Contacts of the strand formed by residues 744 - 753 (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 GLY 744 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B PHE* 3.9 0.8 - - - -
743B ILE* 1.3 80.9 - - - +
745B PHE* 1.3 63.0 + - - -
747B ALA* 5.3 0.2 - - - -
778B ASN* 3.5 5.9 - - - -
779B VAL* 3.2 39.4 + - - +
809B TYR* 3.4 20.6 - - - -
810B THR 3.3 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 745 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B GLN* 3.9 32.5 - - + -
503B PRO 4.8 2.2 - - - -
504B PRO* 3.8 34.5 - - + -
505B VAL 4.4 3.4 - - - -
506B TYR* 4.2 9.6 - + - -
632B GLY* 4.0 17.0 - - - -
633B ARG* 4.2 5.2 - - + -
743B ILE* 3.7 40.8 - - + -
744B GLY* 1.3 75.8 - - - -
746B GLU* 1.3 73.8 + - + +
747B ALA 3.1 3.9 + - - -
777B PRO 4.1 2.0 - - - -
778B ASN* 3.4 22.4 - - - -
809B TYR* 3.8 0.3 - - - -
810B THR* 2.6 41.9 + - - +
811B SER 4.4 9.2 - - - -
812B SER* 4.5 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 746 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B MET* 5.7 0.3 - - - +
499B ARG* 2.6 47.7 + - - +
500B PRO 4.3 0.9 - - - +
501B PRO* 3.8 5.7 - - - +
502B GLN* 3.3 38.8 + - + +
684B GLN* 3.1 32.9 + - + +
745B PHE* 1.3 79.1 - - - +
747B ALA* 1.3 58.8 + - - +
748B VAL* 5.2 1.7 - - - +
777B PRO 3.3 13.8 + - - -
810B THR* 2.7 19.9 + - - +
816B ARG* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 747 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B GLN* 4.8 1.7 + - - +
745B PHE 3.9 1.8 - - - +
746B GLU* 1.3 76.6 - - - +
748B VAL* 1.3 67.2 + - - +
775B SER* 4.2 1.0 + - - -
776B LEU* 2.9 40.5 + - + +
779B VAL* 4.5 9.2 - - + -
807B LEU* 3.7 11.7 - - + -
808B LEU 2.7 20.6 - - - +
809B TYR* 3.1 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 748 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B GLN* 6.1 3.1 - - - +
746B GLU 5.2 1.8 - - - +
747B ALA* 1.3 81.1 - - - +
749B MET* 1.3 62.5 + - - +
773B LEU* 3.9 26.2 - - + -
774B LEU 3.1 13.2 - - - +
775B SER* 4.7 8.7 - - - +
776B LEU* 4.4 1.8 - - - +
806B ALA 3.6 0.7 - - - +
807B LEU* 3.7 3.1 - - - +
808B LEU* 2.8 55.8 + - + +
816B ARG* 6.0 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 749 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B LEU* 4.1 5.4 - - + -
413B PRO* 3.9 15.7 - - - -
748B VAL* 1.3 75.7 - - - +
750B ARG* 1.3 69.3 + - - +
751B ILE* 4.0 24.0 - - + -
773B LEU* 3.3 5.1 + - - -
774B LEU* 2.6 62.8 + - + +
776B LEU* 4.4 8.3 - - + +
785B TYR* 4.0 34.8 - - + -
805B SER* 4.4 4.3 - - - -
806B ALA 3.0 15.7 - - - +
807B LEU* 3.8 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 750 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749B MET* 1.3 78.4 - - - +
751B ILE* 1.3 69.3 + - - +
752B ARG* 4.1 37.4 + - + +
770B SER* 5.0 3.4 + - - -
771B THR 4.5 1.6 + - - -
772B ASP* 2.7 53.5 + - + +
773B LEU* 3.4 40.1 - - + +
804B GLN 3.8 1.4 - - - +
805B SER* 3.3 3.5 - - - -
806B ALA* 3.0 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 751 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B PHE* 4.5 19.5 - - + -
409B LEU* 4.5 8.3 - - + -
411B LEU* 3.4 32.3 - - + -
749B MET* 4.0 17.0 - - + -
750B ARG* 1.3 78.3 - - - +
752B ARG* 1.3 67.9 + - - +
753B CYS* 5.2 0.2 - - - -
759B ILE* 3.7 25.2 - - + +
762B PHE* 4.5 11.7 - - + -
772B ASP* 2.4 40.4 + - - +
774B LEU* 5.0 5.2 - - + -
787B VAL* 4.7 8.5 - - + -
804B GLN 3.6 5.6 - - - +
805B SER* 3.7 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 752 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B ARG* 3.1 29.4 - - - +
434B CYS* 3.0 20.6 + - - -
435B ARG* 3.7 12.6 + - - +
436B THR* 3.3 24.7 - - - +
437B TYR* 4.6 1.2 - - - -
454B LEU* 3.7 13.7 - - + -
750B ARG* 4.2 39.1 + - + +
751B ILE* 1.3 80.8 - - - +
753B CYS* 1.3 66.6 + - - +
772B ASP* 4.6 1.1 - - - +
803B PHE* 3.3 3.8 - - - +
804B GLN* 2.8 47.1 + - + +
806B ALA* 4.5 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 753 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B LEU* 3.9 2.1 - - - +
751B ILE 5.2 0.4 - - - -
752B ARG* 1.3 79.4 - - - +
754B THR* 1.3 73.0 + - - +
757B LEU* 3.0 26.0 - - - +
759B ILE* 3.9 17.7 - - + -
789B MET* 3.5 23.6 - - - -
802B SER 3.2 7.2 - - - -
803B PHE* 3.0 29.2 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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