Contacts of the strand formed by residues 62 - 68 (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 LYS 62 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54U LEU* 4.4 24.2 - - + -
55U VAL 3.7 5.2 - - - +
56U GLU* 3.5 38.3 + - + +
57U PHE* 4.1 3.9 - - - -
60U GLY 4.1 7.8 + - - +
61U VAL* 1.3 85.1 - - - +
63U GLY* 1.3 58.3 + - - +
77U LEU* 3.9 2.1 - - - -
78U PHE* 3.2 38.9 + - + +
113U LEU* 5.2 16.7 - - + +
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Residues in contact with GLY 63 (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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54U LEU* 3.1 11.4 - - - +
55U VAL* 2.7 45.0 + - - -
57U PHE* 4.1 3.6 - - - -
62U LYS* 1.3 76.4 - - - +
64U MET* 1.3 57.9 + - - -
75U ILE* 3.9 10.3 - - - -
76U VAL 3.6 11.4 - - - -
78U PHE* 3.7 5.6 - - - -
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Residues in contact with MET 64 (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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52U GLU* 3.5 52.7 - - + +
53U GLU 3.6 7.6 - - - +
54U LEU* 4.5 1.8 - - + -
55U VAL* 4.3 0.2 - - - -
63U GLY* 1.3 74.6 - - - +
65U ALA* 1.3 67.9 + - - +
66U LEU* 3.8 10.1 + - + +
75U ILE* 3.6 5.9 - - - +
76U VAL* 3.2 38.8 + - + +
78U PHE* 3.7 21.1 - - + -
96U ILE* 5.3 2.5 - - + -
97U VAL* 3.5 26.5 - - + -
131U ALA* 6.5 0.7 - - + -
132U GLN* 6.3 1.3 - - + +
246U TYR* 4.9 12.8 - - + +
247U LEU* 4.5 11.4 - - + -
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Residues in contact with ALA 65 (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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49U ILE* 4.3 12.6 - - + -
50U GLN 4.7 4.9 - - - +
52U GLU* 3.3 26.8 + - - -
53U GLU 3.3 15.5 + - - +
55U VAL* 4.4 1.7 - - + +
64U MET* 1.3 73.1 - - - +
66U LEU* 1.3 64.9 + - - +
68U LEU* 4.1 12.8 - - + -
73U VAL* 3.9 21.3 - - + -
74U GLY 3.2 11.2 - - - +
75U ILE* 4.2 7.5 - - + +
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Residues in contact with LEU 66 (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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51U ALA* 6.2 0.2 - - - +
52U GLU* 3.8 28.3 - - + +
64U MET* 3.8 14.1 + - + +
65U ALA* 1.3 82.5 - - - +
67U ASN* 1.3 69.2 + - - +
68U LEU* 3.7 5.0 - - - +
74U GLY 2.9 5.7 + - - +
76U VAL* 4.2 13.2 - - + -
246U TYR* 5.4 12.3 - - + +
280U TYR* 5.6 6.3 - - + -
283U LEU* 4.1 26.2 - - + -
287U LEU* 4.3 12.6 - - + -
289U ARG* 3.4 29.1 + - - +
16V VAL* 3.3 15.4 - - - +
17V ILE* 3.9 4.2 - - - -
18V GLY* 4.2 3.7 + - - +
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Residues in contact with ASN 67 (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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66U LEU* 1.3 80.9 - - - +
68U LEU* 1.3 61.3 + - - +
69U GLU* 3.0 32.0 + - + +
72U GLN 3.9 0.2 - - - +
73U VAL* 3.4 2.3 - - - -
74U GLY* 2.6 42.7 + - - +
287U LEU* 3.4 41.1 + - + +
289U ARG* 3.4 25.7 + - - +
16V VAL 4.2 1.6 - - - -
17V ILE* 3.9 16.4 - - - +
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Residues in contact with LEU 68 (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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49U ILE* 3.6 20.9 - - + +
50U GLN* 3.2 30.7 - - - +
51U ALA* 3.8 11.7 - - + +
65U ALA* 4.1 9.9 - - + -
66U LEU* 4.8 4.7 - - - +
67U ASN* 1.3 68.0 - - - +
69U GLU* 1.3 63.5 + - - +
73U VAL* 3.7 15.5 - - + -
14V THR 3.8 1.6 - - - +
15V ALA* 3.2 6.6 - - - -
16V VAL* 3.0 55.2 + - + +
17V ILE* 4.8 0.4 - - - -
70V LEU 4.1 6.1 - - - +
72V ARG* 3.3 36.2 + - + +
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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