Contacts of the strand formed by residues 994 - 999 (chain F) in PDB entry 5D6Y
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 SER 994 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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968E THR* 2.3 28.9 + - - +
909F HIS* 3.0 32.1 + - - -
910F LYS* 4.6 15.5 - - - +
990F PHE* 3.1 23.6 + - - -
992F ASP* 3.5 8.8 + - - -
993F GLY* 1.3 75.5 - - - +
995F GLN* 1.3 59.2 + - - +
996F LEU* 5.8 1.7 - - - +
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Residues in contact with GLN 995 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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967E TRP 5.0 2.2 - - - +
968E THR* 3.9 25.5 - - + +
920F VAL* 6.3 1.6 - - + -
987F GLN* 5.5 6.1 - - + -
988F VAL 3.3 11.0 - - - +
989F GLU* 4.4 1.8 - - + +
994F SER* 1.3 73.4 - - - +
996F LEU* 1.3 76.8 + - - +
997F VAL* 5.8 2.2 - - + -
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Residues in contact with LEU 996 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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908F LYS* 3.1 30.1 - - + +
909F HIS 3.9 0.4 - - - -
910F LYS* 3.8 32.3 - - + +
987F GLN* 3.1 4.9 - - - +
988F VAL* 2.6 41.2 + - + -
990F PHE* 3.7 16.4 - - + -
994F SER* 4.3 1.8 + - - +
995F GLN* 1.3 84.9 - - - +
997F VAL* 1.3 62.0 + - - +
998F VAL* 3.8 18.6 - - + -
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Residues in contact with VAL 997 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942E TYR* 3.7 43.5 - - + +
923F THR* 5.1 2.0 - - - +
925F GLU* 5.0 2.7 - - - +
985F MET* 3.5 36.2 - - + +
986F TYR 3.2 7.6 - - - +
987F GLN* 3.9 16.2 - - + +
995F GLN* 5.8 3.1 - - + -
996F LEU* 1.3 79.2 - - - +
998F VAL* 1.3 62.3 + - - +
999F LYS* 5.1 1.2 + - - -
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Residues in contact with VAL 998 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907F SER* 4.9 2.0 - - - -
908F LYS* 5.3 7.4 - - + +
985F MET* 3.5 7.8 - - - -
986F TYR* 2.4 63.5 + - + +
988F VAL* 3.9 14.4 - - + -
996F LEU* 3.8 26.0 - - + -
997F VAL* 1.3 76.1 - - - +
999F LYS* 1.3 68.8 + - - +
1002F ASP* 4.0 18.2 - - + +
1003F VAL* 3.4 32.5 - - + -
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Residues in contact with LYS 999 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983F ILE* 4.7 8.7 - - + -
984F GLN 3.9 10.3 - - - +
985F MET* 3.6 21.7 - - + +
986F TYR* 3.8 4.0 - - - -
997F VAL 5.1 1.0 + - - -
998F VAL* 1.3 88.4 - - - +
1000F ARG* 1.3 67.7 + - + +
1001F ASP* 3.7 13.7 - - + +
1002F ASP* 2.3 69.2 + - - +
1003F VAL* 3.7 4.2 + - - +
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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