Contacts of the helix formed by residues 1064 - 1073 (chain A) in PDB entry 1Y8Z
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
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Residue Dist Surf HB Arom Phob DC
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1040A LYS* 5.6 0.5 - - - +
1058A PRO 4.7 0.2 - - - +
1059A VAL* 3.7 13.3 - - + +
1060A ILE* 2.7 55.2 + - + +
1061A LEU 4.5 0.2 - - - -
1062A ALA 3.8 0.2 - - - -
1063A LYS* 1.3 93.8 - - + +
1065A TYR* 1.3 65.5 + - - +
1066A ASP* 3.1 3.6 - - - +
1067A LYS* 3.1 32.7 + - + +
1068A ALA* 3.0 22.0 + - - +
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Residues in contact with TYR1065 (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 4.0 6.0 + - - -
1063A LYS 3.7 2.4 + - - -
1064A GLU* 1.3 75.5 - - - +
1066A ASP* 1.3 68.1 + - - +
1068A ALA* 3.2 6.7 + - - +
1069A LEU* 2.7 60.3 + - + +
1095A ASN* 3.6 43.5 - - + +
1098A LYS* 3.4 41.7 + - + +
1099A LEU* 3.7 18.8 - - + -
1102A ASN* 3.5 32.2 + - - +
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Residues in contact with ASP1066 (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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1064A GLU* 3.1 1.5 - - - -
1065A TYR* 1.3 92.5 + - - +
1067A LYS* 1.3 62.0 + - - +
1069A LEU* 3.4 6.4 + - - +
1070A LYS* 3.1 41.4 + - - +
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Residues in contact with LYS1067 (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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1057A ILE* 4.4 16.3 - - - +
1058A PRO* 3.0 28.5 + - - +
1059A VAL* 3.8 11.2 - - + -
1064A GLU* 3.1 38.4 + - + +
1066A ASP* 1.3 79.2 - - - +
1068A ALA* 1.3 63.5 + - - +
1070A LYS* 3.5 7.7 + - - +
1071A LEU* 3.2 33.9 + - + +
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Residues in contact with ALA1068 (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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1006A PHE* 5.5 1.1 - - + -
1037A VAL* 6.1 0.2 - - - -
1059A VAL* 3.8 24.0 - - + +
1061A LEU* 4.4 7.2 - - + -
1064A GLU 3.0 12.1 + - - +
1065A TYR* 3.5 10.1 - - - +
1067A LYS* 1.3 75.3 - - - +
1069A LEU* 1.3 65.6 + - - +
1071A LEU* 3.1 8.9 + - - +
1072A VAL* 3.0 28.4 + - + +
1099A LEU* 3.8 24.2 - - + -
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Residues in contact with LEU1069 (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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1065A TYR* 2.7 47.1 + - + +
1066A ASP* 3.7 8.1 - - - +
1067A LYS 3.3 0.2 - - - -
1068A ALA* 1.3 74.8 - - - +
1070A LYS* 1.3 64.7 + - + +
1072A VAL* 3.4 6.3 - - + +
1073A ASN* 3.1 52.8 + - - +
1099A LEU* 3.4 21.7 - - + +
1102A ASN* 3.8 26.5 - - + +
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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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1066A ASP* 3.1 30.1 + - - +
1067A LYS* 4.0 6.7 - - - +
1069A LEU* 1.3 78.1 - - + +
1071A LEU* 1.3 63.2 + - + +
1073A ASN* 3.9 3.7 - - - +
1074A ASP* 3.2 25.3 + - - +
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Residues in contact with LEU1071 (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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1002A ARG* 5.5 0.2 + - - -
1004A CYS* 4.2 10.2 - - - +
1035A THR* 5.1 8.2 + - + -
1037A VAL* 4.0 36.1 - - + -
1057A ILE* 4.0 37.0 - - + -
1059A VAL* 4.6 3.1 - - + -
1067A LYS* 3.2 34.1 + - + +
1068A ALA* 3.1 11.1 + - - +
1070A LYS* 1.3 76.8 - - + +
1072A VAL* 1.3 66.2 + - + +
1074A ASP* 3.0 22.7 + - + +
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Residues in contact with VAL1072 (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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1004A CYS* 4.3 11.4 - - - -
1006A PHE* 4.0 37.0 - - + -
1037A VAL* 5.8 1.8 - - + -
1068A ALA* 3.0 15.6 + - - +
1069A LEU* 3.4 19.5 - - + +
1071A LEU* 1.3 76.2 - - + +
1073A ASN* 1.3 61.0 + - - +
1074A ASP 3.3 0.2 - - - -
1075A CYS* 3.3 22.1 - - - -
1078A LEU* 4.0 22.9 - - + +
1099A LEU* 4.1 11.0 - - + -
1103A ILE* 4.1 22.5 - - + +
1107A ILE* 3.5 6.9 - - - +
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Residues in contact with ASN1073 (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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1069A LEU* 3.1 39.3 + - - +
1070A LYS* 3.9 4.3 - - - +
1072A VAL* 1.3 77.2 - - - +
1074A ASP* 1.3 57.5 + - - +
1075A CYS 3.2 9.8 + - - +
1102A ASN 3.1 22.2 + - - -
1103A ILE* 3.4 5.3 - - - +
1104A LYS* 2.7 65.9 + - + +
1107A ILE* 3.5 6.1 - - - +
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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