Contacts of the helix formed by residues 1064 - 1081 (chain A) in PDB entry 6CNB
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 GLU1064 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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955A LEU* 3.7 30.2 - - + +
962A THR* 3.8 22.2 - - - +
1062A ILE* 4.0 2.2 + - - +
1063A SER* 1.3 74.6 - - - +
1065A LYS* 1.3 74.3 + - + +
1066A SER* 2.7 0.8 + - - -
1067A VAL* 2.4 36.6 + - - +
1068A ARG* 2.7 45.9 + - - +
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Residues in contact with LYS1065 (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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946A THR* 3.1 24.5 + - - +
948A ASN* 6.6 0.4 - - - -
951A ASP* 4.7 12.1 + - - -
1063A SER* 2.7 7.8 + - - +
1064A GLU* 1.3 91.6 - - + +
1066A SER* 1.3 61.4 + - - +
1068A ARG* 3.7 20.0 - - + -
1069A LYS* 2.9 46.0 + - + +
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Residues in contact with SER1066 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939A TRP* 4.7 9.7 - - - -
942A ALA* 3.9 7.7 - - - +
943A TYR* 4.9 9.6 - - - +
946A THR* 3.4 23.5 + - - +
1061A ARG 5.0 0.2 + - - -
1062A ILE* 3.7 17.0 - - - -
1063A SER* 2.5 48.6 + - - -
1064A GLU 2.7 0.4 + - - -
1065A LYS* 1.3 74.0 - - - +
1067A VAL* 1.3 62.4 + - - -
1070A PHE* 3.1 19.2 + - - +
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Residues in contact with VAL1067 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939A TRP* 4.7 10.5 - - + -
955A LEU* 5.3 2.2 - - + -
959A ILE* 4.4 19.7 - - + +
962A THR* 3.9 28.9 - - - +
963A ALA* 4.7 3.6 - - - +
966A ILE* 6.2 0.2 - - + -
1012A ILE* 4.6 13.7 - - + -
1062A ILE* 4.3 19.5 - - + -
1064A GLU* 2.4 17.0 + - - +
1066A SER* 1.3 74.6 - - - +
1068A ARG* 1.3 67.2 + - + +
1070A PHE* 3.0 7.9 + - + +
1071A LEU* 2.9 44.9 + - + +
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Residues in contact with ARG1068 (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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962A THR* 5.0 14.4 - - - +
965A GLU* 5.0 13.7 - - - +
966A ILE* 4.4 23.6 - - + +
1064A GLU* 2.7 44.7 + - - +
1065A LYS* 3.9 15.9 - - + +
1067A VAL* 1.3 78.9 - - + +
1069A LYS* 1.3 65.2 + - + +
1071A LEU* 3.9 4.8 - - - +
1072A GLU* 2.9 24.8 + - - +
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Residues in contact with LYS1069 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942A ALA* 4.3 12.6 - - + +
945A ILE* 5.7 9.2 - - + -
946A THR* 4.3 14.8 - - - +
1065A LYS* 2.9 43.4 + - + +
1066A SER 4.3 0.9 - - - +
1068A ARG* 1.3 74.2 - - + +
1070A PHE* 1.3 61.3 + - - +
1072A GLU* 3.3 11.6 - - + +
1073A ILE* 2.9 33.0 + - + +
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Residues in contact with PHE1070 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935A PHE* 4.1 12.6 - + - -
938A SER* 3.8 14.1 - - - -
939A TRP* 3.4 56.5 - + + -
942A ALA* 3.8 8.7 - - + +
1008A LEU* 3.5 31.2 - - + -
1011A TYR* 4.1 17.3 - + - -
1012A ILE* 4.2 16.8 - - + -
1066A SER 3.1 16.8 + - - +
1067A VAL* 3.0 13.9 + - - +
1069A LYS* 1.3 74.3 - - - +
1071A LEU* 1.3 84.9 + - + +
1073A ILE* 2.9 9.0 + - - +
1074A ALA* 2.9 25.6 + - + +
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Residues in contact with LEU1071 (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 ALA* 4.4 10.1 - - - +
966A ILE* 3.8 36.6 - - + -
967A LEU* 5.4 6.7 - - + -
1008A LEU* 3.5 36.3 - - + -
1012A ILE* 3.7 23.8 - - + -
1067A VAL* 2.9 34.8 + - + +
1068A ARG* 4.0 3.6 - - - +
1070A PHE* 1.3 75.9 - - + +
1072A GLU* 1.3 65.1 + - - +
1074A ALA* 4.3 2.7 - - - -
1075A LEU* 2.9 41.4 + - + +
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Residues in contact with GLU1072 (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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1068A ARG 2.9 20.0 + - - +
1069A LYS* 3.3 14.8 - - + +
1071A LEU* 1.3 74.2 - - - +
1073A ILE* 1.3 70.3 + - + +
1075A LEU* 4.3 8.2 - - - +
1076A PHE* 2.9 35.7 + - + +
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Residues in contact with ILE1073 (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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684A ASP* 6.2 0.2 - - - +
938A SER* 4.2 19.7 - - - +
941A HIS* 4.8 25.8 - - + +
942A ALA* 5.4 6.7 - - + +
1069A LYS* 2.9 25.5 + - + +
1070A PHE* 2.9 9.5 + - - +
1072A GLU* 1.3 78.7 - - + +
1074A ALA* 1.3 69.1 + - - +
1076A PHE* 3.4 8.5 - - + +
1077A LYS* 2.9 47.7 + - + +
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Residues in contact with ALA1074 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
933A VAL* 4.3 33.3 - - + +
938A SER* 5.6 1.5 - - - -
1004A PHE* 4.8 1.1 - - + -
1008A LEU* 4.4 23.1 - - + -
1070A PHE* 2.9 21.5 + - + +
1071A LEU* 3.7 10.5 - - - +
1073A ILE* 1.3 80.0 - - - +
1075A LEU* 1.3 64.4 + - - +
1077A LYS* 3.0 6.7 + - - +
1078A TYR* 2.9 17.0 + - - +
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Residues in contact with LEU1075 (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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966A ILE* 4.4 15.0 - - + -
967A LEU* 5.5 0.9 - - + -
970A LEU* 4.1 25.6 - - + -
1004A PHE* 4.5 10.3 - - + -
1005A TYR* 4.9 11.4 - - + +
1008A LEU* 5.4 5.6 - - + -
1071A LEU* 2.9 31.1 + - + +
1072A GLU* 4.5 7.2 - - - +
1074A ALA* 1.3 77.2 - - - +
1076A PHE* 1.3 59.9 + - + +
1078A TYR* 3.3 12.8 - - + +
1079A ARG* 2.9 32.0 + - + +
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Residues in contact with PHE1076 (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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1072A GLU* 2.9 32.7 + - + +
1073A ILE* 3.4 10.5 - - + +
1075A LEU* 1.3 78.6 - - + +
1077A LYS* 1.3 73.5 + - + +
1078A TYR 3.0 1.3 + - - -
1079A ARG* 3.2 5.1 + - + +
1080A LYS* 2.9 68.9 + - + +
84F TYR* 4.9 10.5 - - - -
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Residues in contact with LYS1077 (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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683A ARG* 4.3 28.0 - - + +
684A ASP* 5.8 2.7 - - - +
927A GLU* 3.5 30.9 + - - +
932A PRO 4.3 12.9 - - - +
933A VAL* 5.0 4.9 - - + +
937A ARG* 4.7 5.3 - - - +
938A SER* 3.4 22.1 + - - +
941A HIS* 6.0 5.5 - - - +
1073A ILE* 2.9 35.6 + - + +
1074A ALA* 3.5 8.3 - - - +
1076A PHE* 1.3 81.1 - - + +
1078A TYR* 1.3 61.3 + - - +
1080A LYS* 4.2 5.1 - - - +
1081A ALA* 3.0 25.5 + - - +
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Residues in contact with TYR1078 (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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919A ASP* 5.1 2.8 + - - -
921A LEU* 3.7 41.3 - - + +
932A PRO* 4.6 8.0 + - + +
1000A ALA* 4.8 2.9 - - - +
1001A GLU* 3.9 39.1 + - + +
1004A PHE* 3.6 55.4 - + + -
1005A TYR* 5.4 4.3 - - - -
1074A ALA 2.9 6.2 + - - +
1075A LEU* 3.3 14.1 - - + +
1076A PHE 3.0 1.4 - - - -
1077A LYS* 1.3 75.6 - - - +
1079A ARG* 1.3 60.7 + - + +
1081A ALA* 2.5 39.7 + - - +
1082A ARG* 3.4 25.4 + - - +
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Residues in contact with ARG1079 (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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1075A LEU* 2.9 22.1 + - + +
1076A PHE* 4.0 4.7 - - + +
1078A TYR* 1.3 80.5 - - + +
1080A LYS* 1.3 59.9 + - - +
1082A ARG* 3.9 43.3 + - - +
82F THR* 4.7 5.6 - - - +
83F PRO* 3.2 40.0 - - - +
84F TYR* 3.1 45.9 + - + +
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Residues in contact with LYS1080 (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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925A GLU* 2.7 23.9 - - - +
1076A PHE* 2.9 57.4 + - + +
1077A LYS* 4.2 5.6 - - - +
1079A ARG* 1.3 77.8 - - + +
1081A ALA* 1.3 59.6 + - - +
1082A ARG* 3.2 4.3 + - - +
84F TYR* 4.0 36.6 - - + -
153F VAL 4.3 19.0 + - - -
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Residues in contact with ALA1081 (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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921A LEU* 3.2 23.2 - - + +
922A ASP 4.7 1.6 - - - +
925A GLU* 3.5 28.7 - - + +
926A MET* 4.6 2.2 - - + +
932A PRO* 4.1 24.0 - - + -
1077A LYS 3.0 18.2 + - - +
1078A TYR* 2.5 21.2 + - - +
1080A LYS* 1.3 68.1 - - - +
1082A ARG* 1.3 62.2 + - - +
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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