Contacts of the strand formed by residues 955 - 959 (chain A) in PDB entry 3LXK
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 ILE 955 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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909A CYS* 3.4 6.8 - - - -
910A LEU* 2.8 47.4 + - + -
933A ILE* 4.2 19.7 - - + -
950A LEU* 4.2 16.4 - - + -
951A ALA 3.6 16.6 - - - +
952A ALA* 3.1 14.1 + - - +
954A ASN* 1.3 86.6 - - + +
956A LEU* 1.3 58.6 + - - +
963A VAL* 3.7 29.6 - - + -
964A LYS 3.5 8.7 - - - +
965A ILE* 3.9 27.8 - - + -
1016A VAL* 5.2 1.8 - - + -
1125A MI1 3.9 3.4 - - - +
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Residues in contact with LEU 956 (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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884A VAL* 3.9 9.6 - - + -
905A LEU* 3.7 34.3 - - + +
908A GLY* 3.3 29.6 - - - +
909A CYS* 4.3 0.4 - - - +
955A ILE* 1.3 73.8 - - - +
957A VAL* 1.3 63.7 + - - +
958A GLU 3.7 0.7 + - - -
963A VAL* 3.2 6.1 - - - +
964A LYS* 2.8 36.2 + - + +
966A ALA* 3.4 20.9 - - + -
1125A MI1 3.5 59.5 - - + +
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Residues in contact with VAL 957 (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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905A LEU* 3.7 15.8 - - - +
907A SER* 3.5 21.5 + - - -
908A GLY 2.9 23.2 + - - +
910A LEU* 3.8 24.0 - - + -
913A PHE* 3.6 49.8 - - + -
929A TYR* 5.3 0.7 - - - +
956A LEU* 1.3 75.1 - - - +
958A GLU* 1.3 60.2 + - - +
959A SER 3.2 30.1 - - - +
962A HIS 3.8 3.6 - - - +
963A VAL* 4.2 4.3 - - + -
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Residues in contact with GLU 958 (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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885A LYS* 5.1 5.7 + - - -
903A GLU* 4.7 2.1 - - - +
905A LEU* 3.6 33.2 - - + +
906A PRO* 6.0 1.6 - - - +
907A SER* 4.9 3.8 + - - -
956A LEU 3.7 3.2 + - - -
957A VAL* 1.3 74.7 - - - +
959A SER* 1.3 64.5 + - - +
962A HIS* 2.8 54.2 + - + +
964A LYS* 2.8 29.5 + - + -
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Residues in contact with SER 959 (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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907A SER* 5.2 3.8 - - - -
913A PHE* 4.9 0.4 - - - -
929A TYR* 4.6 1.0 + - - -
957A VAL* 3.2 16.9 - - - +
958A GLU* 1.3 81.4 - - - +
960A GLU* 1.3 65.4 + - - +
961A ALA* 2.9 16.0 + - - +
962A HIS* 3.0 30.5 + - - +
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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