Contacts of the helix formed by residues 1016 - 1033 (chain A) in PDB entry 1FVR
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 THR1016 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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961A ILE* 3.9 15.6 - - - +
989A GLN 3.9 11.7 - - - +
990A GLU* 3.7 27.4 - - + +
1008A GLU* 4.5 5.7 + - + +
1014A VAL* 5.3 1.8 - - + -
1015A TYR* 1.3 81.0 - - - +
1017A THR* 1.3 63.6 + - - +
1018A ASN* 3.0 26.1 + - - +
1019A SER* 2.8 28.7 + - - -
1020A ASP* 3.0 11.3 + - - -
1079A PRO* 5.5 0.5 - - - +
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Residues in contact with THR1017 (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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956A SER* 3.5 36.3 - - - +
959A GLN* 5.5 2.7 - - - -
960A PHE 3.6 16.6 - - - +
961A ILE* 4.3 6.4 - - + +
989A GLN 5.1 1.0 + - - -
1016A THR* 1.3 74.9 - - - +
1018A ASN* 1.3 68.0 + - - +
1020A ASP* 3.2 12.6 + - - +
1021A VAL* 3.0 26.8 + - - +
1085A PHE* 4.1 3.6 - - - -
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Residues in contact with ASN1018 (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 THR* 3.0 13.4 + - - +
1017A THR* 1.3 86.5 + - - +
1019A SER* 1.3 60.3 + - - +
1021A VAL* 3.3 17.8 + - - +
1022A TRP 3.4 5.4 + - - -
1079A PRO* 3.2 48.7 + - + +
1080A TYR* 4.1 8.6 - - - +
1082A ARG* 3.0 24.0 + - - +
1083A PRO 5.4 1.7 - - - +
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Residues in contact with SER1019 (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 ALA* 3.8 15.2 + - - +
1008A GLU* 3.7 15.2 + - - -
1009A SER* 3.9 12.2 + - - -
1015A TYR* 3.5 13.5 - - - +
1016A THR* 2.8 38.1 + - - -
1018A ASN* 1.3 73.4 - - - +
1020A ASP* 1.3 66.3 + - - +
1021A VAL 3.1 0.2 - - - -
1022A TRP* 3.1 4.4 + - - +
1023A SER* 3.1 23.2 + - - -
1082A ARG* 3.7 8.5 - - - +
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Residues in contact with ASP1020 (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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952A MET* 3.7 9.4 - - + +
960A PHE 4.3 0.7 - - - +
961A ILE* 3.4 11.3 - - - +
962A HIS* 2.8 33.7 + - - +
963A ARG* 2.9 28.1 + - - -
964A ASP 4.8 0.2 + - - -
965A LEU* 3.6 8.3 - - + +
1015A TYR* 5.7 0.2 - - - -
1016A THR 3.0 14.3 + - - +
1017A THR* 3.2 14.4 + - - +
1019A SER* 1.3 80.1 + - - +
1021A VAL* 1.3 58.2 + - - +
1023A SER* 3.1 9.2 + - - -
1024A TYR* 2.8 27.7 + - - +
1085A PHE* 3.9 15.3 - - + -
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Residues in contact with VAL1021 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017A THR* 3.0 17.9 + - - +
1018A ASN* 3.4 13.0 - - - +
1019A SER 3.1 0.2 - - - -
1020A ASP* 1.3 74.5 - - - +
1022A TRP* 1.3 64.4 + - - +
1024A TYR* 3.3 4.7 + - - +
1025A GLY 3.1 16.5 + - - -
1074A CYS* 3.3 25.7 - - + +
1082A ARG* 3.9 16.8 - - + -
1083A PRO* 3.5 27.8 - - + +
1084A SER* 4.7 1.3 - - - -
1085A PHE* 3.6 35.0 - - + +
1088A ILE* 4.2 4.3 - - + -
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Residues in contact with TRP1022 (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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1003A ARG 5.4 0.6 + - - -
1004A TRP 3.4 19.1 + - - -
1005A MET 3.5 14.5 + - - -
1006A ALA* 3.6 22.2 - - + -
1007A ILE* 3.7 25.6 - - + -
1018A ASN 3.4 3.0 + - - -
1019A SER 3.1 9.9 + - - +
1021A VAL* 1.3 78.9 - - - +
1023A SER* 1.3 63.0 + - - +
1025A GLY 3.0 9.9 + - - -
1026A VAL* 3.4 11.4 + - + +
1039A TYR* 4.7 14.2 + - - -
1051A LEU* 4.8 9.4 - - + -
1056A ARG* 3.6 32.1 - - - -
1074A CYS 3.2 12.5 + - - +
1075A TRP* 3.1 56.4 + + + -
1076A ARG 4.0 1.3 - - - -
1077A GLU 5.0 0.2 - - - -
1082A ARG* 3.5 29.2 - - - +
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Residues in contact with SER1023 (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 ARG 5.1 5.0 + - - -
964A ASP* 5.7 0.2 - - - -
965A LEU* 3.5 34.2 + - - -
1004A TRP* 2.8 31.4 + - - +
1005A MET* 4.7 1.7 - - - -
1006A ALA 5.1 0.3 + - - -
1019A SER 3.1 12.8 + - - -
1020A ASP* 3.4 11.3 + - - -
1022A TRP* 1.3 78.0 - - - +
1024A TYR* 1.3 61.3 + - - +
1026A VAL* 3.0 7.9 + - - +
1027A LEU* 2.9 20.4 + - - +
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Residues in contact with TYR1024 (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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945A ALA* 2.7 38.9 + - + +
948A VAL* 3.9 22.2 - - + -
949A ALA* 3.9 14.1 - - + -
965A LEU* 4.1 7.8 - - + +
1020A ASP 2.8 13.7 + - - +
1021A VAL* 3.4 8.7 - - - +
1023A SER* 1.3 75.4 - - - +
1025A GLY* 1.3 60.3 + - - +
1027A LEU* 3.1 14.0 + - + +
1028A LEU* 2.8 45.4 + - + +
1031A ILE* 6.3 0.9 - - + -
1070A LEU* 5.7 0.2 - - + -
1074A CYS* 4.2 5.6 - - - -
1085A PHE* 3.7 24.0 - + + -
1088A ILE* 3.6 37.2 - - + -
1092A LEU* 3.3 15.6 - - - +
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Residues in contact with GLY1025 (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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1021A VAL 3.1 6.7 + - - -
1022A TRP 3.0 4.8 + - - -
1024A TYR* 1.3 79.7 - - - +
1026A VAL* 1.3 60.2 + - - +
1028A LEU* 3.3 7.4 + - - +
1029A TRP* 3.1 16.8 + - - +
1071A MET* 4.0 6.4 - - - +
1074A CYS* 3.8 18.6 - - - -
1075A TRP* 3.4 30.1 - - - -
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Residues in contact with VAL1026 (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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1003A ARG 3.7 19.1 - - - +
1004A TRP* 3.6 27.8 - - + +
1022A TRP* 3.6 27.8 - - + +
1023A SER 3.0 6.0 + - - +
1025A GLY* 1.3 73.0 - - - +
1027A LEU* 1.3 60.8 + - - +
1029A TRP* 3.0 10.0 + - - +
1030A GLU* 2.8 25.8 + - - +
1038A PRO* 3.6 26.5 - - + -
1039A TYR* 5.0 2.5 - - - +
1057A LEU* 4.2 9.6 - - + -
1075A TRP* 3.7 15.0 - - + +
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Residues in contact with LEU1027 (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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910A LEU* 4.2 14.1 - - + -
948A VAL* 4.1 19.3 - - + -
965A LEU* 4.2 7.9 - - + -
966A ALA* 3.7 27.6 - - - +
967A ALA* 3.5 30.3 - - + +
970A ILE* 3.8 17.9 - - + -
1004A TRP* 4.4 0.6 - - - +
1023A SER 2.9 12.4 + - - +
1024A TYR* 3.1 16.6 + - + +
1026A VAL* 1.3 74.7 - - - +
1028A LEU* 1.3 64.9 + - - +
1030A GLU* 3.0 20.1 + - - +
1031A ILE* 3.0 20.9 + - + +
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Residues in contact with LEU1028 (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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942A LEU* 5.1 4.5 - - + -
945A ALA* 3.7 28.0 - - + -
1024A TYR* 2.8 31.0 + - + +
1025A GLY* 3.5 9.6 - - - +
1027A LEU* 1.3 77.2 - - - +
1029A TRP* 1.3 57.6 + - - +
1031A ILE* 3.3 10.7 + - + +
1032A VAL* 3.0 44.1 + - + +
1067A VAL* 4.2 12.3 - - + +
1070A LEU* 4.1 31.0 - - + -
1071A MET* 3.9 26.9 - - + +
1074A CYS* 5.9 0.7 - - - -
1092A LEU* 4.9 4.5 - - + -
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Residues in contact with TRP1029 (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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1025A GLY 3.1 12.6 + - - +
1026A VAL* 3.0 17.4 + - - +
1028A LEU* 1.3 78.0 - - - +
1030A GLU* 1.3 59.5 + - - +
1032A VAL* 3.5 1.2 + - - +
1033A SER* 3.0 47.0 + - - -
1036A GLY 3.5 23.8 - - - -
1037A THR 3.8 13.2 - - - -
1038A PRO* 3.7 25.6 - - + -
1039A TYR 4.7 1.1 - - - -
1040A CYS* 5.7 0.4 - - + -
1057A LEU* 3.8 33.7 - - + +
1058A GLU 2.9 29.5 + - - -
1060A PRO* 3.6 17.8 - - + +
1071A MET* 3.7 28.9 - - - +
1075A TRP* 4.3 1.1 - + + -
1114A ALA* 4.7 8.3 - - + -
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Residues in contact with GLU1030 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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911A LEU* 3.6 17.5 - - - +
914A LEU* 4.0 2.9 - - + -
967A ALA* 2.9 43.1 + - + +
968A ARG 4.8 0.5 + - - -
1004A TRP* 2.8 39.5 + - - -
1026A VAL 2.8 16.2 + - - +
1027A LEU* 3.0 12.4 + - - +
1029A TRP* 1.3 76.4 - - - +
1031A ILE* 1.3 64.6 + - - +
1033A SER* 3.3 6.3 + - - -
1034A LEU 3.1 3.6 + - - -
1035A GLY* 2.7 31.5 + - - -
1036A GLY 4.2 14.2 - - - +
1038A PRO* 4.2 10.4 - - + +
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Residues in contact with ILE1031 (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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910A LEU* 4.1 23.1 - - + -
914A LEU* 3.7 13.6 - - + +
941A LEU* 3.5 50.6 - - + +
942A LEU* 6.3 0.7 - - + -
944A PHE* 4.0 10.8 - - + +
945A ALA* 3.7 35.2 - - + +
948A VAL* 5.4 1.3 - - + -
1024A TYR* 6.3 0.7 - - + -
1027A LEU* 3.0 26.0 + - + +
1028A LEU* 3.3 14.6 + - + +
1030A GLU* 1.3 75.9 - - - +
1032A VAL* 1.3 66.9 + - + +
1034A LEU* 3.1 14.9 + - - +
1103A VAL* 6.1 0.4 - - + -
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Residues in contact with VAL1032 (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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942A LEU* 5.9 0.4 - - + -
1028A LEU* 3.0 28.0 + - + +
1029A TRP 3.8 3.6 - - - +
1031A ILE* 1.3 79.9 - - + +
1033A SER* 1.3 57.7 + - - +
1034A LEU* 3.3 5.4 + - - +
1060A PRO* 3.8 14.4 - - + -
1062A ASN* 3.2 24.4 + - - +
1063A CYS* 3.6 31.4 - - + -
1067A VAL* 3.9 17.0 - - + -
1071A MET* 3.7 17.5 - - + -
1103A VAL* 4.0 27.8 - - + +
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Residues in contact with SER1033 (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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918A ARG* 3.0 15.2 + - - -
1029A TRP* 3.0 34.7 + - - -
1030A GLU* 3.3 2.9 + - - -
1031A ILE 3.3 0.2 - - - -
1032A VAL* 1.3 75.4 - - - +
1034A LEU* 1.3 70.3 + - - +
1036A GLY* 3.1 20.3 + - - -
1060A PRO* 4.6 10.3 - - - -
1062A ASN* 4.8 3.8 - - - -
1113A TYR* 5.7 0.3 - - - -
1114A ALA* 3.7 23.9 + - - +
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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