Contacts of the strand formed by residues 40 - 45 (chain J) in PDB entry 1FSK
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 SER 40 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31J PRO* 4.0 8.1 - - - -
38J ILE 3.7 0.6 - - - -
39J SER* 1.3 85.6 + - - +
41J VAL* 1.3 64.5 + - - +
42J GLU* 5.7 0.7 + - - -
55J LYS 3.8 1.0 - - - +
56J ILE* 3.6 0.9 - - - -
57J SER* 2.7 48.0 + - - +
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Residues in contact with VAL 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J ASP* 3.2 47.0 + - + +
30J PHE* 5.5 0.4 - - + -
31J PRO* 4.4 6.1 - - + +
38J ILE* 3.8 22.9 - - + -
40J SER* 1.3 81.8 - - - +
42J GLU* 1.3 65.5 + - - +
43J ASN* 5.2 1.8 - - - +
54J LYS* 4.1 18.6 - - + -
55J LYS 3.5 2.5 - - - -
56J ILE* 4.0 28.9 - - + -
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Residues in contact with GLU 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40J SER* 5.7 0.9 + - - -
41J VAL* 1.3 77.1 - - - +
43J ASN* 1.3 63.8 + - - +
44J ILE* 3.2 14.4 + - + +
54J LYS* 3.2 3.0 - - - -
55J LYS* 2.8 70.4 + - + +
57J SER* 5.5 1.6 + - - -
101L ARG* 3.2 46.3 + - - +
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Residues in contact with ASN 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41J VAL* 5.2 1.4 - - - +
42J GLU* 1.3 71.7 - - - +
44J ILE* 1.3 59.5 + - - +
45J GLU 3.1 2.0 - - - -
46J GLY 3.6 12.7 + - - +
47J ASN 3.5 4.6 - - - -
48J GLY* 3.1 37.0 - - - +
52J THR* 3.6 9.0 - - + -
53J ILE 3.6 5.6 - - - -
54J LYS* 3.8 20.2 + - - +
101L ARG* 2.9 34.4 - - - +
102L ASP* 2.9 21.9 + - - +
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Residues in contact with ILE 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42J GLU* 3.2 16.6 + - - +
43J ASN* 1.3 70.5 - - - +
45J GLU* 1.3 57.9 + - - +
53J ILE* 2.8 26.7 + - + +
55J LYS* 3.4 49.6 - - + +
68J LYS* 4.6 16.2 - - + +
31L SER* 5.6 2.0 - - - +
32L TYR* 3.1 36.2 + - + +
100L ALA* 3.4 1.0 - - - -
101L ARG* 3.0 21.3 + - - +
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Residues in contact with GLU 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J ASN 3.1 0.8 + - - -
44J ILE* 1.3 74.9 - - - +
46J GLY* 1.3 69.0 + - - +
52J THR* 3.5 4.2 - - - +
53J ILE* 2.9 35.9 + - + +
31L SER 4.4 0.3 - - - +
32L TYR* 2.6 47.7 - - + +
33L TRP* 2.7 38.8 + - + +
35L ASN* 5.1 0.3 + - - -
52L PHE* 5.0 0.2 - - - -
98L ARG* 4.0 0.2 - - - +
99L GLY* 2.7 28.1 + - - -
100L ALA 3.5 13.0 - - - +
104L TRP* 3.5 24.2 - - + -
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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