Contacts of the helix formed by residues 5036 - 5055 (chain d) in PDB entry 3A0B
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 LEU5036 (chain d).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6016b CLA 4.5 23.6 - - + -
5032d TRP 4.1 0.9 + - - +
5033d SER* 2.6 16.1 + - - +
5035d ILE* 1.3 73.4 - - - +
5037d LEU* 1.3 73.9 + - - +
5038d PHE 3.3 0.7 - - - -
5039d PRO* 2.8 16.6 - - - +
5040d CYS* 3.4 8.6 + - - +
5120d PHE* 3.3 34.3 - - + +
5123d ILE* 4.0 13.7 - - + -
5124d GLY* 3.3 25.8 - - - +
5127d LEU* 5.0 0.9 - - + -
6008d CLA 3.5 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5037 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6039a PHO 3.6 17.0 - - - -
6043a PQ9 5.7 6.7 - - + -
5033d SER* 2.9 11.3 + - - +
5036d LEU* 1.3 79.6 - - - +
5038d PHE* 1.3 79.5 + - + +
5041d ALA* 2.6 44.3 + - + +
5121d GLY* 3.4 22.4 - - - +
5124d GLY* 3.6 22.2 - - - +
5125d PHE* 3.5 19.5 - - + -
5128d ARG* 3.8 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE5038 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6043a PQ9 4.4 32.7 - - + +
5028d VAL* 4.9 18.6 - - + -
5029d PHE 4.0 22.7 - - - -
5030d VAL* 4.8 9.2 - - + -
5034d GLY* 3.2 31.4 + - - +
5037d LEU* 1.3 98.6 - - + +
5039d PRO* 1.3 71.1 - - + +
5041d ALA* 3.7 3.9 - - - -
5042d TYR* 3.2 20.1 + - - +
5128d ARG* 4.2 11.0 - - - -
5022f ALA* 5.7 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO5039 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5034d GLY 2.9 24.2 - - - +
5035d ILE* 3.1 19.5 - - - +
5036d LEU* 2.8 25.1 - - - +
5038d PHE* 1.3 73.2 - - + +
5040d CYS* 1.3 53.9 + - - +
5042d TYR* 2.8 22.5 - - + +
5043d LEU* 2.7 25.2 - - + +
6008d CLA 3.5 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS5040 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5036d LEU* 3.4 17.7 + - - +
5039d PRO* 1.3 74.7 - - - +
5041d ALA* 1.3 53.9 + - - +
5042d TYR 2.6 15.9 + - - -
5043d LEU* 3.4 8.3 + - - +
5044d ALA* 3.1 26.3 + - - +
5117d HIS* 3.5 32.0 - - - +
5120d PHE* 4.2 6.3 - - - -
5121d GLY* 3.9 7.0 - - - +
6008d CLA 3.4 50.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA5041 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6039a PHO 3.3 52.0 - - + +
6043a PQ9 3.9 18.1 - - + +
5037d LEU* 2.6 42.8 + - + +
5038d PHE* 3.7 4.5 - - - +
5040d CYS* 1.3 69.4 - - - +
5042d TYR* 1.3 56.8 + - - +
5045d LEU* 4.0 5.7 - - - +
5121d GLY* 4.1 4.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR5042 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6043a PQ9 4.6 12.6 - - + -
5038d PHE 3.2 11.4 - - - +
5039d PRO* 2.8 15.9 - - + +
5040d CYS 2.6 2.2 + - - -
5041d ALA* 1.3 80.5 - - - +
5043d LEU* 1.3 66.6 + - + -
5044d ALA 2.6 4.8 + - - -
5045d LEU* 3.0 6.8 + - + +
5046d GLY* 2.4 38.5 + - - -
6050d BCR 3.5 35.4 - - + +
5025f THR* 2.5 64.6 + - + +
5026f LEU* 4.0 19.9 - - + -
5029f PRO* 4.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5043 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5039d PRO* 2.7 35.7 - - + +
5040d CYS* 3.5 9.0 - - - -
5042d TYR* 1.3 97.1 - - + +
5044d ALA* 1.3 52.2 - - - +
5047d GLY* 2.3 34.6 + - - +
5113d PHE* 3.1 35.8 - - + -
5117d HIS* 3.4 7.4 - - - +
6008d CLA 3.7 37.7 - - + -
6050d BCR 3.3 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA5044 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6039a PHO 4.3 14.4 - - + +
5040d CYS 3.1 16.8 + - - +
5042d TYR 2.6 4.2 + - - -
5043d LEU* 1.3 72.7 - - - +
5045d LEU* 1.3 65.8 + - - +
5046d GLY 2.6 4.2 + - - -
5048d TRP* 3.1 23.7 + - - +
5113d PHE* 4.3 2.0 - - - -
5114d ILE* 4.0 17.0 - - - +
5117d HIS* 4.0 4.3 - - + -
5118d GLY* 3.7 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5045 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6039a PHO 4.7 17.9 - - + +
6043a PQ9 3.3 46.7 - - + -
5041d ALA 4.0 15.3 + - - +
5042d TYR* 3.0 10.8 + - + +
5044d ALA* 1.3 78.2 - - - +
5046d GLY* 1.3 70.2 + - - +
5048d TRP* 3.5 6.8 - - + +
5049d LEU* 3.0 40.5 + - + +
6004d CLA 3.7 25.6 - - + -
6050d BCR 4.4 11.9 - - + -
6059d MGE 4.9 0.9 - - + -
5026f LEU* 5.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY5046 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5042d TYR* 2.4 23.9 + - - -
5043d LEU 3.5 0.2 - - - -
5044d ALA 2.6 0.2 - - - -
5045d LEU* 1.3 71.9 - - - +
5047d GLY* 1.3 52.7 + - - -
5048d TRP 2.6 4.9 + - - -
5049d LEU* 2.5 30.5 + - - +
5050d THR* 3.0 8.7 + - - -
6050d BCR 3.0 33.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY5047 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5043d LEU 2.3 27.5 + - - -
5046d GLY* 1.3 64.8 - - - -
5048d TRP* 1.3 63.0 + - - +
5050d THR* 3.6 1.0 - - - -
5051d GLY* 3.1 18.4 + - - -
5110d LEU* 5.1 8.2 - - - +
5113d PHE* 4.7 4.3 - - - -
5114d ILE* 4.0 17.5 - - - +
6050d BCR 3.7 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP5048 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6039a PHO 3.4 52.3 - - + +
5044d ALA 3.1 18.1 + - - +
5045d LEU* 3.5 8.3 - - + +
5046d GLY 2.6 4.2 + - - -
5047d GLY* 1.3 74.9 - - - +
5049d LEU* 1.3 86.5 + - + +
5052d THR* 2.5 63.3 + - + -
5067d TYR* 5.1 0.2 - - - -
5073d PHE* 4.4 21.5 - + - -
5076d VAL* 6.0 1.3 - - + -
5077d ALA* 5.0 0.8 - - - +
5078d VAL* 3.7 6.1 - - + +
5114d ILE* 4.0 12.9 - - + +
5173d PHE* 3.5 41.8 + + + -
5174d GLY* 4.7 2.2 - - - -
6004d CLA 3.8 24.5 - - + -
6059d MGE 4.0 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU5049 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5045d LEU* 3.0 49.1 - - + +
5046d GLY 2.5 8.8 + - - +
5048d TRP* 1.3 90.3 - - + +
5050d THR* 1.3 65.7 + - - +
5052d THR* 3.2 11.9 - - + -
5053d THR* 3.1 13.2 - - + +
5067d TYR* 6.5 0.2 - - + -
6050d BCR 3.2 50.5 - - + -
6059d MGE 3.4 34.5 - - + -
5033f PHE* 2.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR5050 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5046d GLY 3.0 2.5 + - - -
5047d GLY* 3.6 7.4 - - - -
5048d TRP 3.3 0.2 - - - -
5049d LEU* 1.3 80.7 - - - +
5051d GLY* 1.3 64.1 + - - +
5053d THR 3.3 0.5 + - - -
5054d PHE* 3.1 26.6 + - + +
5055d VAL* 5.4 0.7 - - + -
5101d PHE* 5.5 4.5 - - + -
5110d LEU* 6.3 2.2 - - + -
6050d BCR 2.8 48.6 - - + +
5047e PHE* 3.9 27.4 - - + -
5033f PHE* 3.5 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY5051 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5047d GLY 3.1 9.4 + - - -
5048d TRP 3.9 1.3 - - - -
5050d THR* 1.3 80.2 - - - +
5052d THR* 1.3 63.7 + - - +
5053d THR 2.9 1.6 + - - -
5054d PHE 3.1 8.3 + - - -
5055d VAL* 3.1 43.0 + - - +
5066d SER* 3.9 2.3 + - - -
5077d ALA 4.7 2.2 - - - +
5078d VAL* 4.3 12.3 - - - -
5110d LEU* 4.6 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR5052 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5048d TRP* 2.5 64.0 + - + -
5049d LEU* 3.2 17.3 - - + -
5050d THR 3.1 0.2 - - - -
5051d GLY* 1.3 72.7 - - - +
5053d THR* 1.3 58.7 + - + +
5066d SER* 4.2 0.2 - - - -
5067d TYR* 2.9 45.2 + - + +
5076d VAL* 2.6 36.7 - - + +
5077d ALA* 5.0 0.8 - - - +
5078d VAL* 4.1 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR5053 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5049d LEU* 3.1 19.7 - - - +
5050d THR 3.3 0.6 + - - -
5051d GLY 3.0 0.4 - - - -
5052d THR* 1.3 77.5 - - + +
5054d PHE* 1.3 78.7 + - - +
5066d SER* 2.6 18.6 + - - -
5067d TYR* 3.0 39.9 - - + +
5068d LEU* 3.6 10.6 + - - +
6050d BCR 5.2 2.0 - - + -
5033f PHE* 3.7 19.2 + - + -
5036f ALA* 5.7 0.3 - - - +
5037f ILE* 4.6 4.6 - - + +
5040f MET* 3.7 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE5054 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5050d THR* 3.1 21.0 + - + +
5051d GLY 3.1 1.8 + - - -
5053d THR* 1.3 99.1 - - - +
5055d VAL* 1.3 54.9 + - - +
5066d SER* 3.1 7.9 + - - -
5068d LEU* 4.3 6.2 - - + +
5037e PHE* 3.9 18.4 - + - -
5038e VAL* 4.4 10.3 - - + -
5043e ALA* 3.5 25.8 - - + -
5047e PHE* 3.3 45.7 - + + -
5049e THR* 2.6 30.5 + - - +
5032f PHE* 5.1 4.0 - + - -
5033f PHE* 3.7 29.8 - + - -
5036f ALA* 4.0 22.7 - - + -
5040f MET* 4.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL5055 (chain d).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5050d THR* 5.4 0.7 - - + -
5051d GLY* 3.1 28.7 + - - +
5054d PHE* 1.3 78.6 - - - +
5056d THR* 1.3 81.8 + - + +
5065d SER* 3.1 7.2 - - - -
5066d SER* 3.1 23.5 + - - -
5078d VAL* 6.5 0.2 - - + -
5105d CYS* 3.1 46.7 - - - +
5106d GLN* 4.8 0.9 - - - +
5110d LEU* 3.9 11.2 - - + -
5047e PHE* 3.5 29.6 - - + +
5049e THR* 3.5 1.6 - - - +
----------------------------------------------------------
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