Contacts of the helix formed by residues 1066 - 1086 (chain A) in PDB entry 3H0G
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 MET1066 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A GLU 5.1 2.9 - - - +
854A VAL 4.2 5.6 - - - +
855A MET* 3.2 49.2 - - + +
1065A GLU* 1.3 90.9 - - - +
1067A VAL* 1.3 60.7 + - - +
1068A GLY 3.4 2.0 - - - -
1069A THR* 3.4 37.4 + - + +
1070A LEU* 2.9 27.2 - - - +
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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
----------------------------------------------------------
855A MET* 4.3 3.4 - - - +
856A VAL* 2.6 43.5 - - + +
862A VAL* 4.4 17.3 - - + -
871A GLN* 6.0 0.4 - - - +
874A TYR 3.8 19.5 - - - +
875A GLY* 5.8 0.4 - - - -
1061A VAL* 5.4 5.8 - - + -
1065A GLU* 3.7 6.3 - - + +
1066A MET* 1.3 72.8 - - - +
1068A GLY* 1.3 59.7 + - - +
1070A LEU* 3.6 14.4 - - + +
1071A ALA* 2.9 30.0 + - + +
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Residues in contact with GLY1068 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A MET* 3.5 18.5 - - - +
854A VAL* 3.5 30.4 + - - +
1066A MET* 3.4 0.6 - - - +
1067A VAL* 1.3 78.7 - - - +
1069A THR* 1.3 55.7 + - - +
1071A ALA* 4.3 0.2 - - - -
1072A ALA* 2.6 39.2 + - - +
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Residues in contact with THR1069 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848A VAL* 5.5 10.2 - - + +
851A MET* 4.2 4.4 + - - +
852A GLU* 3.9 31.4 - - + +
854A VAL 4.9 0.4 - - - +
1066A MET* 3.4 39.8 + - + +
1068A GLY* 1.3 74.4 - - - +
1070A LEU* 1.3 72.2 + - - +
1072A ALA* 3.2 5.4 + - - +
1073A GLN* 3.0 36.1 + - - +
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Residues in contact with LEU1070 (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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458A LYS* 5.5 19.6 - - + +
520A PRO* 5.2 22.9 - - + -
521A GLN 6.1 0.7 - - - +
880A ASP* 5.9 2.7 - - - +
881A ALA* 6.0 2.9 - - + -
1065A GLU* 4.1 15.7 - - - +
1066A MET 2.9 24.7 - - - +
1067A VAL* 3.6 19.1 - - + +
1069A THR* 1.3 82.0 + - - +
1071A ALA* 1.3 88.6 + - + +
1073A GLN* 3.3 16.8 + - - +
1074A SER* 3.1 22.5 + - - +
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Residues in contact with ALA1071 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A MET* 4.9 5.2 - - + -
1067A VAL* 2.9 22.7 - - + +
1068A GLY* 3.3 4.2 + - - +
1069A THR 3.3 0.4 - - - -
1070A LEU* 1.3 89.5 - - + +
1072A ALA* 1.3 61.9 + - - +
1074A SER* 2.6 25.0 + - - +
1075A ILE* 3.1 21.0 + - + +
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Residues in contact with ALA1072 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844A GLN* 4.5 1.5 - - - +
847A LEU* 3.7 28.8 - - + +
848A VAL* 4.4 8.1 - - + +
851A MET* 3.6 26.2 - - + +
1068A GLY 2.6 23.2 + - - +
1069A THR* 3.5 5.8 - - - +
1071A ALA* 1.3 74.3 - - - +
1073A GLN* 1.3 63.0 + - + +
1075A ILE* 3.1 18.5 + - - +
1076A GLY* 3.2 10.4 + - - -
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Residues in contact with GLN1073 (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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455A SER 5.6 1.2 + - - -
456A LEU 3.8 18.5 + - - +
457A HIS* 5.3 1.1 + - - -
458A LYS* 3.8 26.3 + - - +
844A GLN* 3.2 24.7 - - - +
848A VAL* 4.9 13.3 - - + +
1069A THR* 3.0 25.4 + - - +
1070A LEU* 3.3 16.0 + - - +
1072A ALA* 1.3 74.8 - - - +
1074A SER* 1.3 63.1 + - - +
1076A GLY* 3.1 11.3 + - - -
1077A GLU* 3.3 19.0 + - - +
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Residues in contact with SER1074 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A GLN* 2.9 59.8 + - - +
1070A LEU 3.1 10.4 + - - -
1071A ALA* 2.6 28.1 + - - -
1073A GLN* 1.3 77.7 - - - +
1075A ILE* 1.3 52.0 + - - +
1077A GLU* 4.3 0.9 - - - -
1078A PRO* 2.3 31.2 - - - +
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Residues in contact with ILE1075 (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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847A LEU* 5.2 15.5 - - + -
851A MET* 4.7 10.8 - - + -
1071A ALA* 3.1 25.2 + - + +
1072A ALA* 3.1 12.5 + - - +
1074A SER* 1.3 73.8 + - - +
1076A GLY* 1.3 57.5 + - - +
1078A PRO* 2.4 31.4 - - + +
1079A ALA* 3.7 8.7 + - - +
1104A LEU* 5.7 6.9 - - + +
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Residues in contact with GLY1076 (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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840A THR 6.1 0.2 - - - -
843A ILE* 4.2 22.6 - - - +
844A GLN* 4.1 15.9 - - - -
847A LEU* 5.6 0.9 - - - -
1072A ALA 3.2 8.0 + - - -
1073A GLN 3.1 8.0 + - - -
1075A ILE* 1.3 74.7 - - - +
1077A GLU* 1.3 61.9 + - - +
1078A PRO* 2.9 5.2 - - - -
1079A ALA* 3.4 4.9 + - - +
1080A THR* 3.2 26.7 + - - +
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Residues in contact with GLU1077 (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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456A LEU* 4.3 17.0 - - + -
457A HIS* 2.3 68.5 + - + +
521A GLN* 2.3 44.5 + - - +
844A GLN* 4.4 1.1 - - - +
1073A GLN 3.3 13.1 + - - +
1074A SER* 3.9 1.8 - - - +
1076A GLY* 1.3 74.6 - - - +
1078A PRO* 1.3 69.2 - - + +
1080A THR* 2.4 30.2 + - - +
1081A GLN* 3.2 15.6 + - - +
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Residues in contact with PRO1078 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A GLN* 4.2 4.2 - - - +
1074A SER 2.3 28.7 - - - +
1075A ILE* 2.4 33.2 - - + +
1077A GLU* 1.3 89.5 - - + +
1079A ALA* 1.3 62.1 + - + +
1081A GLN* 2.9 28.5 + - - +
1082A MET* 3.2 17.0 + - + +
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Residues in contact with ALA1079 (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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843A ILE* 5.1 8.1 - - + -
1075A ILE 4.1 7.6 - - - +
1076A GLY* 3.6 10.8 - - - +
1077A GLU 3.3 0.4 - - - -
1078A PRO* 1.3 80.4 - - - +
1080A THR* 1.3 59.1 + - + +
1082A MET* 2.9 9.9 + - - +
1083A THR* 2.9 30.7 + - - -
1101A VAL* 4.3 14.3 - - + +
1104A LEU* 4.2 24.2 - - + -
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Residues in contact with THR1080 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A LEU* 5.2 9.7 - - + +
836A LYS* 3.7 32.4 + - - -
840A THR* 3.5 37.2 - - + +
843A ILE* 5.3 2.5 - - + -
844A GLN* 5.9 0.7 - - - +
1076A GLY 3.2 16.8 - - - +
1077A GLU* 2.4 29.2 + - - +
1079A ALA* 1.3 76.0 - - + +
1081A GLN* 1.3 60.7 + - - +
1083A THR* 2.9 28.6 - - - +
1084A LEU* 3.9 4.5 + - - +
1101A VAL* 5.5 0.7 - - - -
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Residues in contact with GLN1081 (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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457A HIS* 6.0 2.2 + - - -
521A GLN* 5.7 4.0 + - - +
836A LYS* 4.8 6.1 - - - +
1077A GLU* 3.4 18.4 + - - +
1078A PRO* 2.9 20.5 + - - +
1080A THR* 1.3 83.1 + - - +
1082A MET* 1.3 63.1 + - + +
1084A LEU* 4.6 3.7 - - - +
1085A ASN* 3.3 26.7 + - - +
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Residues in contact with MET1082 (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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1078A PRO 3.6 13.9 - - - +
1079A ALA* 2.9 9.8 + - - +
1081A GLN* 1.3 78.1 - - + +
1083A THR* 1.3 69.7 + - - +
1084A LEU 3.1 1.8 - - - -
1085A ASN* 2.6 26.6 + - + -
1086A THR* 2.8 30.1 + - + -
1100A GLY* 5.5 2.9 - - - -
1101A VAL 5.0 5.2 - - - +
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Residues in contact with THR1083 (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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836A LYS* 4.3 11.0 - - + -
839A GLU* 5.3 2.8 + - - -
840A THR* 5.0 2.7 - - + -
1079A ALA 2.9 9.8 + - - -
1080A THR* 2.9 31.9 - - - +
1082A MET* 1.3 73.6 - - - +
1084A LEU* 1.3 86.7 + - + +
1086A THR* 2.9 19.7 + - - +
1087A PHE* 3.4 7.8 + - - +
1101A VAL* 2.7 52.1 - - + +
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Residues in contact with LEU1084 (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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832A ASP* 3.4 33.0 - - + +
833A THR* 5.0 7.0 - - - +
836A LYS* 3.4 47.3 - - + +
1080A THR 3.9 3.6 + - - +
1081A GLN* 4.6 4.3 - - - +
1082A MET 2.8 3.0 + - - -
1083A THR* 1.3 84.4 - - + +
1085A ASN* 1.3 53.4 + - - +
1087A PHE* 2.8 7.3 + - - +
1088A HIS* 2.4 52.6 + - + +
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Residues in contact with ASN1085 (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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1081A GLN* 3.3 17.5 + - - +
1082A MET* 2.6 22.3 + - + +
1084A LEU* 1.3 70.3 - - - +
1086A THR* 1.3 55.1 + - + +
1087A PHE 2.4 20.4 + - - -
1088A HIS* 2.3 56.1 + - - +
1090A ALA* 4.8 2.1 - - - +
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Residues in contact with THR1086 (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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1082A MET* 2.8 43.9 + - + +
1083A THR* 2.9 15.0 + - - +
1085A ASN* 1.3 69.6 - - - +
1087A PHE* 1.3 70.8 + - - +
1090A ALA* 5.5 1.9 - - - +
1099A LEU* 4.7 8.0 - - - +
1100A GLY* 3.8 35.1 + - - -
1101A VAL* 4.8 0.2 - - - +
1102A PRO* 4.2 6.2 - - - +
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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
------------------------------------------------------------
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