Contacts of the helix formed by residues 1022 - 1043 (chain B) in PDB entry 5UNF
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 ASN1022 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020B ALA* 4.2 0.3 - - - +
1021B ASP* 1.4 79.7 - - + +
1023B ALA* 1.4 62.7 + - - +
1024B ALA* 3.2 15.4 + - + +
1025B GLN* 2.9 66.8 + - - +
1026B VAL* 3.6 11.3 - - - +
1084B VAL* 4.1 6.3 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
1022B ASN* 1.4 71.0 - - - +
1024B ALA* 1.4 59.4 + - - +
1025B GLN 3.3 0.2 - - - -
1026B VAL* 3.4 8.6 + - - +
1027B LYS* 2.9 29.7 + - - +
1079B ALA* 3.5 27.6 - - - +
1082B GLY* 4.2 13.5 - - - -
1084B VAL* 3.6 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1024 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022B ASN* 3.2 14.4 + - - +
1023B ALA* 1.4 76.4 - - - +
1025B GLN* 1.4 56.2 + - - +
1027B LYS* 3.8 18.3 - - - +
1028B ASP* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1025 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016B VAL* 4.3 17.4 - - + +
1019B LYS 4.4 4.4 + - - -
1020B ALA* 3.5 27.4 - - + +
1021B ASP* 3.5 25.1 + - - +
1022B ASN* 2.9 40.6 + - - +
1024B ALA* 1.4 72.7 - - - +
1026B VAL* 1.4 59.6 + - - +
1028B ASP* 3.8 5.2 - - - +
1029B ALA* 3.1 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1026 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017B ILE* 4.0 21.9 - - + +
1020B ALA* 3.7 18.6 - - + -
1022B ASN 3.6 14.6 - - - +
1023B ALA* 3.4 8.3 + - - +
1024B ALA 3.4 0.2 - - - -
1025B GLN* 1.4 72.9 - - - +
1027B LYS* 1.4 58.1 + - - +
1029B ALA* 3.4 5.7 + - - +
1030B LEU* 3.0 52.8 + - + +
1079B ALA* 4.3 3.4 - - + -
1084B VAL* 4.1 18.8 - - + +
1087B ALA* 3.8 23.6 - - + -
1088B GLN* 4.2 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1027 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023B ALA 2.9 17.9 + - - +
1024B ALA* 3.8 17.5 - - - +
1026B VAL* 1.4 75.7 - - - +
1028B ASP* 1.4 54.8 + - - +
1030B LEU* 3.4 3.2 + - - +
1031B THR* 2.7 43.0 + - - +
1076B LEU* 3.9 12.0 - - + +
1079B ALA* 4.0 15.1 - - + +
1080B ASN* 3.3 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1028 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1024B ALA 3.0 19.0 + - - +
1025B GLN* 3.8 6.6 - - - +
1027B LYS* 1.4 78.5 - - - +
1029B ALA* 1.4 60.9 + - - +
1031B THR* 3.3 8.0 + - - -
1032B LYS* 3.2 58.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1029 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013B ASN* 3.5 41.4 - - - +
1016B VAL* 4.2 11.4 - - + -
1017B ILE* 3.8 10.1 - - + -
1025B GLN 3.1 18.6 + - - +
1026B VAL 3.7 4.0 - - - +
1028B ASP* 1.4 74.5 - - - +
1030B LEU* 1.4 58.2 + - - +
1032B LYS* 3.3 6.4 + - - +
1033B MET* 3.0 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1030 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017B ILE* 3.8 22.0 - - + -
1026B VAL* 3.0 36.5 + - + +
1029B ALA* 1.4 73.0 - - - +
1031B THR* 1.3 59.8 + - - +
1032B LYS 3.3 0.2 - - - -
1033B MET* 3.6 10.0 - - - +
1034B ARG* 2.9 24.4 + - - +
1072B ILE* 3.5 27.0 - - + +
1075B ALA* 3.6 49.4 - - + +
1076B LEU* 3.6 23.3 - - + +
1079B ALA* 4.3 2.0 - - + -
1091B ALA* 4.7 0.9 - - + -
1094B LEU* 4.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1031 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027B LYS* 2.7 27.3 + - - +
1028B ASP* 3.3 9.7 + - - -
1030B LEU* 1.3 75.4 - - - +
1032B LYS* 1.3 62.8 + - + +
1034B ARG* 3.5 6.6 + - - +
1035B ALA* 3.3 21.1 + - - +
1076B LEU* 4.1 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1032 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009B THR* 4.4 6.4 - - + +
1013B ASN* 3.4 33.0 + - - +
1028B ASP* 3.2 45.8 + - - +
1029B ALA* 3.3 7.1 + - - +
1031B THR* 1.3 77.7 - - + +
1033B MET* 1.3 56.6 + - - +
1035B ALA* 3.5 7.2 + - - +
1036B ALA* 3.1 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1033 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010B LEU* 3.3 47.9 - - + +
1013B ASN* 3.6 18.4 - - + +
1014B LEU* 3.9 9.9 - - + -
1017B ILE* 3.8 27.8 - - - -
1029B ALA 3.0 18.7 + - - +
1030B LEU* 3.6 11.9 - - - +
1031B THR 3.3 0.2 - - - -
1032B LYS* 1.3 75.4 - - - +
1034B ARG* 1.4 54.9 + - - +
1036B ALA* 3.3 2.1 + - - -
1037B ALA* 2.8 36.0 + - - +
1068B LEU* 5.8 2.2 - - + -
1072B ILE* 3.9 11.9 - - + -
1094B LEU* 3.7 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1034 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030B LEU 2.9 17.1 + - - +
1031B THR* 3.9 7.2 - - - +
1032B LYS 3.5 0.2 - - - -
1033B MET* 1.4 74.4 - - - +
1035B ALA* 1.3 61.0 + - - +
1037B ALA* 3.9 1.9 - - - +
1038B LEU* 3.2 58.0 + - - +
1069B VAL* 3.5 26.1 - - + +
1072B ILE* 3.9 16.6 - - + +
1073B ASP* 2.7 41.2 + - - -
1076B LEU* 4.3 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1035 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1031B THR 3.3 11.0 + - - +
1032B LYS* 3.6 11.2 - - - +
1033B MET 3.2 0.4 - - - -
1034B ARG* 1.3 79.8 - - - +
1036B ALA* 1.4 55.6 + - - +
1038B LEU* 3.6 6.1 + - - +
1039B ASP* 3.1 29.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
1006B ASN* 3.7 36.9 - - - +
1009B THR* 4.0 17.3 - - + -
1010B LEU* 4.1 8.3 - - + -
1032B LYS 3.1 17.5 + - - +
1033B MET* 3.3 4.9 + - - +
1035B ALA* 1.4 72.8 - - - +
1037B ALA* 1.3 59.4 + - - +
1039B ASP* 4.3 1.3 - - - -
1040B ALA* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1037 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010B LEU* 4.2 5.6 - - + +
1033B MET 2.8 16.8 + - - +
1034B ARG 3.9 2.2 - - - +
1035B ALA 3.4 0.2 - - - -
1036B ALA* 1.3 76.8 - - - +
1038B LEU* 1.3 56.3 + - - +
1040B ALA* 3.5 1.4 + - - -
1041B GLN* 3.1 23.7 + - - +
1065B PHE* 3.4 19.5 - - + +
1068B LEU* 4.0 21.8 - - + -
1069B VAL* 3.7 23.3 - - + -
1072B ILE* 4.1 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1038 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034B ARG* 3.2 44.7 + - + +
1035B ALA* 4.1 5.8 - - - +
1037B ALA* 1.3 74.3 - - - +
1039B ASP* 1.4 62.6 + - - +
1041B GLN* 3.5 29.6 - - - +
1042B LYS* 3.4 22.6 - - - +
1066B ASP* 5.8 1.1 - - - +
1069B VAL* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1039 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001B ALA* 3.4 30.7 + - - +
1006B ASN* 3.4 26.1 + - - +
1035B ALA 3.1 19.1 + - - +
1036B ALA* 3.8 3.3 - - - +
1038B LEU* 1.4 74.3 - - - +
1040B ALA* 1.4 61.4 + - - +
1042B LYS* 3.4 22.4 + - - +
1043B ALA* 3.5 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1040 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003B LEU* 3.4 23.8 - - + +
1006B ASN* 3.3 19.7 - - + +
1007B TRP* 4.9 2.2 - - + +
1010B LEU* 5.3 2.0 - - + -
1036B ALA 2.9 19.5 + - - +
1037B ALA 3.5 0.4 + - - +
1039B ASP* 1.4 73.2 - - - +
1041B GLN* 1.4 62.9 + - - +
1043B ALA* 3.2 21.5 + - - +
1061B PHE* 3.8 3.6 - - - -
1065B PHE* 3.6 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1041 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037B ALA 3.1 16.5 + - - +
1038B LEU* 3.5 31.1 - - - +
1039B ASP 3.3 0.2 - - - -
1040B ALA* 1.4 77.6 - - - +
1042B LYS* 1.3 60.0 + - + +
1043B ALA 3.9 4.9 - - - +
1061B PHE* 4.3 1.3 - - - -
1062B ARG* 3.1 54.4 + - + +
1065B PHE* 3.8 25.7 - - + +
1066B ASP* 2.8 30.9 + - - +
1069B VAL* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1042 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038B LEU 3.4 16.2 - - - +
1039B ASP* 3.4 15.9 + - - +
1040B ALA 3.2 0.4 - - - -
1041B GLN* 1.3 74.8 - - + +
1043B ALA* 1.4 62.4 + - - +
1044B THR* 4.1 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1043 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001B ALA 4.5 7.4 - - - +
1002B ASP* 5.6 0.4 - - - -
1003B LEU* 3.9 30.3 - - + +
1039B ASP 3.5 8.7 + - - +
1040B ALA* 3.2 14.1 + - - +
1041B GLN 3.9 1.4 - - - +
1042B LYS* 1.4 82.2 - - - +
1044B THR* 1.3 60.2 + - - +
1045B PRO 4.2 0.2 - - - -
1058B MET* 5.0 2.1 - - - +
1061B PHE* 3.3 25.2 - - - -
----------------------------------------------------------
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