Contacts of the helix formed by residues 1068 - 1080 (chain A) in PDB entry 4QMH
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 SER1068 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1031A CYS* 3.7 29.3 - - - +
1067A ALA* 1.3 80.0 - - - +
1069A LYS* 1.3 66.0 + - - +
1070A LYS* 3.1 3.6 - - - +
1071A ASP* 3.0 18.2 + - - -
1072A ILE* 3.0 21.3 + - - +
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Residues in contact with LYS1069 (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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1061A LEU* 2.8 60.5 + - + +
1062A ASP* 3.8 16.5 + - - +
1065A LYS* 4.0 18.1 - - - +
1066A PRO* 4.3 7.8 - - - +
1067A ALA 3.3 3.1 - - - -
1068A SER* 1.3 76.7 - - - +
1070A LYS* 1.3 58.9 + - + +
1072A ILE* 3.3 1.7 + - - +
1073A LEU* 2.9 32.3 + - + +
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Residues in contact with LYS1070 (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 SER* 3.1 1.2 - - - -
1069A LYS* 1.3 79.6 - - + +
1071A ASP* 1.3 61.9 + - - +
1073A LEU* 3.9 6.4 - - - +
1074A ALA* 3.0 27.2 + - - +
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Residues in contact with ASP1071 (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 ILE* 4.8 7.2 - - + +
1031A CYS* 4.5 11.7 - - - -
1068A SER* 3.0 25.8 + - - +
1070A LYS* 1.3 78.1 - - - +
1072A ILE* 1.3 65.5 + - - +
1074A ALA* 3.3 8.0 + - - +
1075A ALA* 3.0 22.7 + - - +
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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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1027A TYR* 3.5 59.9 - - + +
1030A ILE* 4.8 9.0 - - + -
1031A CYS* 5.0 4.7 - - - -
1061A LEU* 3.7 19.3 - - + -
1066A PRO* 3.3 26.2 - - + -
1067A ALA 3.3 25.1 - - - +
1068A SER* 3.0 11.0 + - - +
1069A LYS 3.8 4.9 - - - +
1071A ASP* 1.3 72.9 - - - +
1073A LEU* 1.3 65.4 + - - +
1075A ALA* 3.1 8.4 + - - +
1076A LEU* 3.0 23.7 + - + +
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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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1054A PHE* 4.5 10.1 - - + -
1058A ASN* 3.6 24.0 - - - +
1061A LEU* 4.0 13.9 - - + +
1069A LYS* 2.9 20.2 + - + +
1070A LYS* 3.9 5.8 - - - +
1072A ILE* 1.3 77.0 - - - +
1074A ALA* 1.3 58.4 + - - +
1076A LEU* 3.1 6.8 + - + -
1077A GLU* 2.8 57.4 + - + +
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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
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1070A LYS 3.0 19.8 + - - +
1071A ASP* 3.5 10.5 - - - +
1072A ILE 3.2 0.2 - - - -
1073A LEU* 1.3 76.9 - - - +
1075A ALA* 1.3 57.2 + - - +
1077A GLU* 3.3 12.8 + - - +
1078A LYS* 2.9 30.0 + - - +
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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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1030A ILE* 4.1 24.2 - - + -
1042A ASN* 4.1 15.0 - - - +
1045A VAL* 3.8 12.7 - - + +
1071A ASP 3.0 13.4 + - - +
1072A ILE 3.4 8.7 - - - +
1074A ALA* 1.3 72.9 - - - +
1076A LEU* 1.3 65.2 + - + +
1078A LYS* 3.3 9.4 + - - +
1079A ALA* 3.1 23.2 + - - +
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Residues in contact with LEU1076 (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 TYR* 3.8 23.8 - - + +
1030A ILE* 6.1 0.4 - - + -
1045A VAL* 4.3 7.6 - - + -
1049A MET* 3.5 21.1 - - + +
1054A PHE* 3.8 15.8 - - + +
1057A MET* 3.6 34.1 - - + +
1058A ASN* 4.0 30.5 - - + +
1061A LEU* 4.3 15.5 - - + -
1072A ILE* 3.0 20.5 + - + +
1073A LEU* 3.6 8.7 - - + +
1075A ALA* 1.3 76.6 - - + +
1077A GLU* 1.3 61.7 + - - +
1079A ALA 3.3 1.0 + - - -
1080A ARG* 3.1 22.0 + - - +
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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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1054A PHE* 4.4 14.4 - - + -
1073A LEU* 2.8 49.3 + - + +
1074A ALA* 3.7 10.7 - - - +
1075A ALA 3.2 0.2 - - - -
1076A LEU* 1.3 76.6 - - - +
1078A LYS* 1.3 58.3 + - - +
1080A ARG* 3.9 6.4 - - - +
1081A PRO* 3.1 25.3 - - - +
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Residues in contact with LYS1078 (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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1074A ALA 2.9 17.0 + - - +
1075A ALA* 3.7 9.4 - - - +
1076A LEU 3.3 0.2 - - - -
1077A GLU* 1.3 77.5 - - - +
1079A ALA* 1.3 59.0 + - - +
1081A PRO* 3.5 13.8 - - - +
1082A ASN* 3.6 11.9 + - - +
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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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1045A VAL* 3.7 22.2 - - + -
1046A LEU* 3.6 27.9 - - + +
1049A MET* 4.2 6.5 - - + -
1075A ALA 3.1 15.8 + - - +
1076A LEU 3.9 2.7 - - - +
1077A GLU 3.3 0.2 - - - -
1078A LYS* 1.3 77.7 - - - +
1080A ARG* 1.3 67.9 + - - +
1081A PRO 3.3 0.2 - - - -
1082A ASN* 2.8 23.8 + - - +
1083A LEU 3.6 3.3 + - - -
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Residues in contact with ARG1080 (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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1049A MET* 3.9 9.9 - - - -
1054A PHE* 3.7 58.2 - - + +
1055A ASP* 4.5 6.5 + - - -
1076A LEU 3.1 16.6 + - - +
1077A GLU* 3.9 7.0 - - - +
1079A ALA* 1.3 76.2 - - - +
1081A PRO* 1.3 70.4 - - + +
1082A ASN 3.0 1.4 + - - -
1083A LEU* 3.1 25.6 + - + +
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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