Contacts of the helix formed by residues 1055 - 1075 (chain A) in PDB entry 6RZ5
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 SER1055 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1051A LYS* 4.4 10.3 - - - -
1052A SER* 3.3 33.8 + - - -
1053A PRO 3.4 2.0 - - - -
1054A ASP* 1.3 79.9 - - - +
1056A PRO* 1.4 68.7 - - - +
1057A GLU* 4.1 7.9 - - - -
1058A MET* 3.0 8.5 + - - +
1059A LYS* 2.9 24.7 + - - +
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Residues in contact with PRO1056 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1054A ASP 4.5 2.0 - - - +
1055A SER* 1.4 84.3 - - - +
1057A GLU* 1.3 59.7 + - + +
1059A LYS* 3.8 10.2 - - + +
1060A ASP* 3.3 22.0 + - - +
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Residues in contact with GLU1057 (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 LYS 5.6 0.5 - - - +
1048A LEU* 5.0 13.5 - - + +
1051A LYS* 5.0 13.9 - - + +
1055A SER* 3.1 6.9 - - - -
1056A PRO* 1.3 78.6 - - + +
1058A MET* 1.4 61.6 + - - +
1060A ASP* 3.7 1.1 + - - -
1061A PHE 3.6 5.0 + - - -
1105A TYR* 2.7 44.6 + - + +
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Residues in contact with MET1058 (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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1048A LEU* 5.5 9.6 - - + +
1051A LYS* 6.1 1.3 - - + +
1052A SER 3.8 15.0 - - - +
1053A PRO* 3.5 22.9 - - + +
1055A SER* 3.0 10.5 + - - +
1057A GLU* 1.4 77.4 - - - +
1059A LYS* 1.4 57.3 + - - +
1061A PHE* 3.4 6.2 + - - +
1062A ARG* 3.1 38.0 + - - +
1105A TYR* 5.4 0.4 - - - -
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Residues in contact with LYS1059 (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 PRO 5.2 0.6 + - - -
1054A ASP 5.4 2.9 - - - +
1055A SER 2.9 14.9 + - - +
1056A PRO* 3.8 11.7 - - + +
1057A GLU 3.4 0.2 - - - -
1058A MET* 1.4 76.7 - - - +
1060A ASP* 1.4 50.9 + - - +
1062A ARG* 3.4 8.7 + - - +
1063A HIS* 2.8 37.5 + - - +
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Residues in contact with ASP1060 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056A PRO 3.3 14.6 + - - +
1057A GLU* 4.7 0.2 - - - -
1058A MET 3.3 0.2 - - - -
1059A LYS* 1.4 75.0 - - - +
1061A PHE* 1.3 59.1 + - - +
1063A HIS* 3.4 5.7 + - - +
1064A GLY* 2.9 26.3 + - - -
1101A TYR* 4.4 11.2 - - - +
1105A TYR* 2.8 35.8 + - - +
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Residues in contact with PHE1061 (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 GLN* 6.0 0.2 - - - -
1045A PRO* 5.1 9.6 - - + -
1048A LEU* 6.4 0.2 - - + -
1057A GLU 3.6 2.4 + - - +
1058A MET* 3.4 10.0 + - - +
1059A LYS 3.4 0.4 - - - -
1060A ASP* 1.3 77.1 - - - +
1062A ARG* 1.4 62.7 + - + +
1064A GLY* 3.3 9.9 + - - -
1065A PHE* 3.3 13.5 + - - +
1101A TYR 4.4 6.8 - - - +
1102A ILE* 5.9 1.8 - - - +
1105A TYR* 3.9 40.8 - - + -
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Residues in contact with ARG1062 (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 GLN* 4.0 26.2 + - + +
1053A PRO* 3.3 27.1 + - - +
1054A ASP* 5.2 5.5 + - - +
1058A MET* 3.1 27.7 + - - +
1059A LYS* 3.7 7.4 - - - +
1061A PHE* 1.4 75.2 - - + +
1063A HIS* 1.4 56.4 + - - +
1065A PHE* 3.7 7.5 + - - +
1066A ASP* 3.3 24.0 + - - +
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Residues in contact with HIS1063 (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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1059A LYS 2.8 22.1 + - - +
1060A ASP* 3.8 6.3 - - - +
1062A ARG* 1.4 70.1 - - - +
1064A GLY* 1.3 56.3 + - - +
1065A PHE 3.3 0.7 - - - -
1066A ASP* 3.0 10.2 + - - +
1067A ILE* 2.9 34.1 + - - +
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Residues in contact with GLY1064 (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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1060A ASP 2.9 16.7 + - - -
1061A PHE 3.3 4.0 + - - -
1063A HIS* 1.3 78.1 - - - +
1065A PHE* 1.3 55.3 + - - +
1067A ILE* 3.6 3.7 + - - +
1068A LEU* 3.2 26.2 + - - +
1097A THR* 3.7 9.5 - - - +
1101A TYR* 3.8 27.1 - - - -
1102A ILE* 5.8 4.5 - - - -
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Residues in contact with PHE1065 (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 ALA* 4.0 14.8 - - + +
1040A ALA* 5.6 1.3 - - + -
1041A GLN* 3.8 33.4 - - + +
1061A PHE 3.3 11.3 + - - +
1062A ARG 4.0 4.7 - - - +
1063A HIS 3.3 0.4 - - - -
1064A GLY* 1.3 73.3 - - - +
1066A ASP* 1.4 59.1 + - - +
1068A LEU* 3.8 11.6 - - + +
1069A VAL* 2.9 29.8 + - - +
1102A ILE* 6.0 0.8 - - - +
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Residues in contact with ASP1066 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062A ARG 3.3 16.0 + - - +
1063A HIS* 3.0 16.7 + - - +
1065A PHE* 1.4 74.3 - - - +
1067A ILE* 1.4 59.9 + - - +
1069A VAL* 3.5 7.2 + - - +
1070A GLY* 3.3 17.8 + - - -
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Residues in contact with ILE1067 (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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1063A HIS 2.9 14.9 + - - +
1064A GLY* 3.9 7.0 - - - +
1066A ASP* 1.4 74.2 - - - +
1068A LEU* 1.4 57.9 + - - +
1070A GLY* 3.6 2.3 + - - -
1071A GLN* 2.9 38.7 + - - +
1097A THR* 4.5 6.1 - - + -
1101A TYR* 6.2 0.2 - - + -
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Residues in contact with LEU1068 (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 LEU* 4.3 29.8 - - + -
1037A ALA* 4.9 10.1 - - + -
1064A GLY 3.2 17.2 + - - +
1065A PHE* 3.8 9.9 - - + +
1066A ASP 3.3 0.2 - - - -
1067A ILE* 1.4 75.2 - - - +
1069A VAL* 1.4 58.8 + - - +
1071A GLN* 3.4 8.5 + - - +
1072A ILE* 3.0 27.4 + - + +
1094A LEU* 3.3 39.4 - - + +
1097A THR* 3.8 14.6 - - + -
1098A ARG* 4.5 16.4 - - + +
1102A ILE* 5.8 6.1 - - + -
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Residues in contact with VAL1069 (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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1034A ARG* 6.0 2.9 - - + +
1037A ALA* 5.2 12.0 - - + +
1038A LEU* 4.9 18.4 - - + -
1065A PHE 2.9 18.5 + - - +
1066A ASP* 3.8 8.3 - - - +
1067A ILE 3.4 0.4 - - - -
1068A LEU* 1.4 71.7 - - - +
1070A GLY* 1.3 64.1 + - - +
1072A ILE* 3.3 8.6 + - - +
1073A ASP* 3.1 32.8 + - - +
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Residues in contact with GLY1070 (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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1066A ASP 3.3 11.1 + - - -
1067A ILE 3.9 3.8 - - - -
1068A LEU 3.3 0.2 - - - -
1069A VAL* 1.3 76.5 - - - +
1071A GLN* 1.4 60.9 + - - +
1073A ASP* 3.5 8.2 + - - +
1074A ASP* 3.2 21.5 + - - +
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Residues in contact with GLN1071 (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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1067A ILE* 2.9 28.9 + - - +
1068A LEU* 3.6 8.1 - - - +
1069A VAL 3.4 0.2 - - - -
1070A GLY* 1.4 71.5 - - - +
1072A ILE* 1.4 62.8 + - - +
1074A ASP* 3.6 8.2 + - - +
1075A ALA* 3.3 22.2 + - - +
1093A GLN* 2.8 39.7 + - + +
1094A LEU* 3.5 17.6 - - + +
1097A THR* 2.7 28.3 + - - +
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Residues in contact with ILE1072 (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 LEU* 5.0 12.9 - - + +
1033A MET* 5.7 5.8 - - + -
1034A ARG* 4.8 23.8 - - + +
1037A ALA* 6.1 1.6 - - + -
1068A LEU 3.0 14.2 + - - +
1069A VAL* 3.4 14.1 - - - +
1070A GLY 3.3 0.2 - - - -
1071A GLN* 1.4 74.1 - - - +
1073A ASP* 1.4 62.6 + - - +
1075A ALA* 3.2 23.1 + - - +
1094A LEU* 5.4 3.1 - - - +
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Residues in contact with ASP1073 (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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1034A ARG* 5.6 3.5 - - - +
1069A VAL* 3.1 24.0 + - - +
1070A GLY* 3.5 10.1 + - - +
1072A ILE* 1.4 72.3 - - - +
1074A ASP* 1.4 64.2 + - - +
1075A ALA 4.3 3.6 - - - -
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Residues in contact with ASP1074 (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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1070A GLY 3.2 17.3 + - - +
1071A GLN* 3.7 10.5 - - - +
1072A ILE 3.3 0.2 - - - -
1073A ASP* 1.4 77.3 - - - +
1075A ALA* 1.3 60.0 + - - +
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Residues in contact with ALA1075 (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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1071A GLN 3.3 10.6 + - - +
1072A ILE* 3.2 19.3 + - - +
1073A ASP 4.3 4.0 - - - -
1074A ASP* 1.3 82.0 - - - +
1091A ALA* 5.6 8.7 - - - +
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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
------------------------------------------------------------
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