Contacts of the helix formed by residues 1040 - 1057 (chain A) in PDB entry 2ZM3
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 SER1040 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1039A ALA* 1.3 75.2 - - - +
1041A MET* 1.3 64.6 + - - +
1042A ARG* 3.6 10.6 + - - +
1043A GLU* 3.2 30.2 + - - +
1044A ARG* 3.1 18.2 + - - +
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Residues in contact with MET1041 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982A SER* 6.0 2.2 - - - -
983A ALA* 4.9 15.5 - - + +
1039A ALA 3.5 2.5 + - - -
1040A SER* 1.3 72.3 - - - +
1042A ARG* 1.3 57.6 + - - +
1044A ARG* 3.4 9.1 + - - +
1045A ILE* 2.9 50.4 + - + +
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Residues in contact with ARG1042 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040A SER* 3.0 10.2 - - - +
1041A MET* 1.3 81.7 - - - +
1043A GLU* 1.3 68.5 + - + +
1045A ILE* 3.4 15.1 + - - +
1046A GLU* 2.9 55.7 + - - +
1049A ASN* 6.1 0.2 - - - +
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Residues in contact with GLU1043 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009A SER 5.1 1.4 - - - +
1010A PHE* 3.4 34.0 - - + -
1035A VAL* 5.4 2.0 - - + -
1039A ALA* 5.3 5.4 - - + -
1040A SER* 3.2 22.5 + - - +
1042A ARG* 1.3 88.4 + - + +
1044A ARG* 1.3 55.5 + - - +
1046A GLU* 3.3 9.6 + - - +
1047A PHE* 2.8 34.1 + - - +
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Residues in contact with ARG1044 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982A SER* 4.5 7.8 - - - -
983A ALA* 3.7 30.7 - - + +
984A ALA 4.5 2.2 - - - +
1035A VAL* 3.0 27.2 + - + +
1036A ASN 2.5 30.7 + - - -
1037A GLU* 3.6 5.6 + - - +
1039A ALA 3.3 20.4 + - - -
1040A SER 3.1 11.9 + - - +
1041A MET* 3.7 8.8 - - - +
1043A GLU* 1.3 74.3 - - - +
1045A ILE* 1.3 59.7 + - - +
1047A PHE* 3.3 8.5 + - + +
1048A LEU* 2.9 38.1 + - + +
1073A GLN* 2.7 34.5 + - - +
1075A THR* 3.3 16.9 + - - +
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Residues in contact with ILE1045 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983A ALA* 4.0 9.2 - - + -
987A TYR* 3.5 48.0 - - + +
1041A MET* 2.9 42.5 + - + +
1042A ARG* 3.6 15.9 - - - +
1044A ARG* 1.3 76.4 - - - +
1046A GLU* 1.3 56.6 + - - +
1048A LEU* 3.3 7.7 + - - +
1049A ASN* 2.9 46.8 + - - +
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Residues in contact with GLU1046 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010A PHE* 3.6 23.3 - - + -
1042A ARG* 2.9 41.2 + - - +
1043A GLU* 3.5 14.6 - - - +
1044A ARG 3.2 0.2 - - - -
1045A ILE* 1.3 75.1 - - - +
1047A PHE* 1.3 64.9 + - - +
1049A ASN* 3.4 10.6 + - - +
1050A GLU* 3.0 28.6 + - - +
1155A GLY 5.6 2.3 - - - +
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Residues in contact with PHE1047 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010A PHE* 3.6 33.6 - + + -
1033A LYS* 3.9 38.6 - - + -
1034A THR 4.5 3.6 - - - -
1035A VAL* 3.3 35.2 - - + -
1043A GLU 2.8 17.3 + - - +
1044A ARG 3.3 8.7 - - - +
1046A GLU* 1.3 75.1 - - - +
1048A LEU* 1.3 84.4 + - + +
1050A GLU* 3.4 3.6 + - - +
1051A ALA* 3.2 20.3 + - - +
1075A THR* 4.2 17.3 - - + -
1077A VAL* 3.3 37.9 - - + +
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Residues in contact with LEU1048 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983A ALA* 3.5 42.8 - - + +
984A ALA* 3.6 8.3 - - + +
987A TYR* 3.9 16.2 - - + -
988A VAL* 3.8 23.5 - - + +
1044A ARG* 2.9 23.8 + - + +
1045A ILE* 3.7 4.3 - - - +
1047A PHE* 1.3 98.6 - - + +
1049A ASN* 1.3 65.7 + - - +
1051A ALA* 3.2 7.5 + - + +
1052A SER* 3.0 23.7 + - - -
1068A VAL* 5.3 2.0 - - + -
1075A THR* 3.9 18.6 - - + -
1077A VAL* 5.2 3.6 - - + -
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Residues in contact with ASN1049 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987A TYR* 3.8 23.5 - - - +
1045A ILE* 2.9 35.9 + - - +
1046A GLU* 3.8 12.4 + - - +
1048A LEU* 1.3 76.6 - - - +
1050A GLU* 1.3 62.3 + - - +
1052A SER* 3.1 19.0 + - - -
1053A VAL* 3.2 18.7 + - + +
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Residues in contact with GLU1050 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009A SER* 4.4 6.1 + - - -
1010A PHE* 3.4 30.0 - - + -
1033A LYS* 4.9 11.8 + - - +
1046A GLU* 3.0 21.5 + - + +
1047A PHE* 3.6 7.4 - - + +
1048A LEU 3.3 0.2 - - - -
1049A ASN* 1.3 76.5 - - - +
1051A ALA* 1.3 60.0 + - - +
1053A VAL* 3.6 9.0 + - - +
1054A MET* 3.5 32.0 + - + +
1153A ASP* 4.9 6.6 - - - +
1154A PHE* 4.7 5.0 + - - +
1155A GLY* 3.8 33.8 + - - +
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Residues in contact with ALA1051 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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988A VAL* 5.2 3.4 - - + -
1047A PHE 3.2 11.9 + - - +
1048A LEU* 3.2 12.5 + - - +
1050A GLU* 1.3 76.8 - - - +
1052A SER* 1.3 65.0 + - - +
1054A MET* 3.2 3.6 + - - -
1055A LYS* 3.0 23.5 + - - +
1065A LEU* 3.3 29.0 - - + +
1068A VAL* 5.0 7.9 - - + -
1077A VAL* 4.0 21.3 - - + -
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Residues in contact with SER1052 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987A TYR 3.6 18.9 + - - -
988A VAL* 4.7 0.3 - - - +
989A PRO* 4.8 1.2 - - - +
1048A LEU 3.0 10.7 + - - -
1049A ASN* 3.1 15.0 + - - -
1051A ALA* 1.3 76.5 - - - +
1053A VAL* 1.3 62.6 + - - +
1055A LYS* 3.2 43.1 - - - +
1056A GLU* 4.2 7.1 + - - +
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Residues in contact with VAL1053 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049A ASN 3.2 15.4 + - - +
1050A GLU* 3.8 9.2 - - - +
1051A ALA 3.2 0.6 - - - -
1052A SER* 1.3 79.2 - - - +
1054A MET* 1.3 61.8 + - + +
1055A LYS 3.4 0.5 + - - -
1056A GLU* 3.5 17.9 + - - +
1057A PHE* 3.9 28.4 - - + -
1131A PHE* 4.4 16.2 - - + -
1154A PHE* 5.5 2.9 - - + +
1157A THR* 4.1 16.8 - - - +
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Residues in contact with MET1054 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033A LYS* 4.5 14.8 - - - +
1050A GLU* 3.5 21.9 + - - +
1051A ALA* 3.2 7.7 + - - +
1053A VAL* 1.3 74.8 - - + +
1055A LYS* 1.3 68.4 + - - +
1056A GLU 2.9 3.7 + - - -
1057A PHE* 3.0 28.1 + - + +
1062A VAL* 5.5 0.2 - - + -
1063A VAL* 3.8 15.0 - - + +
1065A LEU* 4.1 19.4 + - + +
1079A MET* 3.5 32.8 - - + +
1152A GLY 4.8 9.2 - - - +
1153A ASP* 5.9 0.4 - - - -
1154A PHE* 3.5 49.1 - - + -
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Residues in contact with LYS1055 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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988A VAL* 4.3 6.1 - - - +
989A PRO* 3.5 28.2 - - + +
992A TRP* 3.0 81.2 - - + +
1051A ALA* 3.0 18.8 + - - +
1052A SER* 3.2 34.5 - - - +
1053A VAL 3.2 0.2 - - - -
1054A MET* 1.3 76.3 - - - +
1056A GLU* 1.3 69.9 + - - +
1057A PHE 4.2 4.3 - - - +
1058A ASN* 5.6 1.0 - - - +
1065A LEU* 4.3 12.9 - - + +
1068A VAL* 4.3 14.8 - - - +
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Residues in contact with GLU1056 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992A TRP* 4.7 6.5 + - - -
1052A SER 4.2 6.8 - - - +
1053A VAL* 3.8 11.9 - - - +
1054A MET 3.0 0.8 - - - -
1055A LYS* 1.3 87.4 - - - +
1057A PHE* 1.3 68.9 + - + +
1058A ASN* 3.0 13.5 + - - +
1125A TYR* 3.6 5.5 + - - -
1131A PHE* 5.9 5.2 - - + -
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Residues in contact with PHE1057 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1053A VAL* 3.9 33.2 - - + -
1054A MET* 3.0 25.4 + - + +
1055A LYS 4.2 2.9 - - - +
1056A GLU* 1.3 79.6 - - + +
1058A ASN* 1.3 59.3 - - - +
1059A CYS 3.9 1.9 + - - -
1062A VAL* 3.9 20.3 - - + +
1063A VAL 5.3 0.3 - - - +
1064A ARG* 4.5 15.6 - - - +
1065A LEU 5.3 0.3 + - - -
1125A TYR* 3.4 17.7 - + + -
1126A LEU* 3.9 18.6 - - + -
1129A ASN* 5.5 4.3 - - + -
1131A PHE* 3.8 38.6 - + + -
1154A PHE* 3.6 44.9 - + + -
1157A THR* 5.0 2.9 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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