Contacts of the strand formed by residues 6115 - 6119 (chain D) in PDB entry 1LD4
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 LEU6115 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6114D ARG* 1.3 82.9 + - - +
6116D PHE* 1.3 70.5 + - - +
6128D HIS* 3.7 36.6 - - + -
6129D ALA 3.1 16.4 - - - +
6130D LEU* 3.8 21.8 - - + -
6178D PHE* 5.3 3.8 - - + -
6216D GLY 3.9 10.8 - - - +
6217D ARG* 4.0 22.7 - - - +
6218D PRO* 4.0 13.7 - - + -
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Residues in contact with PHE6116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6114D ARG* 3.6 29.8 - - - -
6115D LEU* 1.3 78.3 - - - +
6117D ASP* 1.3 62.5 + - - +
6128D HIS* 3.2 9.2 - - - +
6129D ALA* 2.9 43.9 + - + +
6130D LEU 5.1 0.7 - - - -
6131D ALA* 4.2 12.8 - - + -
6146D ILE* 4.1 19.1 - - + -
6147D ASP 4.6 7.0 - - - +
6148D HIS* 3.7 36.1 - + + -
6151D LEU* 3.8 24.2 - - + -
6173D MET* 4.1 13.9 - - - -
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Residues in contact with ASP6117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6116D PHE* 1.3 74.3 - - - +
6118D VAL* 1.3 58.1 + - - +
6119D LYS* 3.3 29.6 + - + +
6125D VAL* 3.7 28.2 - - + +
6127D GLY 3.8 4.0 - - - -
6128D HIS* 3.7 13.2 + - - -
6146D ILE* 3.4 4.0 - - - +
6147D ASP* 2.7 46.6 + - + +
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Residues in contact with VAL6118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6117D ASP* 1.3 76.5 - - - +
6119D LYS* 1.3 59.3 + - - +
6125D VAL* 3.5 3.6 - - - -
6126D ILE* 2.9 27.4 + - + +
6127D GLY 2.9 22.7 + - - +
6128D HIS 3.7 22.4 - - - +
6129D ALA* 3.9 3.1 - - + +
6138D LYS* 4.1 20.4 - - - -
6142D VAL* 3.8 18.6 - - + -
6144D GLY* 3.5 37.7 - - - +
6145D THR 3.2 5.6 - - - +
6146D ILE* 4.3 10.1 - - + +
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Residues in contact with LYS6119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6117D ASP* 3.3 30.9 + - + +
6118D VAL* 1.3 76.2 - - - +
6120D ASN* 1.3 68.2 + - - +
6123D GLY* 3.2 30.5 - - - +
6124D ASP 3.2 7.9 - - - +
6125D VAL* 4.0 7.5 - - - +
6126D ILE* 4.3 1.1 - - - -
6144D GLY* 3.3 6.2 - - - -
6145D THR* 2.8 40.3 + - - +
6147D ASP* 3.3 31.5 + - + +
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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