Contacts of the strand formed by residues 944 - 949 (chain A) in PDB entry 3OPY
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 GLU 944 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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535A GLU* 3.8 4.2 + - - +
881A ARG* 3.9 5.2 - - - +
940A ILE* 3.4 3.0 - - - -
941A GLN* 3.0 36.1 + - - +
943A SER* 1.4 80.8 - - - +
945A VAL* 1.4 70.5 - - - +
946A THR* 4.1 16.1 - - + +
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Residues in contact with VAL 945 (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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881A ARG* 3.6 38.8 - - + +
882A LEU* 4.1 16.4 - - + -
885A LYS* 4.0 29.9 + - + +
938A ILE* 3.7 28.3 - - + -
939A GLY 3.2 6.1 - - - +
940A ILE* 4.8 3.8 - - + -
944A GLU* 1.4 84.5 - - - +
946A THR* 1.3 62.3 + - - +
947A PHE* 3.9 22.9 - - + -
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Residues in contact with THR 946 (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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734A GLY 3.7 7.4 + - - -
937A VAL 3.1 5.1 - - - +
938A ILE* 3.3 3.5 - - - +
939A GLY 2.7 39.0 + - - -
941A GLN* 3.2 47.9 + - + +
944A GLU* 4.1 16.8 - - - +
945A VAL* 1.3 77.9 - - - +
947A PHE* 1.3 64.9 + - - +
948A THR* 4.1 6.9 + - - -
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Residues in contact with PHE 947 (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* 3.7 37.7 - - + -
888A ASN* 6.4 0.4 - - + -
889A PHE* 3.7 27.1 - + + -
936A VAL* 3.6 16.5 - - + +
937A VAL 3.6 3.8 - - - -
938A ILE* 3.3 35.2 - - + -
945A VAL* 3.9 31.0 - - + -
946A THR* 1.3 75.2 - - - +
948A THR* 1.3 61.3 + - - +
949A PRO* 4.1 4.0 - - - +
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Residues in contact with THR 948 (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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734A GLY* 4.4 7.8 + - - -
936A VAL* 3.4 5.2 - - - +
937A VAL* 2.7 42.7 + - - +
941A GLN* 4.6 3.8 + - - -
946A THR* 4.1 14.9 + - - -
947A PHE* 1.3 76.8 + - - +
949A PRO* 1.3 73.1 - - + +
950A VAL 3.5 0.5 + - - -
952A GLN* 5.6 3.1 - - + -
953A LEU* 3.6 35.2 - - + +
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Residues in contact with PRO 949 (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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932A ASP 3.6 16.6 - - - +
933A ASN* 4.0 24.0 - - + +
935A SER 3.3 8.5 - - - +
936A VAL* 3.9 8.7 - - + -
947A PHE 4.1 4.5 - - - +
948A THR* 1.3 88.8 - - + +
950A VAL* 1.4 64.3 + - - +
951A LYS 4.8 0.2 - - - +
952A GLN* 3.4 37.3 - - + +
953A LEU* 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