Contacts of the strand formed by residues 35 - 41 (chain V) 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 ASN 35 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82S ARG* 2.7 38.2 + - - +
31V PRO* 3.2 24.5 - - + +
32V ALA* 3.4 25.4 + - - +
33V ILE 3.1 3.7 - - - +
34V LEU* 1.3 83.9 - - - +
36V ALA* 1.3 60.6 + - - +
49V GLU* 3.5 5.9 - - - +
50V VAL* 3.2 29.5 + - + +
78V ASP* 4.1 9.6 + - - +
80V GLY 3.2 21.8 + - - -
81V GLY 3.5 7.6 - - - +
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Residues in contact with ALA 36 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35V ASN* 1.3 73.6 - - - +
37V LEU* 1.3 62.4 + - - +
38V GLU* 6.0 0.7 - - + -
47V VAL* 5.2 4.5 - - + -
48V LEU 3.9 5.8 - - - +
49V GLU* 4.9 1.1 - - - +
78V ASP* 3.1 18.7 - - - +
79V THR* 3.3 31.5 + - + +
81V GLY 2.8 9.9 + - - +
82V PRO 4.4 0.2 - - - +
83V ILE* 3.4 37.2 - - + +
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Residues in contact with LEU 37 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23V VAL* 3.9 20.0 - - + -
25V PHE* 3.9 20.0 - - + -
31V PRO* 4.6 4.5 - - + -
36V ALA* 1.3 83.8 - - - +
38V GLU* 1.3 65.4 + - - +
47V VAL* 3.4 6.8 - - - +
48V LEU* 2.8 48.5 + - + +
50V VAL* 4.3 16.4 - - + -
59V VAL* 5.1 0.4 - - + -
61V THR* 3.7 29.2 - - + -
76V VAL* 3.8 14.1 - - + -
77V LEU 3.7 3.1 - - - +
78V ASP* 3.6 27.6 - - + +
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Residues in contact with GLU 38 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36V ALA* 5.6 1.1 - - + -
37V LEU* 1.3 81.2 - - - +
39V ILE* 1.3 69.2 + - - +
45V LYS* 3.4 37.4 + - + +
46V LEU 3.4 8.1 - - - +
47V VAL* 4.5 13.1 - - + +
76V VAL* 3.6 0.5 - - - +
77V LEU* 2.9 57.6 + - + +
79V THR* 3.7 24.9 - - + +
99V ILE* 5.5 1.6 - - - +
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Residues in contact with ILE 39 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13V VAL* 5.5 1.1 - - + -
38V GLU* 1.3 80.4 - - - +
40V LYS* 1.3 64.4 + - - +
41V THR* 5.5 0.4 - - + -
45V LYS* 3.5 7.6 - - - +
46V LEU* 2.9 73.7 + - + +
48V LEU* 3.8 24.5 - - + +
70V LEU* 4.8 12.6 - - + -
74V GLU* 3.2 37.7 - - + -
75V LYS 3.7 11.2 - - - +
76V VAL* 3.7 21.3 - - + -
77V LEU* 4.5 3.1 - - - -
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Residues in contact with LYS 40 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39V ILE* 1.3 77.7 - - - +
41V THR* 1.3 71.8 + - - +
42V PRO* 4.4 3.6 - - - +
44V GLY 4.5 7.0 - - - +
45V LYS* 4.9 0.9 - - - +
70V LEU* 5.9 1.0 - - - +
74V GLU* 4.1 18.2 + - - +
75V LYS 4.9 2.6 + - - +
77V LEU* 5.0 5.3 - - + +
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Residues in contact with THR 41 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39V ILE* 3.5 3.1 + - + +
40V LYS* 1.3 85.5 - - - +
42V PRO* 1.3 75.9 - - + +
43V GLN* 4.0 19.7 + - - +
44V GLY* 2.9 23.5 + - - +
45V LYS* 3.0 28.2 + - - -
46V LEU* 3.9 28.9 - - + -
69V GLY 6.0 1.6 - - - +
70V LEU* 5.0 11.9 - - + -
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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