Contacts of the strand formed by residues 63 - 68 (chain B) in PDB entry 3FPK
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 LEU 63 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B LEU 3.6 0.5 - - - +
23B THR* 3.1 5.4 - - - -
24B VAL* 2.7 52.1 + - + +
26B ALA* 3.9 36.3 - - + +
28B ILE* 3.7 38.1 - - + -
31B PHE* 4.5 1.6 - - + -
54B TYR* 3.9 12.6 - - + +
56B ASN* 3.4 21.3 - - - +
58B PRO 6.1 0.2 - - - +
60B ASN 4.0 4.7 - - - +
61B PRO* 3.0 14.9 + - + +
62B ASN* 1.3 69.7 - - - +
64B GLU* 1.3 58.1 + - - +
65B PHE* 4.1 15.8 - - + -
90B VAL* 5.0 2.0 - - + -
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Residues in contact with GLU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A PRO* 3.7 19.9 - - - +
15B TRP* 5.2 0.2 - - - -
21B SER* 4.2 7.7 - - - -
22B LEU 3.2 9.4 - - - +
23B THR* 4.4 12.8 + - - +
54B TYR 3.7 0.3 - - - -
55B VAL* 2.8 44.9 + - + -
56B ASN* 2.9 14.4 + - - +
60B ASN* 5.8 1.6 + - - -
62B ASN* 3.9 11.3 - - - +
63B LEU* 1.3 75.5 - - - +
65B PHE* 1.3 72.1 + - - +
151B TYR* 2.5 39.1 + - - +
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Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE 3.9 0.7 - - - +
21B SER* 3.1 7.4 - - - -
22B LEU* 2.9 42.7 + - + +
24B VAL* 4.2 18.2 - - + -
37B THR* 3.8 21.8 - - + -
39B LEU* 3.9 31.0 - - + -
52B TYR* 3.8 20.0 - - + -
53B SER 3.4 16.8 - - - -
54B TYR* 3.5 39.9 - + - -
55B VAL* 4.3 1.1 - - - -
63B LEU* 4.1 21.3 - - + -
64B GLU* 1.3 75.8 - - - +
66B TYR* 1.3 62.0 + - - +
67B LEU* 3.7 18.3 - - + +
90B VAL* 5.1 1.6 - - + -
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Residues in contact with TYR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B TRP* 3.8 9.2 - + - -
19B LEU* 3.8 13.0 - - + +
20B PHE 3.8 3.4 - - - -
21B SER* 3.5 18.8 - - - +
55B VAL* 3.8 20.4 - - + +
65B PHE* 1.3 73.4 - - - +
67B LEU* 1.3 56.8 + - - +
115B GLY 3.7 5.1 + - - -
116B THR* 3.4 51.6 - - + +
118B ILE* 3.7 24.2 - - + -
119B GLY* 5.1 0.7 - - - -
141B HIS* 4.4 4.4 - + - -
148B ASP 3.2 15.4 + - - -
150B SER* 2.7 40.5 + - - -
151B TYR* 3.5 14.1 - + + -
301B FAD 2.7 34.5 + - - +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 3.5 6.1 - - - +
20B PHE* 2.7 74.6 + - + +
22B LEU* 5.1 4.9 - - + -
39B LEU* 5.3 0.9 - - + -
52B TYR* 3.5 43.3 - - + +
65B PHE* 3.7 25.4 - - + +
66B TYR* 1.3 83.8 - - - +
68B VAL* 1.3 61.4 - - - +
76B SER* 4.8 4.5 - - - -
79B LEU* 3.6 23.6 - - + -
116B THR* 3.6 5.6 - - - -
301B FAD 3.2 3.8 - - - +
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ALA* 3.4 17.5 - - + +
19B LEU* 3.8 18.4 - - + -
20B PHE* 4.5 0.7 - - - -
67B LEU* 1.3 79.5 - - - +
69B THR* 1.3 68.6 + - - +
70B VAL* 3.2 13.2 + - + +
76B SER* 3.6 14.2 - - - -
116B THR* 3.6 5.4 - - + +
144B ARG* 5.6 8.3 - - - +
301B FAD 3.1 58.0 + - + +
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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