Contacts of the helix formed by residues 1038 - 1057 (chain A) in PDB entry 3S1R
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 THR1038 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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971A PHE* 5.2 1.2 - - - +
973A ILE* 4.4 11.9 - - + +
974A ASP 6.2 1.3 - - - +
979A SER* 4.5 11.9 - - - -
980A ASP* 3.4 13.0 - - - +
981A LEU* 3.6 8.1 - - - -
1036A ARG 4.7 5.6 - - - +
1037A LEU* 1.3 77.4 - - - +
1039A LYS* 1.4 55.9 + - - +
1040A GLN* 4.0 10.4 + - - +
1041A ALA* 3.0 23.3 + - - +
1042A PHE* 2.7 32.1 + - - +
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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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980A ASP* 3.0 35.5 + - - +
981A LEU* 3.6 20.1 - - + +
985A ASP* 3.3 31.9 + - + +
1038A THR* 1.4 68.0 - - - +
1040A GLN* 1.4 57.8 + - - +
1042A PHE* 3.8 4.1 - - + +
1043A ASP* 2.8 71.3 + - - +
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Residues in contact with GLN1040 (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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971A PHE* 3.3 40.4 - - + +
980A ASP* 4.5 2.3 + - - +
1038A THR* 3.2 8.1 + - - +
1039A LYS* 1.4 78.4 - - - +
1041A ALA* 1.3 63.4 + - - +
1043A ASP* 3.8 6.9 + - - +
1044A TRP* 3.7 16.6 + - - +
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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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967A ALA* 4.5 4.2 - - + +
971A PHE* 3.8 23.3 - - + -
973A ILE* 3.8 23.8 - - + -
1037A LEU* 4.3 7.2 - - + -
1038A THR* 3.0 23.0 + - - +
1040A GLN* 1.3 79.6 - - - +
1042A PHE* 1.3 62.0 + - - +
1044A TRP* 3.3 10.4 + - - +
1045A VAL* 3.3 24.6 + - - +
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Residues in contact with PHE1042 (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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981A LEU* 3.6 19.3 - - + -
985A ASP* 4.0 10.1 - - + -
986A ILE* 3.8 35.2 - - + -
989A GLY* 4.6 0.7 - - - -
990A VAL* 4.1 8.1 - - + -
1026A LEU* 4.4 10.1 - - + -
1031A VAL* 3.7 39.9 - - + -
1037A LEU* 3.8 20.6 - - + +
1038A THR 2.7 19.6 + - - +
1039A LYS* 3.8 6.1 - - + +
1041A ALA* 1.3 72.0 - - - +
1043A ASP* 1.4 70.4 + - - +
1045A VAL* 3.1 19.1 + - + +
1046A LEU* 3.2 41.7 + - + +
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Residues in contact with ASP1043 (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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1039A LYS* 2.8 62.2 + - - +
1040A GLN* 4.0 6.8 + - - +
1042A PHE* 1.4 80.4 - - - +
1044A TRP* 1.4 56.2 + - - +
1046A LEU* 3.3 15.9 + - - +
1047A SER* 3.0 28.3 + - - -
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Residues in contact with TRP1044 (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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963A ILE* 3.7 13.0 - - + -
966A ASN* 3.9 21.3 - - + -
967A ALA* 3.6 37.7 - - + -
970A THR* 4.3 15.3 - - + +
971A PHE* 3.9 23.7 - + + -
1040A GLN 3.7 10.8 + - - +
1041A ALA 3.3 8.0 + - - +
1042A PHE 3.3 0.2 - - - -
1043A ASP* 1.4 74.0 - - - +
1045A VAL* 1.4 60.0 + - + +
1047A SER* 3.2 10.7 + - - -
1048A ASN* 2.8 65.4 + - - +
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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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963A ILE* 4.0 19.7 - - + -
964A ILE* 3.9 24.2 - - + -
967A ALA* 3.9 22.4 - - + -
1026A LEU* 4.3 11.7 - - + -
1037A LEU* 4.1 15.5 - - + -
1041A ALA 3.4 14.8 - - - +
1042A PHE* 3.2 11.2 - - - +
1044A TRP* 1.4 76.3 - - + +
1046A LEU* 1.3 55.2 + - + +
1048A ASN* 3.2 1.9 + - - +
1049A ILE* 2.9 53.9 + - + +
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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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989A GLY* 3.4 35.7 - - - +
990A VAL* 5.1 1.1 - - + +
992A ASP* 6.0 0.2 - - + -
993A LEU* 3.3 42.2 - - + +
1026A LEU* 4.7 9.4 - - + -
1042A PHE* 3.2 48.6 + - + +
1043A ASP* 3.3 17.0 + - - +
1045A VAL* 1.3 77.3 - - + +
1047A SER* 1.3 55.8 + - - +
1049A ILE 3.7 0.2 + - - -
1050A GLU* 3.2 23.8 + - - +
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Residues in contact with SER1047 (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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1043A ASP 3.0 16.0 + - - -
1044A TRP* 3.6 12.4 - - - -
1046A LEU* 1.3 72.4 - - - +
1048A ASN* 1.4 60.0 + - - +
1050A GLU* 3.5 8.5 + - - +
1051A ALA* 2.9 30.8 + - - +
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Residues in contact with ASN1048 (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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963A ILE* 3.8 17.9 - - + +
966A ASN* 5.8 1.0 + - - -
1044A TRP* 2.8 63.7 + - - +
1045A VAL* 3.4 4.9 - - - +
1047A SER* 1.4 74.1 - - - +
1049A ILE* 1.4 58.5 + - - +
1051A ALA* 3.6 4.7 + - - +
1052A GLN* 2.9 61.0 + - - +
1055A ARG* 5.6 2.6 + - - -
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Residues in contact with ILE1049 (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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958A VAL* 4.0 7.6 - - + +
960A ILE* 4.1 19.3 - - + -
963A ILE* 3.7 17.5 - - + -
993A LEU* 3.9 17.0 - - + -
997A LEU* 4.0 12.8 - - + -
1018A PHE* 4.1 13.9 - - + -
1022A LEU* 3.8 20.6 - - + -
1026A LEU* 3.7 30.1 - - + -
1045A VAL* 2.9 32.2 + - + +
1046A LEU 4.0 0.2 - - - +
1048A ASN* 1.4 71.8 - - - +
1050A GLU* 1.4 62.1 + - - +
1052A GLN* 3.9 0.7 - - - +
1053A PHE* 2.9 32.6 + - - +
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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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993A LEU* 4.1 5.9 - - + +
996A ASN* 3.4 52.0 + - + +
997A LEU* 4.2 10.1 - - + -
1046A LEU 3.2 17.3 + - - +
1047A SER* 3.7 7.6 - - - +
1049A ILE* 1.4 79.0 - - - +
1051A ALA* 1.4 56.2 + - - +
1053A PHE* 3.3 1.9 + - - +
1054A LEU* 3.0 53.4 + - + +
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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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1047A SER 2.9 19.7 + - - +
1048A ASN* 3.7 6.3 - - - +
1050A GLU* 1.4 73.3 - - - +
1052A GLN* 1.4 62.0 + - - +
1054A LEU* 3.2 11.4 + - - +
1055A ARG* 3.0 45.8 + - - +
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Residues in contact with GLN1052 (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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635A ARG* 5.5 9.7 - - - +
958A VAL* 3.9 17.4 - - + -
959A ASN 4.5 9.9 + - - -
962A ARG* 4.4 16.1 + - - +
963A ILE* 3.5 25.3 - - - +
966A ASN* 5.8 2.2 - - - +
1048A ASN* 2.9 40.6 + - - +
1051A ALA* 1.4 72.9 - - - +
1053A PHE* 1.4 51.5 + - - +
1055A ARG* 3.3 33.0 + - - +
1056A SER* 2.9 37.6 + - - +
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Residues in contact with PHE1053 (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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873A MET* 3.8 23.6 - - + +
957A PRO* 4.5 6.7 - - + -
958A VAL* 3.4 13.6 - - + +
997A LEU* 3.6 40.8 - - + -
998A LEU 3.6 18.6 - - - -
999A VAL* 3.8 6.5 - - + -
1014A ALA 6.0 0.2 - - - -
1015A VAL* 3.6 27.6 - - + -
1018A PHE* 3.6 40.4 - + + -
1049A ILE 2.9 22.4 + - - +
1050A GLU 3.5 3.8 - - - +
1052A GLN* 1.4 67.8 - - - +
1054A LEU* 1.3 66.1 + - + +
1056A SER* 2.9 23.3 + - - -
1057A VAL* 3.3 14.3 + - + +
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Residues in contact with LEU1054 (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 ASN 4.9 2.2 - - - +
998A LEU* 3.8 26.2 - - + +
1001A ARG* 4.0 23.3 - - - +
1050A GLU* 3.0 47.1 + - + +
1051A ALA* 3.6 7.9 - - - +
1053A PHE* 1.3 81.5 - - + +
1055A ARG* 1.4 60.6 + - + +
1057A VAL* 3.5 19.2 + - + +
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Residues in contact with ARG1055 (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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635A ARG 5.5 4.9 + - - -
877A HIS* 3.7 24.0 + - + +
1048A ASN* 5.6 2.4 + - - +
1051A ALA* 3.0 33.6 + - - +
1052A GLN* 3.4 42.4 - - - +
1053A PHE 3.2 0.2 - - - -
1054A LEU* 1.4 73.1 - - + +
1056A SER* 1.3 63.9 + - - +
1057A VAL 3.2 8.6 + - - +
1059A HIS* 4.8 6.6 + - - -
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Residues in contact with SER1056 (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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873A MET* 3.6 7.2 - - - +
874A ASP* 2.9 27.4 + - - +
877A HIS* 3.3 32.3 + - - +
957A PRO* 3.5 28.1 - - - +
958A VAL* 4.0 5.4 + - - -
1052A GLN* 2.9 19.0 + - - +
1053A PHE* 2.9 12.7 + - - -
1055A ARG* 1.3 74.8 - - - +
1057A VAL* 1.3 58.1 + - - +
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Residues in contact with VAL1057 (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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854A ASN* 4.5 9.0 - - - +
872A GLY 3.3 13.5 - - - +
873A MET* 3.8 12.6 - - - -
874A ASP* 3.8 4.7 - - - +
877A HIS* 4.9 0.2 - - - -
998A LEU 4.0 19.7 - - - +
999A VAL* 4.1 20.2 - - + +
1001A ARG* 5.7 4.5 - - - +
1053A PHE* 3.5 17.0 - - + +
1054A LEU* 3.5 14.9 - - + +
1055A ARG 3.2 7.1 - - - +
1056A SER* 1.3 80.9 - - - +
1058A VAL* 1.4 76.8 + - - +
1059A HIS* 3.5 15.4 + - - -
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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
------------------------------------------------------------
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