Contacts of the strand formed by residues 52 - 59 (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 PHE 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B GLU* 1.3 73.8 - - - +
53B THR* 1.3 68.2 + - - +
54B MET* 4.7 9.2 - - - -
67B ALA* 3.8 26.0 - - + -
68B TYR 3.3 22.4 - - - +
69B SER* 3.7 7.4 - - - +
70B ILE* 4.2 2.2 - - - +
110B PRO* 3.1 7.6 - - - +
111B THR* 2.7 70.0 + - + -
112B GLY* 3.8 7.6 - - - -
266B GLU* 3.6 24.2 - - + +
301B FAD 3.6 25.1 - - + -
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Residues in contact with THR 53 (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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45B LEU* 5.3 2.0 - - + -
52B PHE* 1.3 81.8 - - - +
54B MET* 1.3 77.0 + - - +
67B ALA* 3.5 1.9 - - - -
68B TYR* 2.8 33.5 + - - +
70B ILE* 4.1 19.7 - - + +
81B PHE* 4.1 13.7 - - + -
106B ILE* 4.0 18.2 - - + -
107B GLY* 2.7 26.6 + - - +
109B LYS 4.3 3.4 + - - -
110B PRO* 4.1 18.4 - - - +
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Residues in contact with MET 54 (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 PHE* 3.7 26.7 - - + -
52B PHE* 4.7 8.7 - - + -
53B THR* 1.3 81.5 + - - +
55B VAL* 1.3 63.0 - - - +
65B THR* 3.5 21.3 - - - +
66B ARG* 3.4 19.3 - - - -
67B ALA* 3.8 22.9 - - + +
106B ILE* 3.4 3.6 - - - -
107B GLY* 2.6 29.8 + - - -
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Residues in contact with VAL 55 (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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37B PHE* 4.1 17.9 - - + -
53B THR* 4.3 2.0 - - + +
54B MET* 1.3 80.1 - - - +
56B GLY* 1.3 63.9 + - - +
65B THR* 3.8 4.0 - - - -
66B ARG 2.8 27.6 + - - +
68B TYR* 3.7 26.7 - - + -
81B PHE* 3.5 38.8 - - + -
91B LEU* 3.4 7.3 - - - +
95B LEU* 4.7 8.7 - - + -
104B VAL* 4.0 15.9 - - + -
105B LEU 3.2 8.7 - - - +
106B ILE* 3.9 6.1 - - + -
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Residues in contact with GLY 56 (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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55B VAL* 1.3 79.4 - - - +
57B LEU* 1.3 66.2 - - - +
64B LEU 3.1 12.6 - - - -
65B THR* 3.9 5.7 - - - +
91B LEU* 3.9 8.7 - - - -
95B LEU* 4.9 0.9 - - - -
104B VAL* 3.3 11.2 - - - +
105B LEU* 2.9 36.6 + - - -
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Residues in contact with LEU 57 (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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56B GLY* 1.3 83.2 - - - +
58B GLU* 1.3 62.2 + - - +
59B VAL* 3.2 13.4 + - + -
64B LEU* 2.7 38.2 + - - +
91B LEU* 4.0 12.6 - - + -
94B ARG* 3.7 35.4 - - + +
95B LEU* 4.0 18.6 - - + +
98B LEU* 4.2 18.6 - - + -
103B PRO 3.8 21.8 - - - +
104B VAL* 4.4 1.8 - - - +
105B LEU* 3.8 8.0 - - - +
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Residues in contact with GLU 58 (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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57B LEU* 1.3 70.8 - - - +
59B VAL* 1.3 62.1 + - - +
60B ASP 4.2 1.0 + - - -
61B GLY* 5.0 6.3 - - - +
62B LYS 3.7 14.1 - - - +
63B PRO* 4.4 2.0 - - - -
105B LEU* 3.9 15.8 - - + +
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Residues in contact with VAL 59 (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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57B LEU* 3.2 17.0 + - + +
58B GLU* 1.3 76.4 - - - +
60B ASP* 1.3 83.7 + - - +
61B GLY 3.4 0.9 - - - -
62B LYS* 2.9 28.2 + - - +
64B LEU* 3.8 23.8 - - + -
94B ARG* 3.7 54.7 - - - +
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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