Contacts of the strand formed by residues 62 - 68 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54S LEU* 5.1 14.8 - - + -
55S VAL 3.3 12.1 - - - +
56S GLU* 3.6 27.1 - - + +
57S PHE* 4.7 4.5 - - - -
60S GLY 3.7 5.1 + - - +
61S VAL* 1.3 84.7 - - - +
63S GLY* 1.3 60.0 + - - +
77S LEU* 4.0 1.6 - - - +
78S PHE* 3.0 38.4 + - + +
93S THR* 5.8 4.7 - - + -
113S LEU* 4.4 18.7 - - - +
115S ASN* 5.1 9.0 - - - +
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Residues in contact with GLY 63 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54S LEU* 3.3 13.9 - - - +
55S VAL* 3.0 34.3 + - - +
57S PHE* 4.6 1.7 - - - -
62S LYS* 1.3 75.5 - - - +
64S MET* 1.3 63.3 + - - +
75S ILE* 4.5 1.1 - - - -
76S VAL 3.2 15.0 - - - -
77S LEU* 4.3 1.6 - - - -
78S PHE* 3.2 12.7 - - - -
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Residues in contact with MET 64 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52S GLU* 3.8 44.2 - - + +
53S GLU 3.5 11.2 - - - +
54S LEU* 4.1 11.7 - - + -
55S VAL* 4.6 0.7 - - - -
63S GLY* 1.3 74.5 - - - +
65S ALA* 1.3 60.4 + - - +
66S LEU* 4.1 17.5 - - + -
75S ILE* 3.5 7.0 - - - +
76S VAL* 3.0 48.8 + - + +
78S PHE* 4.1 7.2 - - + -
97S VAL* 3.9 9.2 - - + -
243S PRO* 5.1 3.1 - - - -
246S TYR* 5.2 5.8 - - + -
247S LEU* 3.5 36.3 - - + -
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Residues in contact with ALA 65 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49S ILE* 4.2 11.9 - - + -
50S GLN 4.8 2.2 - - - +
51S ALA* 3.9 1.7 - - - -
52S GLU* 2.8 33.3 + - - -
53S GLU 3.1 14.6 + - - +
64S MET* 1.3 70.9 - - - +
66S LEU* 1.3 59.6 + - - +
68S LEU* 4.5 9.0 - - + +
73S VAL* 3.8 17.3 - - + -
74S GLY 3.7 5.4 - - - +
75S ILE* 3.6 23.8 - - + +
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Residues in contact with LEU 66 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51S ALA* 5.6 3.3 - - - +
52S GLU* 4.1 29.2 + - + +
64S MET* 3.6 18.1 + - + -
65S ALA* 1.3 75.5 - - - +
67S ASN* 1.3 67.6 + - - +
68S LEU* 3.8 2.5 + - - +
74S GLY 3.4 4.9 + - - +
76S VAL* 4.0 23.3 - - + +
246S TYR* 5.1 14.4 - - + +
280S TYR* 6.6 0.4 - - + -
283S LEU* 4.9 15.3 - - + -
287S LEU* 3.9 24.0 - - + -
289S ARG* 3.6 28.2 + - - +
16W VAL* 3.7 10.2 - - - +
18W GLY* 3.9 5.0 + - - -
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Residues in contact with ASN 67 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66S LEU* 1.3 78.7 - - - +
68S LEU* 1.3 62.6 + - - +
69S GLU* 3.4 27.3 + - + +
73S VAL* 3.6 8.0 - - - +
74S GLY* 3.0 35.3 + - - +
287S LEU* 3.9 33.5 + - - +
289S ARG* 2.8 40.1 + - - +
16W VAL 4.0 2.7 - - - -
17W ILE* 3.5 21.5 - - + +
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Residues in contact with LEU 68 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49S ILE* 3.7 27.6 - - + +
50S GLN 4.1 5.2 - - - +
51S ALA* 3.8 26.2 - - + +
65S ALA* 4.5 7.0 - - + +
66S LEU 3.8 2.4 + - - +
67S ASN* 1.3 71.8 - - - +
69S GLU* 1.3 62.6 + - - +
72S GLN 4.8 1.3 - - - -
73S VAL* 3.9 17.5 - - + -
15W ALA* 3.1 9.0 - - - -
16W VAL* 2.9 49.7 + - + +
17W ILE* 4.8 0.6 - - - +
70W LEU 3.4 25.4 - - - +
72W ARG* 3.8 25.8 - - + +
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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