 1.3 76.7 - - - +
759A LEU* 1.3 64.4 + - + +
761A VAL* 3.7 6.1 - - - +
762A SER* 3.6 18.0 - - - -
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Residues in contact with LEU 759 (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* 3.5 38.8 - - + +
555A GLN* 3.2 15.1 + - - -
755A HIS* 3.2 43.3 + - + +
756A LEU* 3.8 4.7 - - - +
757A LYS 3.1 0.4 - - - -
758A LYS* 1.3 82.1 - - + +
760A ALA* 1.3 64.0 + - - +
761A VAL 3.4 0.2 - - - -
762A SER* 3.3 18.2 + - - +
763A SER 4.1 1.6 - - - +
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Residues in contact with ALA 760 (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* 4.7 3.4 - - - -
554A CYS* 4.1 13.0 - - + -
555A GLN* 3.0 29.7 + - + +
560A TYR* 3.2 17.0 - - + -
568A PHE* 3.9 32.3 - - + -
756A LEU* 2.8 18.7 + - + +
757A LYS* 3.0 7.6 + - - +
759A LEU* 1.3 77.6 - - - +
761A VAL* 1.3 59.4 + - - +
762A SER 3.8 0.3 - - - +
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Residues in contact with VAL 761 (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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560A TYR* 3.4 31.6 - - + -
561A HIS 3.8 2.7 - - - +
562A LYS* 3.2 12.5 - - - +
563A ASP* 2.6 28.4 + - - +
564A ASP 3.3 35.7 - - - +
565A PRO* 3.4 30.1 - - + +
567A SER* 4.1 0.2 - - - +
568A PHE* 4.5 4.7 - - + -
757A LYS 3.0 17.7 + - - +
758A LYS 3.7 7.9 - - - +
760A ALA* 1.3 72.1 - - + +
762A SER* 1.3 64.2 + - - +
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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
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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