Contacts of the helix formed by residues 1022 - 1042 (chain A) in PDB entry 4YAY
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021A ASP* 1.3 80.7 + - + +
1023A ALA* 1.4 63.2 + - - +
1024A ALA* 3.4 14.3 + - + +
1025A GLN* 2.8 61.9 + - - +
1026A VAL* 3.4 14.2 - - - +
1084A VAL* 3.9 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1023 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022A ASN* 1.4 70.8 - - - +
1024A ALA* 1.4 54.5 + - - +
1026A VAL* 3.2 9.1 + - - +
1027A LYS* 2.8 40.8 + - + +
1079A ALA* 3.5 29.0 - - - +
1082A GLY* 4.3 8.3 - - - +
1084A VAL* 3.4 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1024 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022A ASN* 3.3 13.3 + - - +
1023A ALA* 1.4 77.0 - - - +
1025A GLN* 1.4 60.1 + - - +
1027A LYS* 4.2 11.4 - - + -
1028A ASP* 3.0 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1025 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016A VAL* 4.5 14.0 + - + +
1019A LYS 4.8 2.4 + - - -
1020A ALA* 3.8 27.4 - - + +
1021A ASP* 3.8 17.6 + - - +
1022A ASN* 2.8 48.0 + - - +
1023A ALA 3.3 0.4 - - - -
1024A ALA* 1.4 74.9 - - + +
1026A VAL* 1.3 61.9 + - - +
1028A ASP* 4.6 2.5 - - - +
1029A ALA* 3.5 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1026 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017A ILE* 4.2 24.0 - - + -
1020A ALA* 3.8 18.4 - - + -
1022A ASN 3.4 16.6 - - - +
1023A ALA* 3.2 8.7 + - - +
1025A GLN* 1.3 75.3 - - - +
1027A LYS* 1.4 57.7 + - - +
1029A ALA* 3.4 2.4 + - - +
1030A LEU* 3.0 49.0 + - + +
1079A ALA* 4.6 3.8 - - + -
1084A VAL* 3.8 20.2 - - + +
1087A ALA* 4.1 21.5 - - + -
1088A GLN* 4.6 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1027 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023A ALA* 2.8 28.5 + - + +
1024A ALA* 3.8 9.9 - - - +
1025A GLN 3.5 0.2 - - - -
1026A VAL* 1.4 73.2 - - - +
1028A ASP* 1.4 57.5 + - - +
1030A LEU* 3.4 3.0 + - - +
1031A THR* 2.6 38.9 + - - +
1076A LEU* 4.0 11.6 - - + +
1079A ALA* 3.8 25.8 - - + +
1080A ASN* 3.4 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1028 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1024A ALA* 3.0 22.1 + - - +
1025A GLN* 4.6 3.1 - - - +
1027A LYS* 1.4 78.4 - - - +
1029A ALA* 1.3 60.2 + - - +
1031A THR* 3.6 8.2 + - - -
1032A LYS* 3.4 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1029 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013A ASN* 3.3 28.3 - - - +
1016A VAL* 4.3 12.6 - - + -
1017A ILE* 3.7 21.8 - - + -
1025A GLN 3.5 18.4 + - - +
1026A VAL 3.4 4.9 + - - +
1027A LYS 3.3 0.8 - - - -
1028A ASP* 1.3 78.3 - - - +
1030A LEU* 1.4 58.2 - - - +
1032A LYS* 3.5 1.5 + - - -
1033A MET* 3.2 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1030 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017A ILE* 3.8 20.2 - - + -
1026A VAL* 3.0 37.8 + - + +
1027A LYS 3.4 0.4 + - - +
1029A ALA* 1.4 72.6 - - - +
1031A THR* 1.4 58.6 + - - +
1032A LYS 3.4 0.2 - - - -
1033A MET* 3.6 15.1 - - + +
1034A ARG* 3.0 28.2 + - - +
1072A ILE* 3.7 27.6 - - + +
1075A ALA* 3.8 40.6 - - + +
1076A LEU* 3.7 24.6 - - + +
1079A ALA* 5.1 1.1 - - + -
1087A ALA 5.1 0.9 - - - +
1091A ALA* 4.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1031 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027A LYS* 2.6 25.1 + - - +
1028A ASP* 3.7 9.8 - - - -
1029A ALA 3.3 0.2 - - - -
1030A LEU* 1.4 75.3 - - - +
1032A LYS* 1.4 63.4 + - + +
1034A ARG* 3.4 15.6 + - + +
1035A ALA* 3.4 14.6 + - - +
1076A LEU* 4.3 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1032 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009A THR* 4.6 12.2 - - + +
1013A ASN* 3.4 22.9 - - - +
1028A ASP 3.4 15.4 + - - +
1029A ALA* 3.8 2.0 - - - +
1031A THR* 1.4 77.1 - - + +
1033A MET* 1.3 62.1 + - - +
1035A ALA* 3.7 5.2 + - - +
1036A ALA* 3.2 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1033 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009A THR 4.5 0.9 - - - +
1010A LEU* 3.5 32.9 - - + +
1013A ASN* 3.7 26.2 - - + -
1014A LEU* 4.3 7.2 - - + -
1017A ILE* 3.7 26.9 - - - -
1029A ALA 3.2 9.7 + - - +
1030A LEU* 3.6 16.8 - - + +
1032A LYS* 1.3 75.6 - - - +
1034A ARG* 1.4 61.6 + - - +
1036A ALA* 3.4 4.1 + - - +
1037A ALA* 3.2 21.3 + - - +
1072A ILE* 4.2 28.6 - - + +
1091A ALA* 5.3 2.2 - - + +
1094A LEU* 3.7 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1034 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030A LEU 3.0 17.9 + - - +
1031A THR* 3.5 10.1 - - - +
1032A LYS 3.3 0.4 - - - -
1033A MET* 1.4 74.0 - - - +
1035A ALA* 1.3 63.3 + - - +
1037A ALA* 3.5 4.2 + - - +
1038A LEU* 3.3 49.0 + - + +
1069A VAL* 4.2 20.4 - - + +
1072A ILE* 4.4 14.3 - - + +
1073A ASP* 3.1 35.1 + - - +
1076A LEU* 4.2 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1035 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1031A THR 3.4 11.9 + - - +
1032A LYS* 4.1 4.9 - - - +
1034A ARG* 1.3 77.2 - - - +
1036A ALA* 1.4 61.5 + - - +
1038A LEU* 3.4 20.6 + - + +
1039A ASP* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1036 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006A ASN* 3.8 36.5 - - - +
1009A THR* 4.2 11.9 - - + -
1010A LEU* 4.2 5.8 - - + -
1032A LYS 3.2 18.9 + - - +
1033A MET* 3.4 11.2 - - - +
1034A ARG 3.2 0.2 - - - -
1035A ALA* 1.4 76.1 - - - +
1037A ALA* 1.3 60.0 + - - +
1039A ASP* 3.0 16.9 - - - +
1040A ALA* 3.2 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1037 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010A LEU* 4.7 4.0 - - + +
1033A MET 3.2 13.7 + - - +
1034A ARG 3.5 4.2 + - - +
1036A ALA* 1.3 75.0 - - - +
1038A LEU* 1.4 61.0 + - - +
1040A ALA* 3.9 8.5 - - - -
1041A GLN* 3.3 23.4 + - - +
1065A PHE* 3.8 27.4 - - + +
1068A LEU* 4.1 16.2 - - + -
1069A VAL* 4.3 17.9 - - + +
1072A ILE* 5.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1038 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034A ARG* 3.3 42.7 + - - +
1035A ALA* 3.6 15.9 - - - +
1036A ALA 3.2 1.0 - - - -
1037A ALA* 1.4 77.3 - - - +
1039A ASP* 1.4 60.6 + - - +
1041A GLN* 3.4 28.4 + - - +
1042A LYS* 3.7 15.8 - - - +
1069A VAL* 4.4 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1039 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006A ASN* 3.0 35.7 + - - +
1035A ALA* 3.0 19.1 - - - +
1036A ALA* 3.0 13.2 - - - +
1038A LEU* 1.4 74.2 - - - +
1040A ALA* 1.4 61.8 + - - +
1041A GLN 3.3 1.1 - - - -
1042A LYS* 3.5 36.4 + - + +
1043A ALA* 3.6 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1040 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003A LEU* 4.2 15.5 - - + +
1006A ASN* 4.2 15.7 - - + -
1007A TRP* 6.1 0.9 - - + -
1010A LEU* 6.1 0.9 - - + -
1036A ALA 3.2 18.4 + - - +
1037A ALA* 3.9 10.5 - - - +
1038A LEU 3.3 0.2 - - - -
1039A ASP* 1.4 73.8 - - - +
1041A GLN* 1.4 60.9 + - - +
1042A LYS 3.3 0.7 - - - -
1043A ALA* 3.4 16.2 - - - +
1061A PHE* 3.3 24.1 - - - -
1065A PHE* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1041 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037A ALA 3.3 12.8 + - - +
1038A LEU* 3.4 22.4 - - - +
1040A ALA* 1.4 76.3 - - - +
1042A LYS* 1.4 57.3 + - + +
1043A ALA 3.2 8.3 + - - +
1058A MET* 5.2 0.3 - - - +
1061A PHE* 4.0 6.0 - - - -
1062A ARG* 3.2 60.9 + - + +
1065A PHE* 3.7 12.2 + - + +
1066A ASP* 3.0 39.1 + - - +
1069A VAL* 5.1 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1042 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038A LEU* 3.7 15.7 - - - +
1039A ASP* 3.5 25.8 - - + +
1040A ALA 3.3 0.2 - - - -
1041A GLN* 1.4 74.8 - - + +
1043A ALA* 1.3 60.4 + - - +
1044A THR* 4.9 1.9 + - - -
1058A MET* 5.5 1.8 - - - +
----------------------------------------------------------
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