Contacts of the strand formed by residues 34 - 39 (chain B) in PDB entry 4FK8
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 34 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B TRP* 3.0 29.5 + - + -
31B THR* 3.1 20.6 + - + +
33B THR* 1.3 93.5 - - - +
35B PHE* 1.3 63.3 + - - +
82B PHE* 3.8 32.8 - - + -
83B SER 3.4 10.5 - - - +
84B ILE* 3.9 18.6 - - + -
85B LYS* 3.3 4.0 + - - +
132B THR* 4.0 12.1 - - + -
164B GLU* 3.4 41.3 - - + +
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Residues in contact with PHE 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 4.7 6.7 - - + -
28B HIS 3.1 13.5 - - - +
29B HIS* 3.5 24.7 - + - +
30B TRP* 4.4 3.4 - - - -
34B LEU* 1.3 75.9 - - - +
36B SER* 1.3 68.7 + - - +
37B PHE* 3.9 20.4 - + - -
82B PHE* 3.6 3.4 - - - -
83B SER* 2.6 74.1 + - - +
84B ILE 3.6 6.5 - - - -
85B LYS* 3.5 20.0 - - + -
92B THR* 4.9 1.3 - - - -
95B LEU* 3.3 44.2 - - + -
96B GLN* 3.8 13.9 - - + -
98B LEU* 4.5 2.9 - - + -
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Residues in contact with SER 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 3.6 3.6 - - - +
28B HIS* 2.8 43.0 + - - +
30B TRP* 2.8 23.6 + - - -
35B PHE* 1.3 75.7 - - - +
37B PHE* 1.3 67.1 + - - +
80B GLU* 3.9 6.2 + - - -
81B PHE 3.1 14.4 - - - -
82B PHE* 4.3 1.8 - - - -
167B TYR* 3.6 29.3 - - - -
170B TYR* 5.6 0.3 - - - -
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Residues in contact with PHE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 4.4 6.1 - - + -
26B SER 3.2 16.4 - - - +
27B VAL* 4.2 12.6 - - + +
28B HIS* 4.7 2.2 - - - -
35B PHE* 3.9 14.6 - + - -
36B SER* 1.3 77.3 - - - +
38B THR* 1.3 73.7 + - - +
39B CYS* 4.3 13.2 - - + -
55B VAL* 4.1 18.2 - - + -
68B TYR* 5.9 0.2 - + - -
80B GLU* 3.3 4.5 - - - +
81B PHE* 3.0 71.4 + + + +
83B SER* 5.4 2.9 - - - -
95B LEU* 4.3 16.2 - - + -
98B LEU* 3.8 31.2 - - + -
104B VAL* 4.4 11.2 - - + -
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Residues in contact with THR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 3.6 4.5 - - - +
25B LEU* 2.8 34.4 + - - +
26B SER* 2.7 39.9 + - - +
28B HIS* 5.2 3.6 - - + +
37B PHE* 1.3 79.4 - - - +
39B CYS* 1.3 58.7 + - - +
78B HIS* 3.6 29.8 - - + +
79B LEU 3.1 10.8 - - - +
80B GLU* 4.0 18.8 - - + +
170B TYR* 4.9 3.8 - - - +
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Residues in contact with CYS 39 (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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22B ALA* 4.0 9.6 - - + -
23B THR 3.2 19.7 - - - +
24B VAL* 4.1 1.6 - - - -
25B LEU* 3.6 8.5 - - - -
37B PHE* 4.3 6.7 - - + -
38B THR* 1.3 76.6 - - - +
40B THR* 1.3 71.7 - - - +
78B HIS* 3.3 5.0 - - - +
79B LEU* 2.9 48.5 + - - -
81B PHE* 4.1 7.0 - - - -
104B VAL* 4.0 13.7 - - + -
106B ILE* 4.1 18.6 - - - -
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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
------------------------------------------------------------
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