Contacts of the helix formed by residues 1083 - 1093 (chain B) in PDB entry 4E5W
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 SER1083 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965B LYS* 4.3 16.2 - - - -
1047B TRP* 5.4 3.4 - - - -
1073B GLU* 5.8 0.7 - - - +
1076B THR* 5.6 0.7 - - - -
1078B CYS* 6.5 0.2 - - - +
1079B ASP 3.2 8.2 + - - -
1080B SER* 3.3 19.1 + - - -
1081B ASP 3.5 0.8 - - - -
1082B SER* 1.3 80.9 - - - +
1084B PRO* 1.3 75.4 - - - +
1085B MET* 3.5 10.3 + - - +
1086B ALA* 3.2 16.0 + - - +
1087B LEU* 2.9 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1084 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046B PHE* 4.1 8.7 - - - +
1047B TRP* 3.6 26.0 - - + -
1069B VAL* 3.4 35.2 - - + +
1072B HIS* 5.2 3.6 - - - +
1073B GLU* 3.7 22.2 - - + +
1082B SER 3.7 2.9 - - - +
1083B SER* 1.3 86.1 - - - +
1085B MET* 1.3 55.5 + - - +
1087B LEU* 4.1 0.6 - - + -
1088B PHE* 3.0 37.0 + - - -
1114B LEU* 4.1 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1085 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046B PHE* 3.8 36.6 - - + +
1047B TRP* 4.4 12.4 - - + -
1083B SER* 3.2 8.2 + - - +
1084B PRO* 1.3 76.0 - - - +
1086B ALA* 1.3 61.4 + - - +
1088B PHE* 3.4 1.0 + - - +
1089B LEU* 2.9 54.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1086 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1080B SER 3.8 14.1 - - - +
1081B ASP* 3.9 15.7 - - - +
1083B SER* 3.1 18.6 + - - +
1085B MET* 1.3 79.2 - - - +
1087B LEU* 1.3 58.6 + - - +
1089B LEU* 4.0 6.6 - - - +
1090B LYS* 3.1 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1087 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1072B HIS* 3.6 24.5 - - + -
1081B ASP 4.3 5.6 - - - +
1082B SER* 3.5 34.5 - - - +
1083B SER 2.9 17.0 + - - +
1086B ALA* 1.3 74.2 - - - +
1088B PHE* 1.3 64.9 + - - +
1090B LYS* 3.3 9.4 + - + +
1091B MET* 3.1 28.4 + - - +
1114B LEU* 3.8 16.2 - - + -
1115B PRO* 4.1 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1088 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046B PHE* 3.5 47.6 - + + -
1065B TRP* 5.6 4.5 - + - -
1069B VAL* 5.6 2.9 - - + -
1084B PRO 3.0 25.4 + - - +
1085B MET 4.0 0.2 - - - +
1087B LEU* 1.3 75.8 - - - +
1089B LEU* 1.3 57.5 + - - +
1091B MET* 3.1 32.2 + - + +
1092B ILE* 2.9 38.1 + - + +
1104B LEU* 3.7 23.3 - - + -
1107B THR* 5.1 2.5 - - + -
1108B LEU* 4.0 24.7 - - + -
1112B LYS 5.0 0.4 - - - -
1113B ARG* 4.8 1.8 - - - -
1114B LEU* 3.7 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1089 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046B PHE* 4.0 22.0 - - + -
1085B MET* 2.9 41.4 + - + +
1086B ALA* 4.0 6.1 - - - +
1088B PHE* 1.3 74.8 - - - +
1090B LYS* 1.3 55.1 + - - +
1092B ILE* 4.2 2.9 - - + -
1093B GLY* 2.8 50.6 + - - +
1094B PRO* 3.5 26.7 - - + +
1100B THR* 4.2 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1090 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086B ALA 3.1 18.3 + - - +
1087B LEU* 3.6 10.1 - - + +
1088B PHE 3.2 0.2 - - - -
1089B LEU* 1.3 76.2 - - - +
1091B MET* 1.4 61.9 + - + +
1093B GLY* 4.2 3.5 + - - -
1094B PRO* 5.7 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1091 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087B LEU* 3.1 19.8 + - - +
1088B PHE* 3.1 31.1 + - + +
1090B LYS* 1.4 79.8 - - + +
1092B ILE* 1.3 63.9 - - + +
1107B THR* 3.9 13.7 + - + +
1112B LYS* 3.8 33.0 - - + -
1113B ARG 3.9 21.3 - - - +
1114B LEU* 5.0 6.1 - - - -
1115B PRO* 5.2 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1092 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046B PHE* 4.3 10.1 - - + -
1088B PHE* 2.9 26.3 + - + +
1089B LEU* 4.2 1.8 - - + -
1091B MET* 1.3 74.1 - - + +
1093B GLY* 1.3 67.4 + - - +
1096B HIS* 3.0 19.6 + - + -
1100B THR* 3.6 43.3 - - + +
1103B ARG* 4.0 22.7 + - + +
1104B LEU* 4.0 18.6 - - + +
1107B THR* 3.2 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1093 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1089B LEU* 2.8 22.0 + - - +
1090B LYS 4.2 3.2 + - - -
1091B MET 3.7 1.4 - - - -
1092B ILE* 1.3 83.3 - - - +
1094B PRO* 1.4 70.6 - - - +
1095B THR* 3.4 3.1 - - - -
1096B HIS* 3.3 22.8 + - - +
1100B THR* 5.1 1.4 + - - -
----------------------------------------------------------
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