Contacts of the strand formed by residues 774 - 779 (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 774 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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748B VAL* 3.1 8.1 - - - +
749B MET* 2.6 66.3 + - + +
751B ILE* 5.0 6.7 - - + -
762B PHE* 3.5 38.4 - - + -
766B PHE* 3.6 38.8 - - + -
767B PHE 3.8 2.5 - - - -
768B VAL* 3.5 27.1 - - + -
773B LEU* 1.3 80.7 - - - +
775B SER* 1.3 60.7 + - - +
776B LEU* 3.7 4.2 + - + +
785B TYR* 4.9 1.8 - - + -
787B VAL* 5.9 0.7 - - + -
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Residues in contact with SER 775 (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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681B SER* 3.8 15.1 + - - -
684B GLN* 5.3 6.8 + - - -
747B ALA 4.2 3.9 + - - -
748B VAL* 4.7 7.8 - - - +
766B PHE* 3.3 10.4 - - - +
767B PHE* 2.8 49.9 + - - -
769B ARG* 4.0 26.3 + - - -
773B LEU* 3.5 1.2 + - - -
774B LEU* 1.3 72.3 - - - +
776B LEU* 1.3 58.5 + - - +
777B PRO* 3.8 6.1 - - - +
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Residues in contact with LEU 776 (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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684B GLN* 4.8 0.7 - - - -
710B ALA* 3.7 8.3 - - + -
747B ALA* 2.9 37.0 + - + +
749B MET* 4.4 13.0 - - + +
766B PHE* 3.4 22.7 - - + -
774B LEU* 4.1 12.8 - - + +
775B SER* 1.3 84.9 + - - +
777B PRO* 1.4 56.9 - - - +
778B ASN* 2.7 28.6 + - - +
779B VAL* 3.8 28.0 - - + -
785B TYR* 3.9 25.8 - - + +
807B LEU* 4.0 19.5 - - + -
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Residues in contact with PRO 777 (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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681B SER* 3.6 40.8 - - - +
684B GLN* 3.6 22.4 - - - +
685B VAL 3.4 32.1 - - - +
686B ALA 3.5 2.0 - - - +
709B SER* 3.2 25.8 - - - +
710B ALA* 3.6 4.7 - - + -
745B PHE* 4.1 0.7 - - - -
746B GLU 3.3 17.0 + - - -
775B SER* 3.8 7.0 - - - +
776B LEU* 1.4 82.7 - - - +
778B ASN* 1.3 67.3 + - - +
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Residues in contact with ASN 778 (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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632B GLY 3.8 4.4 - - - +
633B ARG* 3.2 43.2 - - - +
686B ALA* 3.3 24.9 - - + +
688B ASP* 4.8 1.0 + - - -
710B ALA* 3.7 17.9 - - - +
743B ILE* 4.1 12.4 - - + +
744B GLY 3.5 7.6 - - - +
745B PHE* 3.4 20.8 - - - -
776B LEU* 2.7 19.3 + - - +
777B PRO* 1.3 89.0 - - - +
779B VAL* 1.3 62.9 + - - +
780B ASN* 4.2 2.2 - - + +
785B TYR* 5.3 0.9 + - - -
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Residues in contact with VAL 779 (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* 3.2 39.0 - - + -
743B ILE* 3.8 3.8 - - - +
744B GLY* 3.2 36.8 + - - +
747B ALA* 4.5 2.7 - - + -
776B LEU* 3.8 18.4 - - + -
778B ASN* 1.3 77.1 - - - +
780B ASN* 1.3 61.2 + - - +
785B TYR* 4.7 9.0 - - + +
807B LEU* 3.7 29.6 - - + -
809B TYR* 4.3 15.5 - - + -
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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