Contacts of the strand formed by residues 30 - 37 (chain K) 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 30 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21K VAL* 4.5 2.3 - - - +
27K LEU* 3.3 34.5 - - - +
29K GLU* 1.3 85.5 - - + +
31K GLY* 1.3 59.7 + - - +
32K ARG* 5.2 0.3 + - - -
46K LEU* 3.5 11.9 + - - -
89K LEU* 3.7 30.5 - - + +
90K VAL 3.1 5.2 - - - -
91K LYS* 4.2 17.3 - - + -
464X GLU* 2.7 34.1 + - + +
467X VAL* 6.5 0.4 - - + -
468X ALA* 6.4 1.6 - - + -
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Residues in contact with GLY 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K LEU* 4.1 2.2 - - - -
30K THR* 1.3 76.5 - - - +
32K ARG* 1.3 68.7 + - - -
43K VAL* 3.9 10.1 - - - -
44K PHE 3.3 12.8 - - - -
46K LEU* 3.9 6.5 - - - -
88K GLU 2.8 16.5 - - - +
90K VAL* 2.9 25.8 + - - +
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Residues in contact with ARG 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K GLY* 3.5 29.1 - - - -
21K VAL* 3.7 16.9 + - - +
27K LEU* 4.3 26.2 - - + +
31K GLY* 1.3 78.6 + - - -
33K VAL* 1.3 66.2 + - - +
34K LEU* 3.2 0.7 + - - -
43K VAL* 4.1 0.7 - - - -
44K PHE* 2.8 44.5 + - + +
87K GLY* 4.6 7.4 - - - -
88K GLU* 3.5 13.2 - - - +
89K LEU* 3.2 50.8 - - - +
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Residues in contact with VAL 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K GLY 4.0 0.6 + - - -
32K ARG* 1.3 71.6 - - - +
34K LEU* 1.3 61.1 + - - +
35K ALA 3.7 24.2 - - - +
36K VAL* 4.6 0.2 - - + -
41K ALA* 4.8 2.2 - - + -
42K ARG 3.9 4.9 - - - +
43K VAL* 4.0 5.2 - - + +
57K PHE* 3.5 35.2 - - + -
84K VAL* 4.1 9.2 - - + -
85K LYS 3.3 27.6 - - - +
86K GLU* 3.8 5.9 - - - +
87K GLY* 2.8 27.1 + - - +
88K GLU* 3.4 14.3 + - + +
90K VAL* 3.6 12.8 - - + -
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Residues in contact with LEU 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K ARG 3.2 5.5 + - - +
33K VAL* 1.3 74.8 - - - +
35K ALA* 1.3 57.8 + - - +
42K ARG* 2.7 53.3 + - + +
44K PHE* 4.2 29.4 - - + +
72K GLN* 5.3 9.2 - - + +
86K GLU* 3.5 12.3 - - - +
55N GLY* 3.3 23.6 - - - -
56N GLU* 4.7 9.0 - - + +
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Residues in contact with ALA 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K VAL* 3.6 5.6 - - - +
34K LEU* 1.3 81.4 - - - +
36K VAL* 1.3 64.0 + - - +
41K ALA* 3.2 5.2 - - - +
42K ARG* 2.8 54.0 + - - +
86K GLU* 5.0 1.1 - - - -
53N HIS* 3.2 20.2 - - - +
54N LEU 3.5 16.4 - - - +
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Residues in contact with VAL 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K ALA* 1.3 76.1 - - - +
37K GLY* 1.3 61.7 + - - +
40K ILE 3.5 13.2 - - - +
41K ALA* 3.9 4.9 - - + -
77K LEU* 3.6 23.8 - - + -
81K ASP* 4.3 8.3 - - + +
84K VAL* 3.2 41.3 - - + +
85K LYS 4.5 5.4 - - - -
33N ILE* 4.0 5.4 - - + +
52N GLN* 3.7 1.0 - - - +
53N HIS* 2.7 61.7 + - + +
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Residues in contact with GLY 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K VAL* 1.3 78.4 - - - +
38K ASP* 1.3 76.4 + - - +
39K GLY 3.3 2.0 - - - -
40K ILE* 3.0 23.6 + - - +
81K ASP* 3.8 7.9 - - - -
33N ILE* 4.4 5.4 - - - -
51N ALA 4.6 0.7 - - - -
52N GLN* 4.0 16.2 - - - -
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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