Contacts of the strand formed by residues 30 - 37 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26U ASN* 3.4 35.8 + - - +
27U LEU* 2.8 29.7 + - - +
29U GLU* 1.3 88.1 - - + +
31U GLY* 1.3 60.9 + - - +
46U LEU* 3.6 8.4 + - - -
89U LEU* 4.1 21.7 - - + +
90U VAL 3.2 16.8 - - - +
91U LYS* 4.2 10.8 - - + -
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Residues in contact with GLY 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27U LEU* 5.1 2.0 - - - -
30U THR* 1.3 75.6 - - - +
32U ARG* 1.3 67.4 + - - +
43U VAL* 3.7 15.5 - - - -
44U PHE 3.2 13.9 - - - -
46U LEU* 3.7 6.2 - - - +
88U GLU 3.3 2.6 - - - +
89U LEU* 3.7 2.9 - - - +
90U VAL* 3.1 29.5 + - - -
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Residues in contact with ARG 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27U LEU* 5.7 2.0 - - + +
31U GLY* 1.3 78.2 - - - +
33U VAL* 1.3 63.3 + - - +
34U LEU* 5.4 0.9 - - + -
43U VAL* 3.1 6.4 - - - +
44U PHE* 2.6 47.6 + - + +
87U GLY* 4.8 17.5 + - - -
88U GLU 3.3 12.1 - - - +
89U LEU* 5.4 1.6 - - + -
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Residues in contact with VAL 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32U ARG* 1.3 75.6 - - - +
34U LEU* 1.3 67.8 + - - +
35U ALA 3.8 24.2 - - - +
36U VAL* 4.2 9.4 - - + -
41U ALA* 5.0 1.3 - - + -
42U ARG 3.7 8.3 - - - +
43U VAL* 3.9 15.3 - - + -
57U PHE* 4.5 1.6 - - + -
84U VAL* 3.9 17.3 - - + -
85U LYS 3.4 26.9 - - - +
86U GLU* 3.8 5.0 - - - +
87U GLY* 3.0 23.3 + - - +
88U GLU* 3.5 22.3 + - + +
90U VAL* 4.3 5.8 - - + -
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Residues in contact with LEU 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32U ARG* 5.3 0.7 - - + +
33U VAL* 1.3 78.8 - - - +
35U ALA* 1.3 62.7 + - + +
42U ARG* 2.6 32.7 + - + +
44U PHE* 3.9 40.4 - - + +
71U GLY 5.5 0.2 - - - +
72U GLN* 4.6 20.6 - - + +
86U GLU* 3.5 14.6 - - - +
55X GLY* 3.4 19.2 - - - -
56X GLU 4.4 1.0 + - - -
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Residues in contact with ALA 35 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33U VAL* 3.8 3.9 - - - +
34U LEU* 1.3 81.9 - - - +
36U VAL* 1.3 60.8 + - - +
40U ILE* 4.8 0.5 - - - +
41U ALA* 3.7 0.7 - - - -
42U ARG* 2.9 54.5 + - - +
86U GLU* 5.3 0.7 - - - -
53X HIS* 3.1 19.5 - - - +
54X LEU* 3.2 19.1 - - - +
55X GLY* 4.4 0.2 - - - -
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Residues in contact with VAL 36 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33U VAL* 4.2 9.4 - - + -
35U ALA* 1.3 74.4 - - - +
37U GLY* 1.3 69.4 + - - +
40U ILE 3.2 15.7 - - - +
41U ALA* 4.6 2.7 - - + -
77U LEU* 4.5 11.7 - - + -
81U ASP* 4.5 4.7 - - + +
84U VAL* 3.7 44.6 - - + +
85U LYS 4.4 5.8 - - - -
33X ILE* 4.7 4.7 - - + -
52X GLN* 3.6 3.9 - - - +
53X HIS* 2.8 56.5 + - + +
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Residues in contact with GLY 37 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36U VAL* 1.3 85.9 - - - +
38U ASP* 1.3 75.3 + - - +
39U GLY 3.3 2.9 - - - -
40U ILE* 3.1 19.8 + - - +
81U ASP* 4.5 8.3 - - - -
33X ILE* 4.9 1.3 - - - -
51X ALA 4.3 5.6 - - - -
52X GLN* 4.2 13.5 - - - -
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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