Contacts of the strand formed by residues 10 - 17 (chain O) in PDB entry 3FKS
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 10 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8O PRO* 4.1 10.2 + - + +
9O ILE* 1.3 81.2 - - - +
11O GLY* 1.3 58.1 + - - +
25O PHE* 3.0 20.5 - - - +
26O GLU* 4.7 10.2 + - - +
75O LYS* 3.6 37.5 - - + +
76O VAL 3.4 5.8 - - - +
77O LEU* 5.0 9.9 - - + -
179X GLY* 6.3 1.1 - - - -
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Residues in contact with GLY 11 (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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10O THR* 1.3 75.9 - - - +
12O LYS* 1.3 66.1 + - - +
23O VAL* 3.9 8.1 - - - -
24O HIS 3.1 14.6 - - - -
25O PHE* 3.5 10.3 - - - -
26O GLU* 6.4 0.7 - - - -
74O GLU 3.0 2.9 - - - +
75O LYS* 3.6 3.1 - - - +
76O VAL* 2.7 38.7 + - - +
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Residues in contact with LYS 12 (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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11O GLY* 1.3 77.3 - - - +
13O VAL* 1.3 64.9 + - - +
14O THR* 3.4 9.2 + - + +
23O VAL* 3.5 2.6 - - - -
24O HIS* 2.8 43.1 + - + +
26O GLU* 4.4 18.4 - - + +
73O GLY* 3.3 33.6 + - - +
74O GLU 3.1 4.5 - - - +
75O LYS* 5.6 1.3 - - - -
433X ARG* 4.5 17.8 - - - +
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Residues in contact with VAL 13 (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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12O LYS* 1.3 70.2 - - - +
14O THR* 1.3 63.7 + - - +
15O ALA 3.9 4.0 - - - +
16O VAL* 3.5 31.6 - - + -
21O VAL* 3.6 18.2 - - + -
22O ASP 3.9 3.8 - - - -
23O VAL* 4.2 1.6 - - + +
39O ILE* 3.9 12.6 - - + -
70O LEU* 5.5 3.6 - - + -
71O VAL 4.1 9.2 - - - +
72O ARG* 3.2 10.4 - - + +
73O GLY* 2.7 31.4 + - - +
74O GLU* 3.3 22.1 + - + +
76O VAL* 3.6 24.5 - - + -
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Residues in contact with THR 14 (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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70K PRO* 3.2 36.3 - - - +
12O LYS* 3.6 9.0 - - + +
13O VAL* 1.3 73.5 - - - +
15O ALA* 1.3 59.0 + - - +
22O ASP* 2.7 31.3 + - - +
24O HIS* 3.6 29.4 - - + -
58O THR* 4.2 8.5 - - + +
72O ARG* 3.9 17.6 - - - +
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Residues in contact with ALA 15 (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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68K LEU 3.0 12.8 - - - +
69K GLU* 4.4 1.8 - - + -
70K PRO* 3.8 12.8 - - + -
13O VAL* 3.6 1.8 - - - +
14O THR* 1.3 82.4 - - - +
16O VAL* 1.3 66.9 + - - +
17O ILE* 4.3 8.7 - - + -
20O ILE 4.6 0.7 - - - -
21O VAL* 3.2 5.9 - - - +
22O ASP* 2.7 56.7 + - + +
72O ARG* 4.9 1.3 - - - -
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Residues in contact with VAL 16 (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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51K ALA* 4.1 18.6 - - + -
66K LEU 4.0 1.5 - - - +
67K ASN* 3.4 3.1 - - - -
68K LEU* 2.9 49.3 + - + +
13O VAL* 3.5 22.0 - - + -
15O ALA* 1.3 79.7 - - - +
17O ILE* 1.3 64.5 + - - +
18O GLY 4.8 2.2 - - - +
20O ILE 3.9 3.1 - - - -
21O VAL* 3.8 14.6 - - + -
67O THR* 3.9 30.1 - - + +
70O LEU* 4.2 19.1 - - + +
72O ARG* 5.9 1.1 - - + -
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Residues in contact with ILE 17 (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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66K LEU* 5.2 1.3 - - + +
67K ASN* 3.6 28.9 - - + +
68K LEU 4.7 3.1 - - - +
69K GLU* 4.8 15.5 - - + +
289K ARG* 5.0 9.9 - - - +
15O ALA* 5.0 8.3 - - + -
16O VAL* 1.3 84.0 - - - +
18O GLY* 1.3 60.7 + - - +
19O ALA 2.9 9.7 + - - -
20O ILE* 3.1 29.3 + - + +
22O ASP* 5.3 5.6 - - - +
60O ARG* 6.0 3.8 - - - +
271O LEU* 3.7 39.8 - - + +
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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