Contacts of the strand formed by residues 785 - 791 (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 TYR 785 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B LEU* 3.3 4.5 - - - +
411B LEU* 2.8 46.3 + - + +
413B PRO* 3.9 32.1 - - + -
414B PHE* 6.5 0.2 - - + -
710B ALA* 5.3 1.4 + - - +
749B MET* 4.0 15.7 - - + -
763B HIS 3.4 7.9 - - - +
764B GLY* 4.2 1.1 - - - -
765B ASN 3.8 15.8 + - - -
766B PHE* 3.4 39.9 - + + -
774B LEU* 5.6 1.3 - - + -
776B LEU* 3.9 27.6 - - + +
778B ASN 5.3 0.9 + - - -
779B VAL* 4.7 10.0 - - + +
780B ASN* 5.2 1.0 + - - -
783B ALA* 3.6 32.8 - - + +
784B GLY* 1.3 78.2 - - - -
786B ALA* 1.3 61.0 - - - +
787B VAL* 6.2 1.6 - - + -
931B LYS 5.4 0.2 - - - -
932B ASN* 5.4 0.4 - - - -
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Residues in contact with ALA 786 (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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409B LEU 3.2 10.1 - - - +
410B LEU* 4.2 13.7 - - + -
411B LEU* 4.6 0.9 - - - -
763B HIS* 2.7 58.3 + - + +
785B TYR* 1.3 75.7 - - - +
787B VAL* 1.3 66.8 + - - +
846B LEU* 4.5 8.5 - - + -
849B ASN* 4.3 14.6 - - - +
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Residues in contact with VAL 787 (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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408B GLY* 2.8 24.8 - - - -
409B LEU* 2.7 26.3 + - + +
411B LEU* 5.2 6.7 - - + -
751B ILE* 4.7 10.8 - - + -
759B ILE* 3.0 44.9 - - + -
761B THR 3.5 3.6 - - - +
762B PHE* 3.8 28.5 - - + -
763B HIS* 4.4 0.7 - - - -
774B LEU* 5.9 0.7 - - + -
785B TYR* 6.2 1.1 - - + -
786B ALA* 1.3 80.5 - - - +
788B GLN* 1.3 68.7 + - - +
789B MET* 4.5 4.5 - - + +
846B LEU* 3.9 7.4 - - - +
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Residues in contact with GLN 788 (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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406B PRO* 4.2 14.1 - - - +
407B LEU 3.6 9.3 + - - +
408B GLY* 4.1 0.4 - - - -
759B ILE* 3.5 3.3 - - - -
760B HIS* 2.7 66.3 + - + +
761B THR* 3.0 26.2 + - - +
763B HIS* 4.5 6.8 + - - +
787B VAL* 1.3 77.0 - - - +
789B MET* 1.3 58.1 + - - +
846B LEU* 4.7 4.0 - - + +
850B MET* 3.5 45.4 - - - +
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Residues in contact with MET 789 (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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400B LEU* 4.5 2.1 - - - +
407B LEU* 2.8 55.1 + - + +
408B GLY* 3.7 6.1 - - - -
409B LEU* 3.9 25.6 - - + +
753B CYS* 3.5 32.3 - - - -
757B LEU* 4.6 7.0 - - + -
758B SER 3.2 13.2 - - - +
759B ILE* 3.7 13.9 - - + -
760B HIS* 3.5 9.7 - - - -
787B VAL* 4.9 1.3 - - + +
788B GLN* 1.3 75.6 + - - +
790B SER* 1.3 66.5 + - - +
803B PHE* 3.7 28.9 - - + -
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Residues in contact with SER 790 (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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397B GLN* 3.1 22.4 - - - -
400B LEU* 4.4 6.7 - - - -
407B LEU* 4.4 3.6 - - - -
757B LEU* 3.9 3.4 - - - -
758B SER* 3.0 32.1 + - - -
760B HIS* 3.9 16.6 + - - +
789B MET* 1.3 78.4 - - - +
791B VAL* 1.3 60.6 + - - +
792B GLU* 3.2 5.5 + - - +
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Residues in contact with VAL 791 (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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394B PRO* 3.6 19.5 - - + +
395B GLN 3.7 18.4 - - - +
396B THR 3.9 1.8 - - - +
397B GLN* 2.8 50.5 + - - +
400B LEU* 4.4 12.3 - - + -
407B LEU* 4.8 4.3 - - + -
756B GLY 3.5 5.6 - - - +
757B LEU* 4.5 10.8 - - + -
790B SER* 1.3 71.7 - - - +
792B GLU* 1.3 61.8 + - - +
793B GLU 3.3 26.4 + - - +
794B SER* 4.2 0.8 + - - -
795B LEU* 4.1 9.4 - - + -
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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