Contacts of the helix formed by residues 1062 - 1077 (chain A) in PDB entry 4QMI
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 LYS1062 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1028A GLU* 5.2 1.9 + - - -
1061A LEU* 1.3 73.6 - - - +
1063A PRO* 1.4 64.8 - - + -
1064A THR* 2.8 31.7 + - + +
1065A SER* 2.8 27.7 + - - +
1066A LYS 2.7 29.8 + - - -
1068A GLN* 5.9 0.2 - - - +
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Residues in contact with PRO1063 (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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1061A LEU 3.8 1.7 - - - +
1062A LYS* 1.4 88.5 - - + +
1064A THR* 1.3 62.9 + - + +
1066A LYS* 3.7 20.8 - - + +
1067A ASP* 3.0 28.6 + - - +
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Residues in contact with THR1064 (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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1062A LYS* 2.8 27.5 + - + +
1063A PRO* 1.3 80.6 - - + +
1065A SER* 1.3 75.0 + - - +
1067A ASP* 3.3 6.6 + - - +
1068A GLN* 3.3 32.1 + - - +
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Residues in contact with SER1065 (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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1028A GLU* 2.7 35.5 + - - -
1061A LEU* 4.1 18.2 - - - -
1062A LYS* 2.8 35.2 + - - +
1064A THR* 1.3 78.5 + - - +
1066A LYS* 1.3 67.0 + - - +
1068A GLN* 3.2 7.0 + - - +
1069A VAL* 3.0 26.9 + - - +
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Residues in contact with LYS1066 (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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1058A THR* 3.4 31.6 - - - +
1059A GLY* 4.1 15.0 + - - -
1061A LEU* 3.3 32.0 + - + +
1062A LYS 2.7 17.0 + - - +
1063A PRO* 3.7 22.4 - - + +
1065A SER* 1.3 71.3 - - - +
1067A ASP* 1.3 62.8 + - - +
1069A VAL* 4.0 0.7 - - - +
1070A LEU* 3.1 45.5 + - + +
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Residues in contact with ASP1067 (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 PRO 3.0 19.0 + - - +
1064A THR* 3.6 7.9 - - - +
1065A SER 3.1 0.4 - - - -
1066A LYS* 1.3 81.3 - - - +
1068A GLN* 1.3 63.7 + - - +
1070A LEU* 3.7 6.4 + - - +
1071A ALA* 3.3 21.8 + - - +
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Residues in contact with GLN1068 (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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1027A LEU 5.3 0.3 - - - +
1028A GLU* 3.0 38.2 + - - +
1064A THR* 3.3 20.2 + - - +
1065A SER* 3.2 19.1 + - - +
1067A ASP* 1.3 76.4 + - - +
1069A VAL* 1.3 65.6 + - + +
1071A ALA* 3.1 9.5 + - - +
1072A MET* 2.9 39.5 + - + +
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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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1024A TYR* 3.7 46.0 - - + +
1027A LEU* 4.1 20.0 - - + -
1028A GLU* 4.1 11.2 - - + +
1058A THR* 3.8 10.1 - - + -
1061A LEU* 3.7 17.5 - - + -
1065A SER 3.0 18.2 + - - +
1066A LYS 4.0 2.2 - - - +
1068A GLN* 1.3 76.8 - - + +
1070A LEU* 1.3 56.6 + - - +
1072A MET* 3.1 10.1 + - - +
1073A LEU* 2.8 31.9 + - + +
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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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1051A TYR* 4.3 10.1 - - - +
1055A ALA* 4.0 25.4 - - + +
1058A THR* 3.7 23.8 - - + +
1066A LYS* 3.1 40.7 + - + +
1067A ASP* 3.9 7.2 - - - +
1069A VAL* 1.3 74.7 - - - +
1071A ALA* 1.3 56.7 + - - +
1073A LEU* 3.1 8.0 + - + +
1074A GLU* 2.9 41.2 + - + +
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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
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1067A ASP* 3.3 13.4 + - - +
1068A GLN* 3.1 13.1 + - - +
1070A LEU* 1.3 77.5 - - - +
1072A MET* 1.3 63.8 + - + +
1074A GLU* 3.5 11.0 + - - +
1075A LYS* 3.2 32.8 + - - +
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Residues in contact with MET1072 (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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1027A LEU* 3.8 46.4 - - + +
1028A GLU* 6.3 0.2 - - + -
1039A GLN* 4.1 26.9 - - + +
1042A LEU* 3.7 19.1 - - + +
1068A GLN* 2.9 29.3 + - + +
1069A VAL* 3.4 10.8 - - - +
1071A ALA* 1.3 76.7 - - - +
1073A LEU* 1.3 62.2 + - - +
1075A LYS* 3.4 8.4 + - - +
1076A ALA* 3.3 21.7 + - - +
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Residues in contact with LEU1073 (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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1024A TYR* 3.7 25.4 - - + +
1042A LEU* 3.8 28.7 - - + -
1046A MET* 3.5 28.0 - - + +
1051A TYR* 3.8 14.5 - - + -
1054A MET* 3.8 24.5 - - + +
1055A ALA* 3.8 12.3 - - + +
1058A THR* 4.0 12.3 - - + -
1069A VAL* 2.8 18.1 + - + +
1070A LEU* 3.1 14.6 + - + +
1072A MET* 1.3 75.4 - - - +
1074A GLU* 1.3 63.4 + - - +
1076A ALA* 3.2 2.5 + - - +
1077A LYS* 3.1 19.6 + - - +
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Residues in contact with GLU1074 (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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1051A TYR* 2.4 38.0 + - - -
1070A LEU* 2.9 36.4 + - + +
1071A ALA* 3.7 10.3 - - - +
1072A MET 3.4 0.4 - - - -
1073A LEU* 1.3 76.0 - - - +
1075A LYS* 1.3 67.9 + - + +
1077A LYS* 3.2 30.3 + - - +
1078A VAL* 3.7 7.1 + - - +
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Residues in contact with LYS1075 (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 ALA* 3.2 21.6 + - - +
1072A MET* 3.4 9.6 + - - +
1073A LEU 3.2 0.2 - - - -
1074A GLU* 1.3 81.9 - - - +
1076A ALA* 1.3 56.0 + - - +
1078A VAL* 3.2 30.1 - - + +
1079A ASN* 4.0 4.3 - - - +
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Residues in contact with ALA1076 (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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1042A LEU* 4.5 9.0 - - + -
1043A PRO* 4.1 31.8 - - + +
1046A MET* 4.1 13.5 - - + -
1072A MET 3.3 14.0 + - - +
1073A LEU 3.2 7.4 + - - +
1075A LYS* 1.3 73.5 - - - +
1077A LYS* 1.3 56.7 + - - +
1078A VAL 3.1 5.6 - - - -
1079A ASN* 3.2 20.7 + - - +
1080A MET* 3.6 18.5 - - - +
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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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1046A MET* 3.9 4.9 - - - -
1051A TYR* 3.9 48.9 - - + -
1052A GLU* 5.1 3.2 + - - -
1073A LEU 3.1 10.6 + - - +
1074A GLU* 3.2 22.2 + - - +
1075A LYS 3.2 0.4 - - - -
1076A ALA* 1.3 75.4 - - - +
1078A VAL* 1.3 63.2 - - - +
1080A MET* 3.5 26.5 + - + +
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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