Contacts of the strand formed by residues 1142 - 1144 (chain E) in PDB entry 3DLS
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 ILE1142 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063E ASN* 3.0 31.2 + - + +
1090E LEU* 4.4 4.0 - - + -
1108E ILE* 3.7 29.6 - - + +
1111E GLN* 3.3 25.4 + - + +
1112E LEU* 3.7 32.3 - - + +
1115E ALA* 5.9 0.2 - - + -
1134E ILE* 3.9 19.3 - - + -
1135E VAL 3.0 6.5 - - - +
1136E ILE* 3.6 25.8 - - + -
1140E PHE 3.8 5.2 - - - +
1141E THR* 1.3 79.3 - - - +
1143E LYS* 1.3 68.1 + - - +
1144E LEU* 4.9 2.7 - - + +
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Residues in contact with LYS1143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061E HIS 5.3 0.2 - - - -
1062E ALA 3.1 24.7 + - - +
1063E ASN 3.3 1.3 - - - -
1064E ILE 3.9 3.6 - - - -
1065E ILE* 3.7 44.4 - - + +
1082E GLU* 3.5 20.4 - - - -
1084E HIS* 3.4 39.4 + - + +
1134E ILE* 3.4 5.8 - - - -
1135E VAL* 2.7 38.8 + - + +
1141E THR* 3.8 10.9 - - - +
1142E ILE* 1.3 78.8 - - - +
1144E LEU* 1.3 61.9 + - - +
1145E ILE* 3.4 3.7 + - + +
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Residues in contact with LEU1144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063E ASN 2.7 17.6 + - - +
1064E ILE* 3.9 6.0 - - + +
1065E ILE* 3.4 16.3 + - - +
1112E LEU* 4.1 18.2 - - + -
1115E ALA* 4.0 17.9 - - + -
1116E VAL* 4.7 7.2 - - + -
1119E LEU* 3.7 29.6 - - + -
1126E HIS* 3.8 31.2 - - + +
1129E ILE* 4.4 9.6 - - + -
1133E ASN 3.7 16.2 - - - +
1134E ILE* 4.1 15.9 - - + +
1142E ILE* 4.9 2.5 - - + +
1143E LYS* 1.3 68.9 - - - +
1145E ILE* 1.3 59.1 + - - +
1147E PHE* 3.3 17.1 - - + -
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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