Contacts of the strand formed by residues 30 - 36 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26L ASN 3.1 19.7 + - - +
27L LEU* 3.1 14.5 - - - +
28L ASN 3.7 0.2 - - - -
29L GLU* 1.3 88.7 - - + +
31L GLY* 1.3 60.5 + - - +
45L GLY* 3.7 1.6 - - - -
46L LEU* 2.8 27.3 + - - +
89L LEU* 4.0 22.4 - - + -
90L VAL 3.2 12.6 - - - +
91L LYS* 4.2 10.8 - - + -
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Residues in contact with GLY 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L LEU* 4.8 3.6 - - - +
30L THR* 1.3 76.7 - - - +
32L ARG* 1.3 64.7 + - - +
43L VAL* 3.6 17.3 - - - -
44L PHE 3.2 12.6 - - - -
46L LEU* 3.8 2.4 - - - +
88L GLU 3.6 2.8 - - - +
89L LEU* 3.6 5.4 - - - +
90L VAL 3.0 32.1 + - - -
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Residues in contact with ARG 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L LEU* 5.2 11.3 - - + +
31L GLY* 1.3 75.5 - - - +
33L VAL* 1.3 65.2 + - - +
34L LEU* 3.1 4.9 + - + +
43L VAL* 3.6 2.9 - - - +
44L PHE* 2.7 61.4 + - + +
87L GLY* 4.5 20.5 - - - +
88L GLU 3.5 4.3 - - - +
89L LEU* 5.8 2.5 - - + -
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Residues in contact with VAL 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L ARG* 1.3 68.4 - - - +
34L LEU* 1.3 62.5 + - - +
35L ALA 3.6 27.8 - - - +
36L VAL* 4.1 8.5 - - + -
41L ALA* 5.1 2.5 - - + -
42L ARG 3.9 3.8 - - - +
43L VAL* 4.3 4.7 - - + -
57L PHE* 4.1 14.8 - - + -
84L VAL* 4.2 1.8 - - + -
85L LYS 3.3 26.7 - - - +
86L GLU* 3.5 7.5 - - - +
87L GLY* 2.7 28.7 + - - +
88L GLU* 3.1 22.9 + - + +
90L VAL* 3.9 21.1 - - + -
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Residues in contact with LEU 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L ARG* 3.1 7.5 + - + +
33L VAL* 1.3 73.4 - - - +
35L ALA* 1.3 61.2 + - + +
42L ARG* 2.6 26.7 + - + +
44L PHE* 3.7 44.0 - - + +
71L GLY 5.6 0.2 - - - -
72L GLN* 3.6 38.1 - - + +
86L GLU* 3.9 11.0 - - - +
55O GLY* 3.3 19.4 - - - -
56O GLU 4.3 0.7 + - - -
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Residues in contact with ALA 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L VAL* 3.4 8.6 - - - +
34L LEU* 1.3 83.5 - - - +
36L VAL* 1.3 61.8 + - - +
41L ALA* 3.4 1.6 - - - -
42L ARG* 3.0 50.6 + - - +
86L GLU* 5.4 1.1 - - - -
53O HIS* 3.1 23.1 - - - +
54O LEU 3.2 16.8 - - - +
55O GLY* 4.7 0.2 - - - -
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Residues in contact with VAL 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L VAL* 4.1 2.2 - - + -
35L ALA* 1.3 79.6 - - - +
37L GLY* 1.3 61.1 + - - +
40L ILE 3.2 16.4 - - - +
41L ALA* 4.2 5.4 - - + -
77L LEU* 4.4 11.9 - - + -
81L ASP* 4.7 6.1 - - + +
84L VAL* 3.7 52.3 - - + +
85L LYS 4.2 9.0 - - - +
33O ILE* 4.5 3.4 - - + +
52O GLN* 3.6 1.5 - - - +
53O HIS* 2.7 53.1 + - + +
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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