Contacts of the helix formed by residues 1062 - 1073 (chain A) in PDB entry 4Z4Q
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 SER1062 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1060A ARG 3.3 3.1 + - - -
1061A LYS* 1.3 72.6 - - - +
1063A ALA* 1.3 62.3 + - - +
1065A SER* 3.3 8.3 + - - -
1066A VAL* 3.0 26.3 + - - +
1082A TYR* 3.6 20.7 - - - -
1085A MET* 4.7 5.1 - - - +
1101A MET* 4.1 8.1 - - - +
1116A MET* 3.6 8.3 - - - -
1119A THR* 2.5 44.5 + - - -
1120A GLU* 3.7 8.3 + - - -
1121A ALA* 4.2 3.0 - - - +
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Residues in contact with ALA1063 (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 LYS* 3.1 3.2 - - + +
1062A SER* 1.3 76.1 - - - +
1064A LYS* 1.3 61.8 + - - +
1066A VAL* 3.9 0.9 - - - +
1067A GLY* 3.1 21.5 + - - -
1116A MET* 3.1 45.9 + - + +
1117A ARG* 4.7 0.2 - - - -
1063B ALA 5.1 0.2 - - - +
1067B GLY* 3.9 11.2 - - - -
1070B MET* 3.9 32.3 - - + -
1078B ASP* 5.8 0.2 - - + -
1116B MET* 6.2 0.4 - - + -
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Residues in contact with LYS1064 (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 ARG* 4.5 30.0 - - + +
1061A LYS* 2.9 15.2 + - + +
1063A ALA* 1.3 78.0 - - - +
1065A SER* 1.3 63.9 + - - +
1067A GLY* 3.6 0.5 + - - -
1068A ASN* 3.2 33.6 + - - +
1067B GLY 3.5 22.4 + - - +
1068B ASN* 3.7 26.0 - - - +
1071B GLY* 4.4 16.6 - - - -
1072B ASN* 3.0 31.9 + - - +
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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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1047A SER* 4.5 0.9 + - - -
1048A MET* 4.4 18.4 - - - +
1051A ASP* 5.7 1.3 - - - -
1053A ASN* 3.5 22.2 + - - -
1060A ARG* 4.4 6.0 + - - +
1061A LYS 3.5 9.5 + - - -
1062A SER* 3.3 9.0 + - - -
1064A LYS* 1.3 79.1 - - - +
1066A VAL* 1.3 63.5 + - - +
1068A ASN* 3.1 11.7 + - - +
1069A ILE* 3.0 27.4 + - - +
1085A MET* 4.4 16.7 - - - -
1121A ALA* 5.3 2.3 + - - +
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Residues in contact with VAL1066 (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 SER 3.0 16.9 + - - +
1063A ALA 3.9 3.6 - - - +
1065A SER* 1.3 79.7 - - - +
1067A GLY* 1.3 57.9 + - - +
1069A ILE* 3.2 10.1 + - - +
1070A MET* 3.0 33.1 + - + +
1078A ASP* 3.9 23.1 - - + +
1081A ILE* 4.2 13.4 - - + +
1082A TYR* 4.1 34.8 - - + -
1085A MET* 4.2 9.9 - - - -
1116A MET* 3.8 22.2 - - + -
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Residues in contact with GLY1067 (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 ALA 3.1 15.8 + - - -
1064A LYS 4.1 0.9 - - - -
1066A VAL* 1.3 76.2 - - - +
1068A ASN* 1.3 61.0 + - - +
1070A MET* 3.8 6.0 - - - +
1071A GLY 2.8 24.6 + - - -
1063B ALA* 3.9 25.4 - - - -
1064B LYS* 3.5 18.8 + - - +
1067B GLY* 5.6 0.7 - - - -
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Residues in contact with ASN1068 (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 SER* 4.1 7.1 + - - +
1051A ASP* 3.2 29.8 + - - +
1060A ARG* 6.2 1.0 - - - +
1064A LYS* 3.2 32.2 + - - +
1065A SER* 3.1 12.6 + - - +
1067A GLY* 1.3 78.2 - - - +
1069A ILE* 1.3 56.6 + - - +
1072A ASN* 3.0 41.2 + - - +
1064B LYS* 3.7 24.1 - - - +
1068B ASN* 3.7 15.5 + - - +
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Residues in contact with ILE1069 (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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1040A VAL* 5.6 0.4 - - + +
1043A ARG* 4.1 15.9 - - + +
1044A ILE* 3.8 36.6 - - + +
1047A SER* 3.6 24.5 - - - +
1048A MET* 5.0 2.2 - - + -
1065A SER* 3.0 31.0 + - - +
1066A VAL* 3.2 6.9 + - + +
1068A ASN* 1.3 75.8 - - - +
1070A MET* 1.3 56.0 + - - +
1073A PHE* 2.8 32.2 + - + -
1074A HIS* 3.0 32.2 + - + +
1081A ILE* 3.7 24.0 - - + -
1085A MET* 5.3 2.0 - - - -
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Residues in contact with MET1070 (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 VAL* 3.0 21.6 + - + +
1067A GLY* 3.8 4.5 - - - +
1069A ILE* 1.3 78.8 - - - +
1071A GLY* 1.3 60.3 + - - +
1072A ASN 3.6 0.2 + - - -
1074A HIS 3.4 17.3 - - - +
1075A PRO* 4.6 3.0 - - + +
1076A HIS 3.6 20.6 - - - +
1078A ASP* 3.1 46.2 - - + +
1081A ILE* 3.9 4.9 - - + -
1145A PHE* 3.9 11.4 - - - -
1061B LYS* 4.2 19.1 - - + +
1063B ALA* 3.8 26.0 - - + -
1117B ARG* 4.0 22.9 - - - +
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Residues in contact with GLY1071 (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 GLY 2.8 21.2 + - - -
1068A ASN 4.1 0.4 - - - -
1070A MET* 1.3 74.3 - - - +
1072A ASN* 1.3 66.9 + - - +
1145A PHE* 3.6 13.0 - - - -
1146A ASP* 4.0 12.6 - - - +
1061B LYS* 4.1 21.0 - - - +
1064B LYS* 4.4 10.3 - - - +
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Residues in contact with ASN1072 (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 SER* 5.2 0.6 + - - -
1050A LYS* 5.9 1.4 - - - +
1051A ASP* 5.8 2.2 + - - -
1068A ASN* 3.0 28.5 + - - +
1071A GLY* 1.3 86.3 - - - +
1073A PHE* 1.3 86.8 + - + +
1144A ASN* 2.8 31.4 + - - +
1145A PHE* 3.9 4.7 - - - -
1149A GLU* 3.7 21.2 + - - +
1064B LYS* 3.1 30.9 + - - +
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Residues in contact with PHE1073 (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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1043A ARG* 3.6 39.5 + - + -
1046A TYR* 3.8 22.0 - + - -
1047A SER* 3.8 35.9 - - - -
1050A LYS* 4.6 3.4 - - + -
1069A ILE* 2.8 17.2 + - - +
1072A ASN* 1.3 100.7 - - + +
1074A HIS* 1.3 58.3 + - - +
1075A PRO* 3.5 4.7 - - - +
1144A ASN* 4.5 2.9 - - + -
1145A PHE* 3.4 20.4 - - - -
1149A GLU* 3.4 30.3 - - + -
1150A LYS 4.0 8.5 - - - -
1151A GLU* 3.7 38.9 - - + +
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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