Contacts of the strand formed by residues 946 - 950 (chain Z) in PDB entry 5WTI
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 LEU 946 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B U 3.8 8.5 + - - -
928Z LEU* 6.0 0.7 - - + -
938Z ILE* 4.9 13.5 - - + -
939Z SER 3.4 8.3 - - - +
940Z LEU* 3.5 21.0 - - + +
945Z LYS* 1.3 81.3 - - - +
947Z VAL* 1.3 64.0 + - - +
948Z THR* 5.0 9.9 - - - +
1086Z LEU* 4.5 9.2 - - + +
1089Z LYS* 3.7 27.0 - - + +
1090Z LEU* 4.2 33.4 - - + +
1093Z GLN* 5.9 4.0 - - + -
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Residues in contact with VAL 947 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B U 3.6 29.2 - - - +
882Z HIS* 4.0 30.3 - - + +
884Z LYS* 5.0 4.7 - - - +
937Z PHE* 3.7 1.5 - - + +
938Z ILE* 3.1 7.6 - - - +
939Z SER* 2.9 61.5 + - - +
940Z LEU* 3.7 11.0 - - - +
941Z SER* 4.4 7.0 - - - +
945Z LYS 4.6 2.0 - - - +
946Z LEU* 1.3 75.2 - - - +
948Z THR* 1.3 66.8 + - - +
949Z THR* 4.3 1.3 - - - +
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Residues in contact with THR 948 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B C 2.6 45.5 + - - +
13B U 2.7 23.7 + - - +
928Z LEU* 4.3 11.0 - - + +
936Z LYS* 3.7 31.9 - - + -
937Z PHE 3.4 4.0 - - - +
938Z ILE* 3.5 18.6 - - + +
946Z LEU* 5.0 7.6 - - - +
947Z VAL* 1.3 74.4 - - - +
949Z THR* 1.3 63.2 + - - +
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Residues in contact with THR 949 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B C 4.5 2.9 - - - -
13B U 3.9 8.5 + - - -
14B U 3.4 34.9 + - - -
882Z HIS* 4.6 9.6 - - + -
936Z LYS* 3.4 11.7 - - - +
937Z PHE* 2.8 51.9 + - + +
947Z VAL* 5.3 1.3 - - + -
948Z THR* 1.3 75.2 - - - +
950Z HIS* 1.3 76.2 + - - +
954Z ASN* 3.7 20.4 + - + +
957Z GLN* 5.5 1.7 + - - -
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Residues in contact with HIS 950 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B U 3.6 21.5 + - - +
19B U 3.5 38.5 + - - +
20B C 4.8 2.7 + - - -
579Z GLN* 3.8 8.0 + - - -
617Z ASN* 3.3 29.0 + - - -
935Z GLU* 3.7 20.5 + - + +
936Z LYS* 4.8 2.9 - - - +
949Z THR* 1.3 76.8 + - - +
951Z ALA* 1.3 60.3 + - - +
952Z ASP* 3.2 25.3 + - + -
953Z ILE* 3.1 28.3 + - + +
954Z ASN* 2.9 31.9 + - - +
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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