Contacts of the strand formed by residues 980 - 985 (chain J) in PDB entry 6ALG
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 THR 980 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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960J LEU* 3.7 32.1 - - + -
961J SER 3.3 8.7 - - - +
962J ASN 3.1 6.4 + - - -
963J VAL* 3.6 13.1 - - + -
975J ILE* 3.3 23.5 - - + +
977J SER* 2.3 33.9 + - - -
978J ARG 3.1 3.8 + - - +
979J ASN* 1.3 77.3 - - - +
981J GLU* 1.3 60.4 + - - +
996J LYS* 4.1 3.4 - - - +
997J VAL* 3.0 33.1 + - + +
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Residues in contact with GLU 981 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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960J LEU* 3.0 12.0 - - - +
961J SER* 2.9 41.7 + - - +
979J ASN 3.8 2.2 + - - +
980J THR* 1.3 73.5 - - - +
982J LEU* 1.3 69.9 + - - +
983J LYS* 2.9 40.3 + - + -
994J SER* 3.2 21.1 + - - -
995J TYR 3.3 15.7 - - - +
996J LYS* 4.5 23.1 + - + +
997J VAL* 4.4 3.4 - - - -
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Residues in contact with LEU 982 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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950J ILE* 3.7 34.1 - - + -
952J VAL* 5.6 6.1 - - + -
958J ILE* 3.8 26.0 - - + -
960J LEU* 3.7 25.8 - - + -
981J GLU* 1.3 70.6 - - - +
983J LYS* 1.3 66.7 + - - +
984J LEU* 5.1 1.1 - - + +
993J GLU 3.6 0.3 - - - +
994J SER* 3.1 6.6 + - - -
995J TYR* 2.9 50.4 + - + +
997J VAL* 4.0 16.6 - - + +
1003J LEU* 6.2 2.7 - - + -
1017J VAL* 3.7 22.7 - - + -
1018J ALA* 5.7 0.2 - - + -
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Residues in contact with LYS 983 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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958J ILE* 3.7 3.6 - - - -
959J LYS* 2.9 44.7 + - + +
961J SER* 3.4 22.4 - - - +
981J GLU* 2.9 46.5 + - + +
982J LEU* 1.3 79.9 - - - +
984J LEU* 1.3 59.5 + - - +
985J ILE* 3.7 11.3 + - + -
991J THR* 3.9 29.5 + - + +
993J GLU 3.1 5.6 - - - +
994J SER* 3.9 6.1 + - - -
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Residues in contact with LEU 984 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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952J VAL* 3.8 17.7 - - + -
954J ASN* 3.7 37.0 - - + +
955J LYS 4.2 1.3 - - - +
956J GLY* 3.5 27.8 - - - +
957J SER 3.3 16.2 - - - +
958J ILE* 3.7 16.6 - - + -
982J LEU* 4.2 1.7 - - + +
983J LYS* 1.3 70.3 - - - +
985J ILE* 1.3 58.7 + - - +
991J THR 3.5 0.2 - - - -
992J LYS* 2.5 41.3 + - + +
993J GLU* 2.9 36.6 + - + +
1011J VAL* 4.7 3.4 - - + -
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Residues in contact with ILE 985 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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878J ASP* 5.4 0.2 - - - +
956J GLY* 3.5 5.2 - - - -
957J SER* 2.9 40.6 + - - +
959J LYS* 3.7 29.2 - - + +
983J LYS* 4.2 14.1 - - + +
984J LEU* 1.3 76.5 - - - +
986J ASP* 1.3 71.4 + - - +
989J GLY* 4.1 15.9 - - - +
990J ARG 3.3 12.1 - - - +
991J THR* 3.3 30.5 - - - +
992J LYS* 5.2 0.7 - - - -
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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