Contacts of the strand formed by residues 1010 - 1018 (chain A) in PDB entry 1DJO
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 ALA1010 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1008A LYS 3.9 1.4 + - - -
1009A LEU* 1.3 76.1 - - - +
1011A ASN* 1.3 61.2 + - - +
1012A VAL* 3.9 2.5 - - + -
1054A LEU 4.7 1.2 + - - -
1055A ALA* 3.0 22.8 - - + +
1056A ASN* 3.1 10.7 + - - +
1092A ASP* 3.4 23.1 - - + +
1148A SER* 4.0 36.8 - - - +
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Residues in contact with ASN1011 (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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1009A LEU 4.7 3.3 + - - -
1010A ALA* 1.3 72.0 - - - +
1012A VAL* 1.3 60.4 + - - +
1013A VAL* 5.4 1.1 - - + -
1056A ASN* 3.5 29.0 + - - +
1089A ASN 5.1 2.0 + - - -
1090A ASP* 3.2 35.2 + - - +
1091A VAL* 3.8 2.8 - - - -
1092A ASP* 2.8 48.5 + - - +
1093A GLY 3.3 4.5 + - - +
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Residues in contact with VAL1012 (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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1010A ALA* 4.5 3.1 - - + -
1011A ASN* 1.3 79.1 - - - +
1013A VAL* 1.3 74.2 + - - +
1014A ILE* 5.1 1.7 - - + +
1055A ALA* 4.3 6.1 - - + -
1056A ASN 3.0 10.7 + - - +
1057A VAL* 3.2 34.5 - - + +
1058A ARG* 3.4 4.4 + - - +
1093A GLY 3.3 19.5 - - - +
1095A VAL* 4.1 11.9 - - + -
1144A VAL* 4.8 9.0 - - + +
1147A ALA* 4.0 28.3 - - + +
1148A SER* 3.4 27.8 - - - +
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Residues in contact with VAL1013 (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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1011A ASN* 5.4 0.7 - - + -
1012A VAL* 1.3 77.2 - - - +
1014A ILE* 1.3 66.0 + - - +
1015A LEU* 4.0 23.3 - - + -
1058A ARG* 3.6 36.3 - - + +
1060A GLU* 4.3 11.7 - - + +
1085A LEU* 4.4 14.4 - - + -
1090A ASP 5.3 1.1 - - - +
1091A VAL* 3.7 32.3 - - + -
1093A GLY 3.2 6.9 + - - +
1094A ILE* 3.6 8.2 - - + +
1095A VAL 2.9 25.8 + - - +
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Residues in contact with ILE1014 (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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1012A VAL* 5.1 1.8 - - + +
1013A VAL* 1.3 74.8 - - - +
1015A LEU* 1.3 64.5 + - - +
1016A ALA 3.6 0.6 + - - +
1041A VAL* 3.9 20.3 - - + +
1044A LEU* 6.1 0.9 - - + -
1045A ILE* 4.0 23.3 - - + -
1051A LEU* 4.4 7.6 - - + -
1057A VAL* 4.7 9.0 - - + -
1058A ARG 3.1 12.5 + - - +
1059A GLY* 3.6 1.0 - - - -
1060A GLU* 3.0 27.5 + - - +
1095A VAL* 3.2 22.2 - - + +
1097A THR* 4.2 23.6 - - + -
1140A LEU* 3.9 23.6 - - + -
1144A VAL* 4.1 15.3 - - + -
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Residues in contact with LEU1015 (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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1013A VAL* 4.0 20.2 - - + -
1014A ILE* 1.3 71.2 - - - +
1016A ALA* 1.3 62.6 + - - +
1017A THR* 5.4 0.4 - - + -
1060A GLU* 3.5 25.1 - - + +
1062A VAL* 4.1 15.7 - - + -
1078A LEU* 4.5 5.8 - - + -
1081A ARG* 4.2 18.6 - - + -
1082A VAL* 3.9 26.0 - - + -
1085A LEU* 4.8 7.6 - - + -
1094A ILE* 3.8 27.6 - - + -
1095A VAL 2.7 11.4 + - - +
1096A ILE* 3.3 17.5 - - + +
1097A THR* 3.1 21.2 + - - -
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Residues in contact with ALA1016 (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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1014A ILE* 3.6 2.2 + - + -
1015A LEU* 1.3 73.4 - - - +
1017A THR* 1.3 62.3 + - - +
1018A GLY 4.8 1.1 - - - +
1039A VAL 5.9 0.4 - - - +
1041A VAL* 3.5 33.2 - - + +
1044A LEU* 5.1 4.5 - - + -
1060A GLU 2.9 8.8 + - - +
1061A GLN* 3.3 20.0 - - - +
1062A VAL* 3.0 25.6 + - - +
1063A MET 3.4 4.0 + - - +
1097A THR* 3.1 14.6 - - - +
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Residues in contact with THR1017 (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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1015A LEU 4.0 2.0 - - - +
1016A ALA* 1.3 78.0 - - - +
1018A GLY* 1.3 58.3 + - - +
1062A VAL* 4.8 3.4 - - + -
1063A MET* 3.1 31.6 - - + +
1065A ILE* 3.1 32.5 + - - +
1078A LEU* 3.9 23.1 - - + -
1096A ILE* 3.8 19.7 - - + -
1097A THR* 2.5 25.3 + - - +
1098A HIS* 3.3 20.9 - - + +
1099A GLY 4.4 1.0 + - - -
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Residues in contact with GLY1018 (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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1016A ALA* 3.8 1.6 - - - +
1017A THR* 1.3 82.5 + - - +
1019A GLY* 1.3 63.9 + - - -
1021A ILE* 3.5 19.9 - - - +
1022A ALA* 3.8 9.3 - - - +
1037A ALA* 4.1 3.4 - - - -
1061A GLN* 4.3 1.0 - - - +
1063A MET 3.7 1.2 + - - -
1064A GLN* 3.5 22.3 + - - -
1065A ILE 3.6 4.0 - - - -
1097A THR* 4.4 6.0 + - - +
1098A HIS 4.5 0.2 - - - -
1099A GLY 4.4 5.9 + - - -
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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