Contacts of the helix formed by residues 210 - 225 (chain 7) in PDB entry 5LN3
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 ALA 210 (chain 7).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597 VAL* 3.9 28.7 - - + -
607 LYS 5.2 1.1 - - - +
617 PHE* 4.4 19.9 - - + +
667 VAL* 4.6 7.4 - - + +
1997 LEU* 6.1 2.9 - - + -
2057 LEU* 5.3 6.7 - - + -
2087 THR* 3.7 4.7 + - - +
2097 GLU* 1.3 71.2 - - - +
2117 ARG* 1.3 64.3 + - - +
2127 ASP* 3.0 7.0 - - - -
2137 LEU* 2.9 26.9 + - + +
2147 VAL* 3.4 8.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 211 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617 PHE* 5.7 4.2 - - - -
667 VAL* 4.7 9.4 - - + +
2097 GLU* 3.6 46.1 + - - +
2107 ALA* 1.3 71.9 - - - +
2127 ASP* 1.4 66.7 + - - +
2147 VAL* 3.1 11.1 + - - +
2157 GLU* 2.9 29.3 + - - +
2347 ILE* 4.4 20.8 - - + +
2367 THR* 5.8 6.2 + - - +
2457 GLU* 5.3 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 212 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2087 THR* 3.8 12.0 + - - +
2097 GLU 2.9 24.8 - - - +
2117 ARG* 1.4 78.7 + - - +
2137 LEU* 1.4 83.0 + - + +
2157 GLU* 3.3 8.2 + - - +
2167 ARG* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597 VAL* 6.4 0.4 - - + -
1947 LEU 6.0 0.4 - - - +
1957 LEU* 4.4 14.4 - - + +
1987 VAL* 3.7 45.3 - - + -
1997 LEU* 5.6 5.4 - - + -
2087 THR* 4.2 14.8 - - + -
2107 ALA* 2.9 17.1 + - + +
2127 ASP* 1.4 88.8 - - + +
2147 VAL* 1.4 67.0 + - + +
2167 ARG* 3.4 8.1 + - + +
2177 CYS* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 214 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577 LEU* 4.4 17.7 - - + +
587 GLY* 6.3 1.6 - - - -
597 VAL* 4.0 31.6 - - + -
667 VAL* 4.7 7.2 - - + -
677 ILE* 5.9 0.2 - - - -
687 ALA* 3.7 31.6 - - + +
1957 LEU* 4.9 3.8 - - + -
2107 ALA* 3.4 16.6 - - + +
2117 ARG* 3.1 10.5 + - - +
2137 LEU* 1.4 82.1 - - + +
2157 GLU* 1.3 60.7 + - - +
2177 CYS* 3.1 22.4 - - - -
2187 MET* 3.4 10.4 + - - +
2347 ILE* 4.9 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 215 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2117 ARG 2.9 16.5 + - - +
2127 ASP* 3.6 9.0 - - - +
2147 VAL* 1.3 76.1 - - - +
2167 ARG* 1.3 61.9 + - - +
2187 MET* 3.6 5.9 + - - +
2197 ARG* 3.2 55.0 + - - +
2327 PHE* 4.5 25.9 - - + -
2347 ILE* 5.8 3.1 - - + +
2487 LEU* 6.3 0.7 - - + -
2517 GLU* 3.2 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 216 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2127 ASP 3.1 10.0 + - - +
2137 LEU* 3.5 13.9 - - + +
2157 GLU* 1.3 77.8 + - - +
2177 CYS* 1.3 66.0 + - - +
2197 ARG* 3.2 45.5 + - - +
2207 VAL* 3.2 46.2 + - + +
2237 TYR* 5.0 1.0 - - - -
2537 ASN* 3.3 27.9 + - - +
2547 TRP* 5.7 5.3 - - - -
2567 ILE* 3.4 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 217 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577 LEU* 3.7 21.5 - - - -
1917 ALA* 4.5 16.0 - - + +
1947 LEU* 4.8 13.6 - - + +
1957 LEU* 3.7 26.2 - - + -
2137 LEU 3.1 13.9 + - - +
2147 VAL* 3.1 28.7 - - - -
2167 ARG* 1.3 80.6 - - - +
2187 MET* 1.3 56.0 + - - +
2207 VAL* 3.2 11.2 + - - +
2217 LEU* 2.9 28.1 + - - +
2247 ARG* 4.4 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 218 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557 SER* 5.9 1.6 - - - +
577 LEU* 3.8 19.1 - - + -
687 ALA* 3.7 30.3 - - + -
697 ALA* 3.8 17.3 - - - +
707 ASP* 4.9 10.5 - - - +
2147 VAL 3.4 16.2 + - - +
2157 GLU* 3.7 7.9 - - - +
2177 CYS* 1.3 79.6 - - - +
2197 ARG* 1.3 57.1 + - - +
2217 LEU* 3.3 20.9 + - - +
2227 TYR* 3.1 28.9 + - + +
2327 PHE* 3.9 44.9 - - + -
2507 THR* 4.6 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 219 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2157 GLU* 3.2 41.1 + - - +
2167 ARG* 3.2 49.4 + - - +
2177 CYS 3.2 0.4 - - - -
2187 MET* 1.3 75.7 - - - +
2207 VAL* 1.4 64.4 + - - +
2227 TYR* 3.4 1.7 + - - +
2237 TYR* 3.2 34.4 + - + -
2507 THR* 3.9 23.8 - - + -
2517 GLU* 3.4 50.5 + - - +
2527 THR 5.7 0.4 - - - -
2537 ASN* 3.8 22.4 + - - +
2547 TRP* 5.8 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 220 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1947 LEU* 4.6 11.0 - - + -
2167 ARG* 3.2 45.3 - - + +
2177 CYS* 3.2 10.9 + - - +
2197 ARG* 1.4 75.3 - - - +
2217 LEU* 1.4 62.3 + - - +
2237 TYR* 3.5 9.7 + - + +
2247 ARG* 3.2 61.5 + - + +
2567 ILE* 6.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557 SER* 3.8 28.5 - - - +
577 LEU* 4.6 12.1 - - + -
707 ASP* 5.7 1.1 - - - +
1867 TYR* 4.4 12.6 - - + -
1877 GLY* 4.2 24.0 - - - +
1907 LEU* 4.9 6.9 - - + +
1917 ALA* 5.1 5.2 - - + -
2177 CYS 2.9 16.7 + - - +
2187 MET* 3.4 27.1 - - - +
2197 ARG 3.2 0.2 - - - -
2207 VAL* 1.4 77.9 - - - +
2227 TYR* 1.3 60.6 + - - +
2247 ARG* 3.4 20.1 - - - +
2257 ASP* 3.2 34.8 + - + +
2287 SER* 3.9 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 222 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2187 MET* 3.1 16.8 + - + +
2197 ARG 3.4 3.3 + - - +
2217 LEU* 1.3 72.9 - - - +
2237 TYR* 1.3 76.5 + + - +
2257 ASP 2.5 21.6 - - - +
2267 ALA* 5.7 0.4 - - - -
2287 SER* 3.6 23.1 - - - -
2297 TYR 3.6 21.8 - - - +
2307 ASN* 3.4 36.7 + - + +
2507 THR* 3.2 34.3 - - + -
2627 GLY* 3.3 39.8 + - - +
2637 PHE* 4.0 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 223 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2167 ARG* 5.0 1.6 - - - -
2197 ARG* 3.2 23.6 + - + +
2207 VAL* 3.9 9.6 - - + +
2217 LEU 3.4 0.2 - - - -
2227 TYR* 1.3 98.4 - + - +
2247 ARG* 1.3 59.0 + - + +
2257 ASP 4.4 1.4 - - - +
2267 ALA* 6.0 0.7 - - - +
2507 THR* 5.1 3.6 - - - -
2517 GLU 3.0 24.1 + - - -
2527 THR* 3.5 7.3 - - - +
2537 ASN* 3.1 30.9 + - + +
2567 ILE* 4.1 25.8 - - + -
2577 ALA* 4.8 4.2 - - - +
2607 ILE* 4.0 28.9 - - + +
2617 SER* 3.5 24.0 - - - +
2627 GLY* 4.1 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 224 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1907 LEU* 3.8 49.6 + - + +
1917 ALA* 4.4 8.3 - - - +
1947 LEU* 4.1 15.0 - - - +
2177 CYS 4.4 2.2 + - - -
2207 VAL* 3.2 38.3 + - + +
2217 LEU* 3.4 31.6 - - - +
2237 TYR* 1.3 73.6 - - + +
2257 ASP* 1.3 58.4 + - - +
2267 ALA 4.1 1.2 + - - -
2607 ILE* 4.4 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 225 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1867 TYR* 3.3 33.3 - - + -
1907 LEU* 5.8 4.3 - - + -
2217 LEU* 3.2 19.0 + - + +
2227 TYR 2.5 24.9 - - - +
2237 TYR 4.6 1.3 - - - -
2247 ARG* 1.3 79.5 - - + +
2267 ALA* 1.3 54.3 + - - +
2277 ARG* 2.9 43.3 + - - +
2287 SER* 2.7 37.5 + - - +
----------------------------------------------------------
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