Contacts of the helix formed by residues 237 - 255 (chain 1) in PDB entry 6AH0
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 237 (chain 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2361 PRO* 1.3 68.9 - - - +
2381 ARG* 1.3 55.0 + - - -
2391 ALA 2.5 20.3 + - - -
2401 LYS* 3.0 14.6 + - - -
2411 GLY 3.4 5.0 + - - -
3001 GLU 5.9 4.7 - - - -
3021 ASP 5.9 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 238 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2331 ASP* 3.2 24.3 + - - +
2361 PRO 3.2 3.6 + - - -
2371 GLY* 1.3 69.0 - - - -
2391 ALA* 1.3 61.9 + - - +
2411 GLY* 3.4 12.0 + - - +
2421 SER 3.9 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2371 GLY 2.5 10.5 + - - -
2381 ARG* 1.3 69.9 - - - +
2401 LYS* 1.3 66.3 + - - +
2411 GLY 2.8 1.8 + - - -
2421 SER* 3.6 6.8 + - - -
2431 GLU 4.2 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 240 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2371 GLY 3.0 9.9 + - - -
2391 ALA* 1.3 70.8 - - - +
2411 GLY* 1.3 65.7 + - - +
2431 GLU* 2.9 15.1 + - - +
2441 THR* 3.0 10.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 241 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2291 SER* 6.0 4.7 - - - -
2321 TRP 5.5 2.9 - - - -
2331 ASP* 5.2 10.5 - - - -
2361 PRO 6.3 0.4 - - - -
2371 GLY 3.4 6.2 + - - -
2381 ARG* 3.4 12.3 + - - -
2391 ALA 2.8 5.5 + - - -
2401 LYS* 1.3 76.2 - - - +
2421 SER* 1.3 64.2 + - - -
2441 THR* 3.0 0.9 + - - -
2451 PRO* 3.0 23.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 242 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2381 ARG 3.9 4.6 + - - -
2391 ALA 3.6 5.7 + - - -
2401 LYS 3.5 0.2 - - - -
2411 GLY* 1.3 72.6 - - - +
2431 GLU* 1.3 63.6 + - - +
2451 PRO* 5.7 0.2 - - - -
2461 GLY* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 243 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2391 ALA 4.2 2.8 + - - -
2401 LYS* 2.9 12.3 + - - +
2421 SER* 1.3 77.1 - - - +
2441 THR* 1.3 65.1 + - - +
2461 GLY* 4.0 0.2 - - - -
2471 ALA* 3.0 13.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 244 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2401 LYS 3.0 11.1 + - - -
2411 GLY 3.0 1.7 + - - -
2431 GLU* 1.3 73.4 - - - +
2451 PRO* 1.3 54.1 - - - +
2471 ALA* 2.4 32.2 + - - +
2481 THR 2.9 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 245 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2291 SER* 6.0 6.7 - - - -
2411 GLY 3.0 14.5 - - - +
2441 THR* 1.3 68.9 - - - -
2461 GLY* 1.3 55.9 + - - +
2481 THR* 3.3 3.7 + - - +
2491 PRO* 2.9 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 246 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2421 SER* 3.0 18.3 + - - +
2441 THR 2.7 5.1 + - - -
2451 PRO* 1.3 69.4 - - - +
2471 ALA* 1.3 64.7 + - - -
2491 PRO* 3.0 3.6 - - - +
2501 GLY* 3.0 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 247 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2431 GLU 3.0 9.7 + - - -
2441 THR* 2.4 17.2 + - - +
2461 GLY* 1.3 67.1 - - - -
2481 THR* 1.3 63.3 + - - +
2501 GLY* 3.2 3.4 + - - -
2511 SER* 3.0 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 248 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2441 THR 2.9 10.8 + - - -
2451 PRO* 3.3 5.6 + - - -
2471 ALA* 1.3 75.4 - - - +
2491 PRO* 1.3 64.1 - - - +
2511 SER* 2.8 15.3 + - - +
2521 LYS* 2.9 11.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 249 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2451 PRO 2.9 15.0 - - - +
2461 GLY* 3.0 3.1 - - - +
2481 THR* 1.3 72.7 - - - +
2501 GLY* 1.3 62.3 + - - +
2521 LYS* 4.6 1.8 - - - +
2531 ILE* 2.9 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 250 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2461 GLY 3.0 13.3 + - - -
2471 ALA* 3.6 3.6 - - - -
2481 THR 2.9 0.8 + - - -
2491 PRO* 1.3 77.5 - - - +
2511 SER* 1.3 63.5 + - - +
2521 LYS 2.9 1.6 + - - -
2531 ILE* 3.8 0.3 - - - -
2541 TRP* 2.9 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 251 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2471 ALA 3.0 9.6 + - - -
2481 THR* 2.8 10.0 + - - +
2501 GLY* 1.3 71.7 - - - +
2521 LYS* 1.3 56.8 + - - +
2541 TRP* 3.9 1.1 - - - +
2551 ASP* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 252 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2481 THR 2.9 13.1 + - - -
2491 PRO* 3.8 2.5 - - - -
2511 SER* 1.3 76.6 - - - +
2531 ILE* 1.3 66.8 + - - +
2561 PRO* 2.9 22.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 253 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2491 PRO 2.9 14.4 + - - -
2501 GLY* 3.8 1.8 - - - -
2521 LYS* 1.3 74.3 - - - +
2541 TRP* 1.3 58.1 + - - +
2561 PRO* 3.2 2.1 - - - +
2571 THR* 2.9 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 254 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2501 GLY 2.9 16.2 + - - -
2511 SER* 4.1 0.7 - - - +
2531 ILE* 1.3 71.9 - - - +
2551 ASP* 1.3 53.9 + - - +
2561 PRO 2.8 4.7 - - - -
2571 THR* 2.7 24.5 + - - +
2581 PRO 3.0 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 255 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2511 SER 2.9 19.5 + - - -
2521 LYS* 3.9 0.9 - - - -
2541 TRP* 1.3 71.3 - - - +
2561 PRO* 1.3 58.5 - - - +
2571 THR 3.4 0.2 - - - -
2581 PRO* 3.8 9.7 - - - -
2591 SER* 3.9 9.4 + - - -
----------------------------------------------------------
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