Contacts of the strand formed by residues 70 - 75 (chain O) in PDB entry 3K9Q
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 LYS 70 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22O GLN* 4.7 18.3 - - - +
28O GLU* 4.5 36.6 + - - +
66O ARG* 3.2 5.1 - - - -
67O VAL* 2.8 46.0 + - + +
68O ASN* 3.3 7.6 - - - +
69O GLY* 1.3 75.0 - - - +
71O GLU* 1.3 66.4 + - - +
72O VAL* 3.5 5.6 + - + +
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Residues in contact with GLU 71 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29O VAL 4.7 2.9 - - - +
30O VAL* 4.3 6.8 - - - +
61O VAL* 4.2 19.0 - - + +
62O ASP 3.5 21.3 - - - +
63O GLY 4.9 0.2 - - - -
65O PHE 3.8 2.0 - - - -
66O ARG* 4.3 8.9 - - + +
69O GLY 4.1 2.0 + - - -
70O LYS* 1.3 75.1 - - - +
72O VAL* 1.3 66.8 + - - +
73O LYS* 3.9 33.1 + - + +
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Residues in contact with VAL 72 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18O PHE* 3.8 28.9 - - + -
29O VAL* 3.8 14.6 - - + +
30O VAL 3.8 6.3 - - - +
31O ALA 4.2 3.1 - - - +
32O VAL* 4.0 19.3 - - + +
63O GLY 4.6 0.2 - - - -
64O GLY* 3.3 3.3 - - - -
65O PHE* 2.8 64.1 + - + +
67O VAL* 4.5 3.8 - - + -
70O LYS* 4.4 7.2 - - + +
71O GLU* 1.3 79.9 - - - +
73O LYS* 1.3 74.9 + - - +
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Residues in contact with LYS 73 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30O VAL 2.9 17.3 + - - +
31O ALA* 3.1 5.6 - - + +
32O VAL 2.8 25.3 + - - +
62O ASP 5.5 0.7 - - - -
63O GLY* 3.5 16.6 - - - +
71O GLU* 3.9 30.0 - - + +
72O VAL* 1.3 75.3 - - - +
74O SER* 1.3 58.9 - - - +
75O PHE* 4.0 23.9 - - + -
88O LEU* 4.6 20.9 - - + +
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Residues in contact with SER 74 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32O VAL* 3.2 7.6 - - - -
38O ASP* 2.4 35.7 + - - -
41O LEU* 4.0 17.7 - - - +
63O GLY* 3.0 14.8 + - - +
64O GLY* 3.7 6.7 - - - -
65O PHE* 4.3 9.2 - - - -
72O VAL 3.7 0.4 + - - -
73O LYS* 1.3 74.1 - - - +
75O PHE* 1.3 75.2 + - - +
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Residues in contact with PHE 75 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31O ALA* 4.3 4.0 - - + -
32O VAL 2.9 16.0 + - - +
33O ASN* 3.0 21.2 - - - +
34O ASP* 3.2 15.6 + - - +
36O THR 4.8 2.5 - - - +
41O LEU* 5.2 3.8 - - - +
73O LYS* 4.0 24.7 - - + -
74O SER* 1.3 81.9 - - - +
76O SER* 1.3 62.4 + - - +
77O GLU* 4.5 2.7 - - + +
83O LEU* 3.9 13.0 - - + -
84O PRO* 3.5 32.5 - - + -
85O TRP* 4.6 8.5 - + - -
88O LEU* 3.8 28.7 - - + -
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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