Contacts of the helix formed by residues 1038 - 1052 (chain B) in PDB entry 1GKU
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 ASP1038 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036B GLU 3.4 5.4 + - - -
1037B LEU* 1.3 92.6 - - + +
1039B TYR* 1.3 63.6 + - - +
1040B LEU* 2.6 44.2 + - - +
1041B LYS* 3.3 30.0 + - + -
1042B ALA 3.4 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1039 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA 5.4 0.3 + - - -
21B ALA* 3.8 28.5 + - - -
574B PHE 4.6 6.8 + - - -
576B PRO* 5.7 2.6 - - - +
682B LYS* 3.6 59.2 - - + -
685B VAL* 5.4 8.3 - - + -
686B VAL* 4.1 16.0 - - + +
1032B ILE* 3.9 14.1 - - + -
1037B LEU 3.2 4.6 + - - -
1038B ASP* 1.3 74.2 + - - +
1040B LEU* 1.3 93.8 + - + +
1042B ALA* 3.2 17.4 - - - +
1043B LEU* 3.6 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1040 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B ARG 4.8 13.2 - - - +
574B PHE* 5.2 5.4 - - + +
1038B ASP* 2.6 20.3 + - - +
1039B TYR* 1.3 105.7 - - + +
1041B LYS* 1.3 72.9 + - + +
1042B ALA 2.9 5.6 + - - -
1043B LEU* 2.9 11.5 + - + +
1044B GLU* 2.8 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1041 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037B LEU* 4.6 10.1 - - + -
1038B ASP* 3.3 32.6 + - + +
1040B LEU* 1.3 83.5 - - - +
1042B ALA* 1.3 56.9 + - - +
1044B GLU* 3.5 36.3 + - - +
1045B ASP* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1042 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686B VAL* 4.4 18.8 - - + -
1028B ARG* 5.2 13.0 - - + +
1032B ILE* 5.7 1.6 - - + -
1037B LEU* 3.8 24.6 - - + +
1038B ASP 3.4 3.6 + - - +
1039B TYR* 3.2 15.3 - - - +
1040B LEU 2.9 0.8 + - - -
1041B LYS* 1.3 80.1 - - - +
1043B LEU* 1.3 58.9 + - - +
1045B ASP* 3.3 4.7 + - - +
1046B MET* 2.8 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1043 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B VAL* 6.1 2.2 - - + -
574B PHE* 3.9 38.1 - - + +
576B PRO* 6.0 5.6 - - + -
685B VAL* 5.6 4.0 - - + -
686B VAL* 3.7 34.5 - - + -
689B ILE* 4.5 24.0 - - + -
693B TRP* 4.2 1.9 - - + -
1039B TYR* 3.8 35.7 - - + +
1040B LEU* 2.9 7.7 + - + +
1042B ALA* 1.3 72.0 - - - +
1044B GLU* 1.3 57.9 + - - +
1046B MET* 3.1 9.7 + - - +
1047B TYR* 2.6 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1044 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B PHE* 4.5 14.7 - - + -
1040B LEU 2.8 16.2 + - - +
1041B LYS* 3.5 42.2 + - - +
1043B LEU* 1.3 77.1 - - - +
1045B ASP* 1.3 66.9 + - - +
1047B TYR* 3.2 4.7 + - - +
1048B ALA* 3.2 16.1 + - - +
1051B LYS* 5.7 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1045 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025B LEU* 5.0 4.5 - - - +
1028B ARG* 3.1 29.7 + - - +
1041B LYS 2.9 19.5 + - - +
1042B ALA* 3.4 5.0 - - - +
1044B GLU* 1.3 79.4 - - + +
1046B MET* 1.3 57.7 + - - +
1048B ALA* 2.7 37.8 + - - +
1049B GLU* 3.3 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1046 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686B VAL* 3.7 26.7 - - + +
689B ILE 4.6 0.2 - - - -
690B GLU* 3.3 49.1 - - + +
693B TRP* 4.1 14.4 - - + -
694B ILE* 4.3 13.9 - - + -
715B ARG* 5.1 4.0 - - - +
1025B LEU* 4.7 16.2 - - + -
1028B ARG* 6.5 1.1 - - - -
1029B MET* 4.9 5.4 - - + -
1042B ALA* 2.8 25.0 + - + +
1043B LEU* 3.5 13.5 - - - +
1045B ASP* 1.3 78.0 + - - +
1047B TYR* 1.3 59.0 + - - +
1049B GLU* 3.8 10.1 - - - +
1050B ILE* 2.8 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1047 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B PHE* 3.7 29.9 - + - -
570B VAL* 3.3 31.2 - - + +
571B ASN* 4.8 4.4 + - - -
572B GLY 5.9 0.9 - - - -
574B PHE* 3.4 27.1 - + + -
693B TRP* 3.7 20.2 - + - -
1043B LEU 2.6 18.9 + - - +
1044B GLU 3.4 6.7 - - - +
1045B ASP 3.0 0.2 - - - -
1046B MET* 1.3 73.2 - - - +
1048B ALA* 1.3 64.5 + - - +
1050B ILE* 3.3 14.6 - - + +
1051B LYS* 3.3 46.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1048 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1044B GLU 3.2 10.0 + - - +
1045B ASP* 2.7 20.2 + - - +
1047B TYR* 1.3 72.0 - - - +
1049B GLU* 1.3 52.1 + - - +
1050B ILE 2.9 4.0 - - - -
1051B LYS* 2.7 48.6 + - + +
1052B SER* 3.5 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1049 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694B ILE* 4.0 8.9 - - - +
715B ARG* 2.4 47.4 + - - -
1015B LYS* 4.4 3.6 - - - +
1016B PHE* 4.0 13.4 - - + +
1021B ARG* 3.5 29.3 + - - +
1025B LEU* 4.9 4.9 - - - +
1045B ASP* 3.3 14.0 + - - +
1046B MET* 3.8 17.9 - - - +
1048B ALA* 1.3 77.4 - - - +
1050B ILE* 1.3 63.1 + - + +
1051B LYS 3.3 0.2 - - - -
1052B SER* 3.5 23.2 - - - -
1053B ILE* 4.0 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1050 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B PHE* 4.1 25.8 - - + -
693B TRP* 4.1 16.4 - - + -
694B ILE* 3.3 44.4 - - + +
697B VAL* 4.2 18.4 - - + -
1046B MET 2.8 24.5 - - - +
1047B TYR* 3.3 11.4 - - + +
1048B ALA 2.8 0.8 + - - -
1049B GLU* 1.3 78.8 - - - +
1051B LYS* 1.3 66.6 + - + +
1052B SER 3.1 0.2 - - - -
1053B ILE* 3.0 31.4 + - + +
1054B ASP* 3.8 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1051 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1044B GLU 5.7 0.8 + - - -
1047B TYR* 3.3 50.9 - - + +
1048B ALA* 2.7 19.9 + - + +
1050B ILE* 1.3 73.8 - - + +
1052B SER* 1.3 55.4 + - - +
1053B ILE 2.8 20.5 + - - +
1054B ASP* 5.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1052 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013B TYR* 4.4 10.6 - - - -
1015B LYS* 4.0 14.2 + - - -
1016B PHE* 3.9 15.1 - - - -
1048B ALA 3.5 2.5 + - - -
1049B GLU* 3.5 23.0 + - - -
1050B ILE 3.1 1.0 - - - -
1051B LYS* 1.3 76.2 - - - +
1053B ILE* 1.3 69.9 + - - +
----------------------------------------------------------
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