Contacts of the helix formed by residues 1032 - 1049 (chain A) in PDB entry 2B7A
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 SER1032 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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973A ILE* 3.5 21.0 - - - +
1006A GLU 3.3 21.8 - - - -
1007A PTR 4.2 6.7 - - - -
1024A GLU* 4.5 4.9 + - - +
1030A LYS 5.3 0.9 + - - -
1031A PHE* 1.3 74.6 - - - +
1033A VAL* 1.3 65.0 + - - +
1034A ALA* 3.4 12.3 + - - +
1035A SER* 2.7 35.0 + - - -
1036A ASP 3.0 6.6 + - - -
1110A VAL* 4.5 5.1 - - - +
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Residues in contact with VAL1033 (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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965A GLU* 6.2 0.4 - - - +
968A GLY* 4.7 21.8 - - - +
971A ARG* 6.1 0.9 - - - -
972A TYR 5.0 1.1 - - - +
973A ILE* 3.4 19.6 - - + +
1001A LEU* 5.0 7.9 - - + -
1006A GLU* 4.8 1.0 + - - +
1032A SER* 1.3 73.8 - - - +
1034A ALA* 1.3 56.0 + - - +
1036A ASP* 3.1 11.4 + - - +
1037A VAL* 2.9 31.6 + - + +
1115A SER* 6.1 1.8 - - - -
1116A PHE* 4.1 25.4 - - + +
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Residues in contact with ALA1034 (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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1032A SER* 3.1 6.5 + - - +
1033A VAL* 1.3 80.5 - - - +
1035A SER* 1.3 56.6 + - - +
1037A VAL* 3.4 8.8 + - - +
1038A TRP 3.1 18.5 + - - -
1110A VAL* 3.5 44.6 - - + +
1113A ARG* 3.1 23.9 + - + +
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Residues in contact with SER1035 (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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973A ILE* 4.4 1.7 - - - +
1022A ALA* 4.0 7.3 + - - +
1024A GLU* 3.8 11.9 - - - -
1025A SER* 3.7 21.8 - - - -
1030A LYS 4.3 1.1 - - - -
1031A PHE* 3.4 13.1 - - - +
1032A SER* 2.7 39.9 + - - -
1034A ALA* 1.3 73.5 - - - +
1036A ASP* 1.3 65.1 + - - +
1038A TRP* 3.3 4.0 + - - +
1039A SER* 3.1 25.3 + - - -
1113A ARG* 3.8 7.3 - - - +
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Residues in contact with ASP1036 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964A MET* 3.2 28.5 - - + +
972A TYR 4.3 1.7 - - - +
973A ILE* 3.5 17.9 - - - +
974A HIS* 2.8 24.8 + - - +
975A ARG* 3.0 26.5 + - - -
976A ASP 4.8 0.2 + - - -
977A LEU* 3.5 11.0 + - + +
1032A SER 3.0 7.0 + - - +
1033A VAL* 3.1 13.9 + - - +
1035A SER* 1.3 78.6 + - - +
1037A VAL* 1.3 51.8 + - - +
1039A SER* 3.3 5.8 + - - -
1040A PHE* 2.8 32.7 + - - +
1116A PHE* 3.8 6.1 - - + -
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Residues in contact with VAL1037 (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 VAL* 2.9 23.8 + - + +
1034A ALA* 3.5 12.3 - - - +
1035A SER 3.3 0.2 - - - -
1036A ASP* 1.3 73.9 - - - +
1038A TRP* 1.3 66.6 + - - +
1040A PHE* 3.1 5.2 + - - +
1041A GLY 3.0 17.5 + - - -
1105A CYS* 3.5 25.9 - - + +
1113A ARG* 4.0 15.5 - - + -
1114A PRO* 3.5 28.9 - - + +
1115A SER* 5.0 0.2 - - - -
1116A PHE* 3.6 32.3 - - + +
1119A LEU* 4.1 6.3 - - + -
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Residues in contact with TRP1038 (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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1019A PHE 5.5 0.8 + - - -
1020A TRP 3.4 17.7 + - - -
1021A TYR 3.1 17.0 + - - -
1022A ALA* 3.6 19.7 - - + -
1023A PRO* 3.4 25.8 - - + -
1034A ALA 3.1 11.4 + - - +
1035A SER 3.3 8.7 + - - +
1037A VAL* 1.3 75.2 - - - +
1039A SER* 1.3 58.5 + - - +
1041A GLY* 2.9 16.5 + - - -
1042A VAL* 3.3 16.3 + - + +
1061A PHE* 5.8 2.8 - + - -
1082A LEU* 3.8 21.8 - - + -
1087A ARG* 3.4 27.6 - - + -
1105A CYS 3.6 14.8 + - - +
1106A TRP* 3.3 54.4 + + + -
1107A ASN 3.7 5.8 - - - -
1113A ARG* 3.6 17.9 - - - +
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Residues in contact with SER1039 (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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975A ARG 5.8 3.3 - - - -
976A ASP 6.0 0.2 - - - -
977A LEU* 3.9 27.8 + - - +
1020A TRP* 2.6 29.6 + - - +
1021A TYR* 4.7 4.2 - - - -
1022A ALA 5.0 0.2 + - - -
1035A SER 3.1 11.7 + - - -
1036A ASP* 3.6 10.0 + - - -
1037A VAL 3.3 0.2 - - - -
1038A TRP* 1.3 78.6 - - - +
1040A PHE* 1.3 56.8 + - - +
1042A VAL* 3.0 8.9 + - - +
1043A VAL* 2.9 31.4 + - - +
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Residues in contact with PHE1040 (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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957A THR* 3.5 31.6 - - + -
960A ILE* 4.1 23.1 - - + -
961A CYS* 3.3 29.4 - - - -
977A LEU* 4.2 6.4 - - + +
1036A ASP 2.8 17.5 + - - +
1037A VAL 3.1 7.4 + - - +
1039A SER* 1.3 73.0 - - - +
1041A GLY* 1.3 57.3 + - - +
1043A VAL* 3.2 15.8 + - + +
1044A LEU* 2.9 41.1 + - + +
1101A ILE* 4.6 1.1 - - + -
1105A CYS* 3.9 9.6 - - - -
1116A PHE* 3.8 17.9 - + + -
1119A LEU* 3.8 35.0 - - + -
1123A VAL* 5.2 1.6 - - + -
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Residues in contact with GLY1041 (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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1037A VAL 3.0 7.3 + - - -
1038A TRP 2.9 11.4 + - - -
1040A PHE* 1.3 78.3 - - - +
1042A VAL* 1.3 56.0 + - - +
1044A LEU* 3.4 7.7 + - - +
1045A TYR 3.0 22.2 + - - -
1102A MET* 3.6 6.5 - - - +
1105A CYS* 3.8 18.4 - - - -
1106A TRP* 3.3 24.1 - - - -
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Residues in contact with VAL1042 (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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1019A PHE 4.1 7.9 - - - +
1020A TRP* 3.4 37.9 - - + +
1038A TRP* 3.7 21.1 - - - +
1039A SER* 3.0 12.7 + - - +
1041A GLY* 1.3 72.7 - - - +
1043A VAL* 1.3 55.3 + - - +
1045A TYR* 3.2 3.3 + - - +
1046A GLU* 2.8 37.2 + - - +
1057A PRO* 3.6 25.1 - - + -
1061A PHE* 5.9 0.7 - - + -
1088A LEU* 4.2 8.7 - - + -
1106A TRP* 3.6 22.2 - - + +
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Residues in contact with VAL1043 (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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960A ILE* 4.2 28.5 - - + -
977A LEU* 3.7 13.2 - - + +
978A ALA* 3.6 35.7 - - - +
979A THR* 4.0 16.8 - - + +
982A ILE* 5.2 2.7 - - + -
1039A SER 2.9 18.7 + - - +
1040A PHE* 3.4 16.2 - - + +
1042A VAL* 1.3 76.1 - - - +
1044A LEU* 1.3 61.9 + - - +
1046A GLU* 3.2 11.1 + - - +
1047A LEU* 3.0 27.9 + - + +
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Residues in contact with LEU1044 (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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954A LEU* 4.8 2.9 - - + -
957A THR* 3.5 33.2 - - + +
1040A PHE* 2.9 25.8 + - + +
1041A GLY* 3.5 10.1 - - - +
1043A VAL* 1.3 75.1 - - - +
1045A TYR* 1.3 63.1 + - - +
1047A LEU* 3.4 6.5 + - + +
1048A PHE* 3.2 53.6 + - + +
1098A ILE* 4.0 18.4 - - + +
1101A ILE* 3.6 32.3 - - + -
1102A MET* 3.8 19.7 - - + +
1123A VAL* 5.7 0.7 - - + -
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Residues in contact with TYR1045 (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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1041A GLY 3.0 12.2 + - - +
1042A VAL* 3.3 7.6 - - - +
1044A LEU* 1.3 75.0 - - - +
1046A GLU* 1.3 66.2 + - - +
1048A PHE* 3.2 3.3 + - - -
1049A THR* 3.1 44.1 + - + +
1055A LYS* 2.6 31.4 + - - +
1057A PRO* 4.0 21.3 - - + -
1060A GLU* 3.2 22.0 + - - +
1088A LEU* 3.7 32.1 - - + -
1089A PRO* 3.1 30.9 - - + +
1091A PRO* 3.6 11.3 - - + +
1102A MET* 3.5 29.2 - - + -
1106A TRP* 3.9 6.5 - - + -
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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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938A ARG* 4.6 8.5 + - - +
978A ALA* 3.5 2.4 - - - +
979A THR* 2.7 47.3 + - + -
980A ARG* 4.8 0.7 + - - -
1020A TRP* 2.8 44.2 + - + +
1042A VAL 2.8 19.3 + - - +
1043A VAL* 3.3 14.5 - - - +
1045A TYR* 1.3 73.7 - - - +
1047A LEU* 1.3 62.9 + - - +
1049A THR* 2.6 25.6 + - - -
1050A TYR 3.3 4.3 + - - -
1051A ILE* 3.6 17.8 + - + +
1057A PRO* 4.3 13.6 - - + +
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Residues in contact with LEU1047 (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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937A LEU* 3.7 29.2 - - + -
941A LEU* 3.4 29.7 - - + +
953A LEU* 3.4 32.9 - - + +
956A TYR* 4.8 2.9 - - + -
957A THR* 3.5 26.2 - - - +
960A ILE* 4.5 11.0 - - + -
979A THR* 3.9 13.5 - - + -
1043A VAL* 3.0 28.0 + - + +
1044A LEU* 3.7 11.4 - - + +
1045A TYR 3.3 0.2 - - - -
1046A GLU* 1.3 76.7 - - - +
1048A PHE* 1.3 62.8 + - + +
1050A TYR* 3.1 15.9 + - - -
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Residues in contact with PHE1048 (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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950A HIS* 3.6 48.5 + + + -
953A LEU* 4.0 24.9 - - + -
954A LEU* 3.7 26.9 - - + -
957A THR* 4.9 0.7 - - - -
1044A LEU* 3.2 33.7 + - + +
1045A TYR 3.2 2.4 + - - -
1047A LEU* 1.3 77.1 - - + +
1049A THR* 1.3 58.5 + - - +
1050A TYR* 3.2 12.3 + - - -
1091A PRO* 3.5 28.4 - - + +
1092A ASP 4.0 4.7 - - - +
1094A CYS* 4.1 18.2 - - + -
1095A PRO* 3.9 11.0 - - + -
1098A ILE* 3.7 20.6 - - + -
1102A MET* 5.6 0.7 - - - -
1112B GLN* 3.6 11.6 + - - +
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Residues in contact with THR1049 (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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1045A TYR* 3.1 51.8 + - + +
1046A GLU* 2.6 21.8 + - - -
1048A PHE* 1.3 75.6 - - - +
1050A TYR* 1.3 66.9 + - - +
1051A ILE* 3.2 11.3 + - - -
1052A GLU* 3.2 18.5 + - - +
1055A LYS* 4.0 23.5 + - + +
1056A SER* 5.7 1.4 - - - -
1057A PRO* 6.0 0.3 - - - +
1091A PRO* 3.9 11.9 - - + -
1112B GLN* 3.7 13.1 + - - +
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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