Contacts of the strand formed by residues 40 - 45 (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 ILE 40 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36K VAL* 3.5 2.8 - - - +
37K GLY 3.0 39.7 + - - +
38K ASP* 2.9 11.2 + - + +
39K GLY* 1.3 85.2 - - - +
41K ALA* 1.3 63.8 + - - +
42K ARG* 5.9 7.2 - - + -
74K GLY* 5.7 2.9 - - - -
75K ILE 3.2 12.6 - - - +
76K VAL* 4.7 12.1 - - + -
77K LEU* 4.2 2.0 - - - -
283K LEU* 5.7 4.0 - - + -
286K LEU* 4.4 15.3 - - + +
287K LEU* 3.9 37.2 - - + -
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Residues in contact with ALA 41 (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* 4.8 0.9 - - + -
35K ALA 3.2 13.0 - - - +
36K VAL* 3.9 11.0 - - + -
40K ILE* 1.3 78.1 - - - +
42K ARG* 1.3 62.3 + - - +
43K VAL* 3.4 3.2 + - + -
57K PHE* 4.3 13.7 - - + -
73K VAL 3.3 3.5 - - - +
74K GLY* 4.7 1.1 - - - -
75K ILE* 2.9 34.3 + - - +
77K LEU* 3.9 22.4 - - + -
84K VAL* 4.4 4.7 - - + -
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Residues in contact with ARG 42 (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* 3.9 0.3 - - - -
34K LEU* 2.7 69.1 + - + +
35K ALA* 2.8 22.8 + - - +
40K ILE* 5.9 8.1 - - + -
41K ALA* 1.3 68.6 - - - +
43K VAL* 1.3 54.5 + - - +
72K GLN* 3.1 39.5 + - + +
73K VAL 3.6 5.6 - - - -
74K GLY* 4.8 3.1 - - - -
54N LEU 3.7 19.2 + - - -
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Residues in contact with VAL 43 (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* 3.9 16.8 - - - -
32K ARG 3.8 3.4 - - - +
33K VAL* 4.0 12.8 - - + -
41K ALA 4.1 4.9 - - - +
42K ARG* 1.3 75.4 - - - +
44K PHE* 1.3 73.7 + - - +
45K GLY 3.8 0.7 + - - -
46K LEU* 3.5 24.2 - - + -
57K PHE* 4.1 10.8 - - + -
72K GLN* 3.5 3.9 - - - -
73K VAL* 2.8 38.7 + - + +
75K ILE* 3.8 24.9 - - + -
90K VAL* 3.9 20.6 - - + -
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Residues in contact with PHE 44 (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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23K ASP 5.5 0.2 - - - -
24K GLU* 3.5 37.2 - - + -
27K LEU* 4.0 14.8 - - + +
31K GLY* 3.3 5.4 - - - -
32K ARG* 2.8 51.6 + - + +
34K LEU* 4.2 27.3 - - + +
42K ARG 4.0 1.8 + - - -
43K VAL* 1.3 71.9 - - - +
45K GLY* 1.3 62.4 + - - +
71K GLY* 3.4 26.0 - - - -
72K GLN* 4.7 1.1 - - + +
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Residues in contact with GLY 45 (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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24K GLU* 5.4 1.1 - - - -
27K LEU* 4.1 17.5 - - - -
43K VAL 3.8 0.6 + - - -
44K PHE* 1.3 85.1 - - - +
46K LEU* 1.3 73.7 + - - +
47K ASN* 3.1 13.3 + - - +
71K GLY 4.0 7.5 + - - +
73K VAL* 3.8 7.3 - - - +
72O ARG* 3.2 14.4 + - - -
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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