Contacts of the helix formed by residues 1019 - 1036 (chain B) in PDB entry 2WIN
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 LYS1019 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
979B LYS* 4.1 28.3 - - - +
982B ILE* 5.7 2.9 - - - +
1012B TRP* 4.2 2.0 - - - -
1015B PHE* 3.5 46.4 + - + +
1016B GLY* 3.1 11.6 + - - +
1017B LEU 3.0 0.6 - - - -
1018B GLU* 1.3 99.8 - - - +
1020B ARG* 1.3 63.9 + - - +
1021B GLN 3.3 2.2 - - - -
1022B GLY* 3.2 13.2 + - - +
1023B ALA* 3.4 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1020 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 3.4 31.1 - - + -
41A PRO* 3.4 23.0 - - - +
42A GLY* 3.6 20.8 + - - +
1003B VAL* 4.1 4.0 - - - +
1007B ASP* 3.4 29.1 + - - -
1012B TRP* 3.5 42.4 - - + +
1017B LEU 3.2 11.9 + - - +
1019B LYS* 1.3 76.1 - - - +
1021B GLN* 1.3 63.1 + - - +
1023B ALA* 2.8 17.2 + - - +
1024B LEU* 3.0 50.7 + - + +
1069B ASN 5.9 0.4 + - - -
1070B LEU* 4.3 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1021 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A THR* 5.7 0.7 - - - +
96A GLU* 2.8 44.7 + - + +
1017B LEU 4.4 2.4 + - - +
1018B GLU* 4.7 9.6 - - - +
1019B LYS 3.3 0.4 - - - -
1020B ARG* 1.3 80.8 + - - +
1022B GLY* 1.3 60.7 + - - +
1023B ALA 3.3 0.5 + - - -
1024B LEU* 3.6 12.5 + - - +
1025B GLU* 3.2 50.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1022 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982B ILE* 5.1 2.7 - - - -
1018B GLU 4.8 1.8 + - - -
1019B LYS* 3.2 11.6 + - - +
1020B ARG 3.1 0.8 - - - -
1021B GLN* 1.3 78.1 - - - +
1023B ALA* 1.3 58.0 + - - +
1025B GLU* 4.1 12.3 + - - +
1026B LEU* 3.2 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1023 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982B ILE* 4.1 28.0 - - + -
999B THR* 3.8 3.5 - - + +
1003B VAL* 3.7 23.8 - - + -
1012B TRP* 4.6 2.5 - - + -
1019B LYS 3.4 9.2 + - - +
1020B ARG* 2.8 13.1 + - - +
1022B GLY* 1.3 76.7 - - - +
1024B LEU* 1.3 65.4 + - - +
1025B GLU 3.1 1.3 - - - -
1026B LEU* 3.1 4.4 + - - +
1027B ILE* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1024 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003B VAL* 4.3 10.8 - - + -
1020B ARG* 3.0 65.4 + - + +
1021B GLN* 4.0 16.2 - - - +
1023B ALA* 1.3 77.2 - - + +
1025B GLU* 1.3 56.9 + - + +
1027B ILE* 3.4 8.5 + - + +
1028B LYS* 3.0 30.0 + - - +
1070B LEU* 3.4 42.0 - - + +
1071B ILE* 4.2 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1025 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 6.0 2.4 - - - +
96A GLU* 4.9 0.7 - - - +
1021B GLN* 3.2 42.9 + - - +
1022B GLY* 4.2 10.7 - - - +
1023B ALA 3.1 0.6 - - - -
1024B LEU* 1.3 79.1 - - - +
1026B LEU* 1.3 60.0 + - + +
1028B LYS* 4.0 5.8 - - - +
1029B LYS* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1026 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982B ILE* 3.6 33.0 - - + +
983B VAL 4.4 1.8 - - - +
984B THR* 3.7 42.8 - - + +
985B PRO* 3.2 24.2 - - + +
999B THR* 4.2 7.4 - - + -
1022B GLY 3.2 18.1 + - - +
1023B ALA 3.1 6.8 + - - +
1025B GLU* 1.3 78.0 - - + +
1027B ILE* 1.3 61.3 + - - +
1029B LYS* 3.7 11.6 - - + +
1030B GLY 3.0 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1027 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985B PRO* 5.3 1.6 - - - -
996B MET* 5.8 2.0 - - - +
999B THR* 3.5 21.8 - - + +
1000B VAL* 3.8 32.8 - - + +
1003B VAL* 3.6 31.4 - - + -
1023B ALA 2.9 19.1 + - - +
1024B LEU* 3.7 9.2 - - + +
1025B GLU 3.3 0.2 - - - -
1026B LEU* 1.3 75.0 - - - +
1028B LYS* 1.3 64.5 + - - +
1030B GLY* 3.2 2.4 + - - -
1031B TYR* 3.1 21.1 + - - +
1067B ALA* 4.7 7.9 - - + -
1070B LEU* 4.0 17.5 - - + -
1071B ILE* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1028 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1024B LEU 3.0 18.3 + - - +
1025B GLU* 4.0 5.4 - - - +
1027B ILE* 1.3 77.0 - - - +
1029B LYS* 1.3 61.3 + - - +
1031B TYR* 3.3 7.4 + - + +
1032B THR* 3.1 35.1 + - - +
1071B ILE* 3.9 27.6 - - + -
1072B ALA* 6.4 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1029 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984B THR* 5.1 10.7 - - + +
985B PRO* 4.7 6.3 + - + +
1025B GLU 2.9 20.2 + - - +
1026B LEU* 3.7 20.4 - - + +
1027B ILE 3.2 0.2 - - - -
1028B LYS* 1.3 77.6 - - - +
1030B GLY* 1.3 60.7 + - - +
1032B THR* 3.5 5.8 + - - -
1033B GLN* 2.8 62.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1030 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985B PRO* 3.8 26.6 - - - +
992B ASN* 3.2 13.7 + - - -
993B MET* 5.7 1.4 - - - +
996B MET* 4.6 9.1 - - - +
1026B LEU 3.0 11.6 + - - -
1027B ILE 3.2 4.4 + - - -
1029B LYS* 1.3 73.4 - - - +
1031B TYR* 1.3 64.2 + - - +
1033B GLN* 4.6 0.4 - - - -
1034B GLN* 3.2 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1031 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027B ILE 3.1 6.3 + - - +
1028B LYS* 3.5 12.3 - - + +
1029B LYS 3.3 0.2 - - - -
1030B GLY* 1.3 75.9 - - - +
1032B THR* 1.3 71.0 + - - +
1034B GLN* 3.3 15.4 + - - +
1035B LEU* 3.3 46.0 + - + +
1064B PHE* 3.3 43.1 - + + -
1071B ILE* 3.7 23.1 - - + -
1072B ALA 4.0 16.8 + - - -
1073B ILE* 3.8 18.4 - - + -
1074B ASP* 3.2 34.4 + - - +
1077B VAL* 4.4 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1032 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028B LYS* 3.1 23.8 + - - +
1029B LYS* 3.8 7.9 - - - -
1031B TYR* 1.3 87.2 - - - +
1033B GLN* 1.3 62.0 + - + +
1035B LEU* 3.1 26.5 + - + +
1036B ALA* 3.8 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1033 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985B PRO 3.3 18.5 + - - +
986B SER* 3.7 10.4 - - - +
987B GLY 4.7 2.8 + - - +
992B ASN* 3.2 34.9 + - - +
1029B LYS* 2.8 52.5 + - + +
1031B TYR 3.3 0.4 - - - -
1032B THR* 1.3 78.7 - - + +
1034B GLN* 1.3 57.2 + - - +
1035B LEU 3.2 0.2 - - - -
1036B ALA* 3.4 10.1 + - - +
1037B PHE* 3.1 29.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1034 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989B GLY* 3.1 32.0 + - - +
992B ASN* 3.3 13.0 + - - +
993B MET* 3.4 32.1 - - - +
1030B GLY 3.2 16.6 + - - +
1031B TYR 3.6 6.5 - - - +
1032B THR 3.1 0.8 - - - -
1033B GLN* 1.3 73.8 - - - +
1035B LEU* 1.3 63.8 + - - +
1036B ALA 3.2 0.9 - - - -
1037B PHE* 3.3 18.9 + - - +
1038B ARG* 3.8 7.4 + - - +
1056B LEU* 5.2 5.1 - - - +
1060B VAL* 3.9 17.4 - - + +
1064B PHE* 4.1 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1035 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1031B TYR* 3.3 48.2 - - + +
1032B THR* 3.1 19.4 + - + +
1034B GLN* 1.3 75.7 - - + +
1036B ALA* 1.3 55.7 + - - +
1037B PHE 3.0 9.9 + - - -
1038B ARG* 3.3 23.3 + - + +
1064B PHE* 5.2 2.2 - - + -
1077B VAL* 4.0 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1036 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032B THR 3.8 4.1 + - - +
1033B GLN* 3.4 15.3 + - - +
1034B GLN 3.2 0.8 - - - -
1035B LEU* 1.3 76.4 - - - +
1037B PHE* 1.3 73.9 + - + +
1038B ARG 3.7 0.4 - - - -
1048B VAL* 4.1 8.5 - - - +
----------------------------------------------------------
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