Contacts of the strand formed by residues 172 - 188 (chain 1) in PDB entry 5NEM
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 ARG 172 (chain 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461 ASP* 3.2 42.1 + - - +
821 HIS* 3.2 2.6 - - - -
831 GLU* 2.7 65.0 + - + +
1701 ALA* 3.2 2.6 - - - -
1711 THR* 1.3 83.4 - - + +
1731 VAL* 1.3 65.1 + - - +
1741 THR* 3.7 10.9 + - - +
138B ARG* 4.2 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 173 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441 PRO* 4.2 10.8 - - + +
451 LYS 3.1 20.2 - - - +
461 ASP* 3.1 22.1 + - - +
471 GLN 4.2 7.2 - - - +
491 ASN* 3.3 26.0 - - - +
801 VAL* 3.6 28.5 - - + -
811 LYS 3.7 2.2 - - - -
821 HIS* 4.1 4.9 - - + +
861 LEU* 5.7 0.2 - - + -
1681 ILE* 4.8 5.6 - - + -
1701 ALA* 4.6 8.2 - - + +
1721 ARG* 1.3 78.7 + - - +
1741 THR* 1.3 63.2 + - - +
1751 GLU 3.9 9.6 - - - +
1761 LEU* 4.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 174 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411 LYS* 5.2 2.3 + - - -
441 PRO* 3.8 13.7 - - - +
811 LYS* 2.6 32.7 + - + -
821 HIS* 4.9 1.2 - - - -
831 GLU* 4.9 6.9 + - - +
1721 ARG* 3.7 17.5 + - - +
1731 VAL* 1.3 75.1 - - - +
1751 GLU* 1.3 61.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 175 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411 LYS* 3.4 33.4 + - - +
441 PRO* 4.5 3.1 - - - -
791 ALA 4.5 0.2 - - - -
801 VAL* 3.4 8.5 - - - +
811 LYS* 3.0 59.5 + - + +
1121 LEU* 6.4 0.7 - - - -
1731 VAL* 3.7 2.9 - - - +
1741 THR* 1.3 82.2 - - + +
1761 LEU* 1.3 70.9 + - - +
1771 LEU* 4.4 18.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411 LYS* 3.8 2.1 - - - +
421 VAL* 3.2 41.6 + - + +
441 PRO* 4.2 16.1 - - + +
491 ASN* 3.8 30.5 - - + +
511 LEU* 4.6 1.1 - - + -
551 GLN* 5.8 1.1 - - - +
781 VAL* 3.6 16.4 - - + -
791 ALA 3.5 2.2 - - - -
801 VAL* 3.6 26.7 - - + -
1681 ILE* 3.7 12.1 - - + -
1731 VAL* 4.8 1.6 - - + -
1751 GLU* 1.3 79.6 - - - +
1771 LEU* 1.3 69.8 + - - +
1781 TYR* 3.9 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391 PHE* 3.7 28.3 - - + -
401 VAL* 3.3 6.5 - - - +
411 LYS* 3.5 29.6 - - + +
421 VAL 4.9 0.2 - - - +
771 GLU 3.8 0.2 - - - +
781 VAL* 3.5 5.5 - - - +
791 ALA* 3.0 46.3 + - + +
1121 LEU* 5.6 2.5 - - + -
1751 GLU* 4.4 19.5 - - + +
1761 LEU* 1.3 83.6 - - - +
1781 TYR* 1.3 70.4 + - - +
143 LEU* 4.2 17.9 - - + -
163 THR* 4.7 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 178 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381 ARG 3.1 2.4 - - - +
391 PHE* 3.1 5.2 - - - -
401 VAL* 2.9 42.4 + - + +
421 VAL* 3.8 23.7 - - + +
491 ASN* 5.5 0.2 - - - +
501 VAL 3.9 4.7 + - - -
511 LEU* 3.3 45.4 - - + +
521 ASP 3.2 26.7 + - - -
531 LEU* 4.3 15.0 - - + -
551 GLN* 4.4 5.6 + - + -
561 THR* 4.0 12.1 - - + -
761 LEU* 4.5 13.5 - - + -
771 GLU 3.7 2.7 - - - -
781 VAL* 4.4 9.9 - - + -
1761 LEU* 3.9 27.6 - - + +
1771 LEU* 1.3 82.1 - - - +
1791 ARG* 1.3 59.8 + - - +
1801 MET* 5.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 179 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371 ASP* 2.7 40.0 + - - +
381 ARG 3.3 15.7 - - - +
391 PHE* 3.7 29.7 - - + +
761 LEU* 3.7 3.9 - - - +
771 GLU* 2.9 62.1 + - + +
1781 TYR* 1.3 75.5 - - - +
1801 MET* 1.3 61.6 + - - +
1811 LYS* 3.2 13.4 + - - +
163 THR 3.6 22.4 + - - -
173 THR* 4.1 2.4 - - - +
183 ASP* 2.8 33.2 + - - -
193 PRO* 4.5 0.4 - - - +
203 LYS 4.2 8.0 + - - -
174 ASN* 3.6 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 180 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331 SER 5.1 0.2 - - - +
361 LEU* 3.4 34.3 + - + +
371 ASP* 3.4 17.8 - - - +
381 ARG 4.2 0.2 + - - -
531 LEU* 3.7 31.4 - - + -
621 VAL* 4.2 23.1 - - + +
661 LEU* 3.6 31.0 - - + -
721 TYR* 4.4 8.5 - - + -
731 PHE 4.8 0.9 - - - +
741 ALA* 3.7 23.8 - - + -
751 ASP 3.7 4.0 - - - -
761 LEU* 4.4 4.3 - - + -
1781 TYR* 5.8 2.0 - - + -
1791 ARG* 1.3 74.2 - - - +
1811 LYS* 1.3 61.6 + - - +
1821 ARG 4.3 0.2 + - - -
1831 ALA* 4.2 18.3 - - + +
1841 GLU 5.9 0.2 - - - +
1851 THR* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 181 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371 ASP* 3.4 18.6 - - - +
741 ALA* 3.3 3.3 - - - +
751 ASP* 2.8 49.4 + - + +
761 LEU 5.2 0.7 - - - -
771 GLU* 2.0 39.8 + - + +
1791 ARG* 3.2 29.2 - - - +
1801 MET* 1.3 72.5 - - - +
1821 ARG* 1.3 71.9 + - + +
1831 ALA 3.2 2.2 - - - -
203 LYS 4.7 0.9 - - - -
213 THR* 3.6 33.4 - - + +
223 ALA 4.3 0.4 - - - +
314 GLN* 5.4 2.4 - - - +
324 ASN* 4.9 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 182 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331 SER* 4.6 8.5 + - - -
371 ASP* 5.5 1.6 + - - +
731 PHE* 3.6 18.7 - - + +
751 ASP* 3.3 26.7 + - - +
1801 MET 4.3 0.4 + - - -
1811 LYS* 1.3 76.9 - - + +
1831 ALA* 1.3 65.3 + - - +
1841 GLU* 3.2 11.8 + - - +
313 ASN* 4.4 0.6 - - - +
343 ARG* 3.6 11.3 + - - +
154 SER* 5.1 12.6 - - - +
324 ASN* 3.7 23.5 - - - +
334 SER* 2.7 29.7 + - - -
354 ASP* 2.7 40.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321 VAL* 4.0 15.3 - - + +
331 SER* 3.2 25.1 + - - +
361 LEU* 4.0 37.9 - - + -
731 PHE 3.3 9.6 - - - +
741 ALA* 3.9 3.4 - - + -
1801 MET* 4.2 17.2 + - + +
1811 LYS 3.2 0.6 - - - -
1821 ARG* 1.3 76.0 - - - +
1841 GLU* 1.3 62.5 + - - +
403 ARG* 5.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 184 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321 VAL* 5.0 0.7 - - - -
721 TYR* 3.2 5.5 - - - +
731 PHE* 2.8 34.9 + - + +
1801 MET* 5.9 0.2 - - - +
1821 ARG* 3.2 9.3 + - - +
1831 ALA* 1.3 75.6 - - - +
1851 THR* 1.3 67.7 + - - +
1861 TYR* 2.6 37.4 + - + +
343 ARG* 2.9 40.7 + - - +
403 ARG* 3.8 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 185 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321 VAL* 3.6 21.2 - - + +
361 LEU* 4.3 14.4 - - + -
651 LEU 5.5 2.9 - - - +
661 LEU* 5.4 2.9 - - + -
691 ALA* 3.6 13.9 - - + -
711 TYR 3.5 5.8 - - - -
721 TYR* 4.5 7.4 - - + -
1801 MET* 6.2 0.4 - - + -
1831 ALA* 5.4 0.2 - - + -
1841 GLU* 1.3 82.2 - - - +
1861 TYR* 1.3 67.8 + - - +
403 ARG* 3.5 7.9 - - - +
413 PHE* 3.0 60.7 + - + +
443 PHE* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 186 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691 ALA* 3.6 2.3 - - - +
701 THR 3.0 17.0 + - - -
711 TYR* 3.0 38.3 + - + +
721 TYR 4.5 0.2 - - - -
731 PHE* 5.0 0.9 - - + -
1251 VAL* 4.1 20.0 - - + -
1841 GLU* 2.6 40.6 + - + -
1851 THR* 1.3 75.6 - - - +
1871 CYS* 1.3 71.9 + - - +
1881 PRO 3.8 1.1 - - - -
343 ARG* 4.2 14.6 + - - +
373 LEU* 3.8 35.7 - - + -
383 PRO 4.1 9.9 - - - +
393 GLY 3.3 7.0 - - - +
403 ARG* 3.5 44.7 + - + -
413 PHE* 4.0 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 187 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701 THR* 2.7 42.8 + - - +
711 TYR* 4.3 17.9 - - - -
1861 TYR* 1.3 75.9 - - - +
1881 PRO* 1.3 72.5 - - - +
362 TYR* 3.6 40.6 - - + +
1272 PRO* 4.4 5.6 - - + -
1632 VAL* 4.5 7.4 - - - -
383 PRO 3.6 18.6 - - - -
393 GLY 2.9 14.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 188 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681 THR 3.4 15.9 - - - +
1861 TYR 3.8 0.4 - - - -
1871 CYS* 1.3 89.2 - - - +
1891 ARG* 1.3 60.5 + - - +
362 TYR* 4.1 3.5 + - + -
1422 LEU* 4.1 21.2 - - + +
1432 PHE* 3.5 19.4 - - - -
413 PHE* 3.7 17.5 - - + -
473 VAL* 4.1 24.0 - - + -
903 PHE* 5.8 2.9 - - + -
684 PHE* 3.4 39.9 - - + -
----------------------------------------------------------
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