Contacts of the helix formed by residues 1034 - 1053 (chain A) in PDB entry 4QMH
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 ASN1034 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992A PRO* 3.8 23.7 - - + +
996A THR* 4.3 1.4 + - - -
1032A ASP* 2.8 16.0 + - - +
1033A ARG* 1.3 82.4 - - + +
1035A ALA* 1.3 59.7 + - - +
1036A ASP* 2.8 38.9 + - - +
1037A VAL* 3.0 21.6 + - + +
1038A ARG* 3.0 30.2 + - - +
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Residues in contact with ALA1035 (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 ARG 3.7 4.2 + - - -
1034A ASN* 1.3 73.9 + - - +
1036A ASP* 1.3 61.6 + - - +
1038A ARG* 3.5 27.4 + - - +
1039A LYS* 3.1 27.7 + - - +
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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
----------------------------------------------------------
996A THR* 3.6 25.5 + - + +
1034A ASN* 2.8 16.1 + - - +
1035A ALA* 1.3 74.9 - - - +
1037A VAL* 1.3 68.4 + - - +
1039A LYS* 3.4 6.7 + - - +
1040A ASN* 3.0 30.3 + - - +
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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
----------------------------------------------------------
992A PRO* 3.7 13.7 - - + +
995A LYS* 3.9 26.9 - - + -
996A THR* 3.6 21.1 - - - +
999A TRP* 4.5 4.2 - - + -
1029A HIS* 3.8 20.9 - - + -
1032A ASP* 3.4 28.0 - - + +
1034A ASN* 3.0 24.9 + - + +
1036A ASP* 1.3 72.8 - - - +
1038A ARG* 1.3 59.1 + - - +
1040A ASN* 3.3 1.0 + - - +
1041A ALA* 2.8 30.1 + - - +
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Residues in contact with ARG1038 (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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1029A HIS 3.5 7.6 - - - -
1030A ILE 3.7 15.9 - - - +
1031A CYS* 4.0 5.8 - - - +
1032A ASP 2.8 54.8 + - - +
1033A ARG* 3.1 22.8 + - - +
1034A ASN 3.0 12.9 + - - +
1035A ALA* 3.5 28.7 - - - +
1037A VAL* 1.3 76.1 - - - +
1039A LYS* 1.3 63.9 + - - +
1041A ALA* 4.0 0.3 - - - +
1042A ASN* 2.8 34.8 + - - +
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Residues in contact with LYS1039 (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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1035A ALA 3.1 15.7 + - - +
1036A ASP* 3.7 9.0 - - - +
1037A VAL 3.3 0.2 - - - -
1038A ARG* 1.3 79.0 - - - +
1040A ASN* 1.3 73.0 + - - +
1042A ASN* 3.8 5.7 - - - +
1043A GLU* 2.8 57.8 + - + +
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Residues in contact with ASN1040 (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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996A THR* 2.8 43.9 + - - +
999A TRP* 3.7 21.4 - - + +
1000A ALA* 3.7 19.6 - - - +
1003A ALA* 4.4 0.2 - - - +
1036A ASP* 3.0 14.6 + - - +
1037A VAL 4.1 1.3 - - - +
1039A LYS* 1.3 93.0 + - - +
1041A ALA* 1.3 66.4 + - - +
1043A GLU* 3.2 13.5 + - - +
1044A ALA* 3.1 21.1 + - - +
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Residues in contact with ALA1041 (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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999A TRP* 3.8 23.0 - - + +
1026A LEU* 3.4 18.4 - - + +
1029A HIS* 3.8 36.3 - - + +
1030A ILE* 3.9 4.7 - - - +
1037A VAL 2.8 22.5 + - - +
1038A ARG 4.1 0.4 - - - +
1040A ASN* 1.3 72.2 - - - +
1042A ASN* 1.3 64.4 + - - +
1044A ALA* 3.0 10.3 + - - +
1045A VAL* 3.3 8.3 + - - +
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Residues in contact with ASN1042 (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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1030A ILE* 3.5 40.4 + - - +
1038A ARG* 2.8 32.7 + - - +
1039A LYS* 3.8 5.1 - - - +
1041A ALA* 1.3 76.6 - - - +
1043A GLU* 1.3 63.0 + - + +
1045A VAL* 3.2 25.0 + - - +
1046A LEU 4.6 0.5 + - - -
1075A ALA* 4.1 14.0 - - - +
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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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1000A ALA* 5.9 1.7 - - - -
1003A ALA* 3.6 21.4 - - + +
1039A LYS* 2.8 53.8 + - + +
1040A ASN* 3.6 15.3 - - - +
1041A ALA 3.2 0.4 - - - -
1042A ASN* 1.3 77.2 - - + +
1044A ALA* 1.3 58.9 + - - +
1045A VAL 3.6 0.3 + - - -
1046A LEU* 4.2 8.8 + - - +
1047A GLY 4.7 2.6 + - - -
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Residues in contact with ALA1044 (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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999A TRP* 3.5 43.1 - - + +
1002A LEU* 4.7 3.1 - - + -
1003A ALA* 3.7 14.4 - - + +
1006A LEU* 5.2 0.7 - - + +
1026A LEU* 4.5 0.9 - - + -
1040A ASN 3.1 8.3 + - - +
1041A ALA 3.0 10.6 + - - +
1043A GLU* 1.3 77.0 - - - +
1045A VAL* 1.3 64.8 + - - +
1046A LEU 3.3 1.3 - - - -
1047A GLY* 3.3 3.6 + - - +
1048A ILE* 3.0 27.1 + - + +
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Residues in contact with VAL1045 (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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1026A LEU* 4.1 13.5 - - + -
1030A ILE* 3.8 26.2 - - + -
1041A ALA 3.3 10.0 + - - +
1042A ASN* 3.2 19.8 + - - +
1044A ALA* 1.3 78.3 - - - +
1046A LEU* 1.3 58.0 + - - +
1048A ILE* 3.3 2.6 + - - +
1049A MET* 2.9 29.7 + - + +
1057A MET* 4.5 2.6 - - + +
1075A ALA* 3.8 22.2 - - + +
1076A LEU* 4.3 17.3 - - + -
1079A ALA* 3.7 21.3 - - + -
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Residues in contact with LEU1046 (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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1007A PRO* 5.6 5.6 - - + -
1042A ASN 4.6 0.4 + - - -
1043A GLU 4.2 8.5 + - - +
1044A ALA 3.3 0.2 - - - -
1045A VAL* 1.3 78.7 - - - +
1047A GLY* 1.3 58.8 + - - +
1049A MET* 3.1 2.6 + - - -
1050A ILE* 2.8 40.9 + - + +
1079A ALA* 3.6 36.3 - - + +
1082A ASN* 3.9 30.3 - - + +
1083A LEU* 3.8 20.6 - - + -
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Residues in contact with GLY1047 (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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1002A LEU 5.2 1.6 - - - -
1003A ALA 5.4 0.9 + - - -
1006A LEU* 3.8 14.5 - - - +
1007A PRO* 3.9 26.9 - - - +
1043A GLU 4.7 1.6 + - - -
1044A ALA* 3.3 8.7 + - - +
1046A LEU* 1.3 79.7 - - - +
1048A ILE* 1.3 61.0 + - - +
1050A ILE* 3.4 8.1 + - - +
1051A HIS* 3.3 26.0 - - - -
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Residues in contact with ILE1048 (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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999A TRP* 4.5 13.0 - - + -
1002A LEU* 5.4 0.4 - - + -
1006A LEU* 3.7 22.0 - - + +
1019A ILE* 3.7 26.1 - - + +
1022A MET* 4.1 23.8 - - + -
1023A VAL* 4.3 7.2 - - + -
1026A LEU* 4.1 14.8 - - + -
1044A ALA* 3.0 16.6 + - + +
1045A VAL 3.6 5.6 - - - +
1047A GLY* 1.3 73.6 - - - +
1049A MET* 1.3 64.3 + - - +
1051A HIS* 3.0 7.3 + - - +
1052A LEU* 3.0 27.6 + - + +
1057A MET* 3.6 24.7 - - + -
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Residues in contact with MET1049 (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 VAL* 2.9 15.9 + - + +
1046A LEU* 3.1 6.0 + - - +
1048A ILE* 1.3 75.0 - - - +
1050A ILE* 1.3 62.4 + - - +
1053A GLY* 2.7 29.5 + - - +
1054A PHE* 3.6 32.5 - - + +
1057A MET* 3.5 14.1 - - - -
1076A LEU* 3.5 50.5 - - + +
1079A ALA* 4.2 9.0 - - + -
1080A ARG* 3.9 17.3 - - - -
1083A LEU* 3.7 30.7 - - + +
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Residues in contact with ILE1050 (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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1006A LEU 4.7 2.9 - - - +
1007A PRO* 3.8 37.7 - - + +
1009A LEU 5.3 2.0 - - - +
1046A LEU* 2.8 33.0 + - + +
1047A GLY* 3.6 7.6 - - - +
1048A ILE 3.2 0.4 - - - -
1049A MET* 1.3 76.5 - - - +
1051A HIS* 1.3 76.1 + - + +
1053A GLY 4.9 0.2 + - - -
1083A LEU* 3.9 9.9 - - + -
1084A PRO* 3.8 33.9 - - + -
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Residues in contact with HIS1051 (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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1006A LEU* 2.8 40.3 + - + +
1009A LEU 3.2 21.9 + - - -
1010A PRO 4.1 4.0 - - - -
1011A PRO* 4.1 15.5 - - + +
1014A VAL* 3.5 36.7 + - + +
1016A LYS* 4.1 21.9 - - + +
1019A ILE* 4.4 17.3 - - + -
1047A GLY 3.3 22.4 - - - +
1048A ILE 3.0 6.3 + - - +
1049A MET 3.0 0.4 - - - -
1050A ILE* 1.3 88.2 + - + +
1052A LEU* 1.3 65.9 + - + +
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Residues in contact with LEU1052 (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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1016A LYS* 3.6 40.4 + - + +
1019A ILE* 3.7 25.4 - - + -
1020A HIS* 3.6 31.9 - - + +
1023A VAL* 3.7 30.5 - - + -
1048A ILE* 3.0 14.8 + - + +
1051A HIS* 1.3 83.2 - - - +
1053A GLY* 1.3 61.0 + - - +
1056A ALA* 3.4 20.4 + - + +
1057A MET* 4.1 17.3 - - + +
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Residues in contact with GLY1053 (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 MET* 2.7 30.6 + - - -
1050A ILE 4.9 0.6 + - - -
1051A HIS 3.7 0.6 - - - -
1052A LEU* 1.3 77.7 - - - +
1054A PHE* 1.3 64.6 + - - -
1055A ASP 3.4 2.7 - - - -
1056A ALA 3.6 0.6 + - - -
1057A MET* 3.3 21.8 + - - +
1083A LEU* 5.2 3.1 - - - -
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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
------------------------------------------------------------
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