Contacts of the strand formed by residues 62 - 69 (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 LYS 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B GLU* 4.3 3.1 - - - -
59B VAL* 2.9 36.1 + - - +
60B ASP 3.0 7.2 + - - +
61B GLY* 1.3 79.3 - - - +
63B PRO* 1.3 75.1 - - + +
64B LEU* 3.3 0.9 + - - +
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Residues in contact with PRO 63 (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* 4.0 20.0 - - + -
57B LEU 3.7 5.8 - - - +
58B GLU* 4.4 1.3 - - + -
61B GLY 4.5 2.0 - - - +
62B LYS* 1.3 87.7 - - + +
64B LEU* 1.3 60.2 + - - +
65B THR* 3.9 12.2 + - + +
105B LEU* 3.6 24.5 - - + -
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Residues in contact with LEU 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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56B GLY* 3.1 2.9 - - - -
57B LEU 2.7 40.1 + - - +
59B VAL* 3.8 29.2 - - + -
62B LYS 3.3 1.0 + - - +
63B PRO* 1.3 72.5 - - - +
65B THR* 1.3 60.5 + - - +
66B ARG* 3.7 27.6 - - - +
90B PRO* 3.6 37.5 - - + +
91B LEU* 3.6 17.4 - - + +
94B ARG* 4.5 4.0 - - - +
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Residues in contact with THR 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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19B PHE* 3.7 35.6 - - + -
54B MET* 3.5 19.8 - - - +
55B VAL 3.3 16.8 - - - -
56B GLY* 3.9 12.6 - - - +
63B PRO* 3.9 17.9 + - + +
64B LEU* 1.3 80.8 - - - +
66B ARG* 1.3 82.2 + - - +
91B LEU* 4.5 0.9 - - - -
105B LEU* 4.3 5.4 - - + -
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Residues in contact with ARG 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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54B MET* 3.4 10.0 - - - -
55B VAL 2.8 30.2 + - - +
64B LEU* 3.7 22.5 - - - +
65B THR* 1.3 88.9 + - - +
67B ALA* 1.3 63.0 + - - +
68B TYR* 3.5 7.0 - - + -
90B PRO* 3.7 24.7 - - - +
91B LEU* 3.6 22.2 - - + -
301B FAD 3.0 72.3 + - - +
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Residues in contact with ALA 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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52B PHE* 3.8 21.8 - - + -
53B THR 3.5 5.6 - - - -
54B MET* 3.8 12.2 - - + +
66B ARG* 1.3 73.4 - - - +
68B TYR* 1.3 67.0 + - - +
301B FAD 2.7 66.9 + - + +
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Residues in contact with TYR 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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37B PHE* 5.9 0.2 - + - -
52B PHE* 3.6 5.1 - - - +
53B THR 2.8 30.5 + - - +
55B VAL* 3.7 18.4 - - + -
66B ARG* 3.5 11.2 - - + -
67B ALA* 1.3 84.8 - - - +
69B SER* 1.3 64.6 + - - +
70B ILE 3.4 0.5 + - - -
81B PHE* 3.6 31.0 - + + -
82B PHE 3.8 4.5 - - - -
83B SER* 2.7 34.4 + - - -
91B LEU* 4.0 19.5 - - + +
92B THR* 3.3 7.6 - - - +
95B LEU* 3.6 12.7 - - + +
301B FAD 2.7 65.2 + + - -
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Residues in contact with SER 69 (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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50B GLY 5.1 0.8 + - - -
51B GLU 3.9 2.5 - - - -
52B PHE* 3.7 9.5 - - - +
68B TYR* 1.3 72.9 - - - +
70B ILE* 1.3 62.0 + - - +
71B VAL* 3.4 8.1 + - - +
81B PHE* 3.4 12.4 - - - -
135B ALA* 3.9 2.9 - - - -
136B PRO* 3.2 47.9 - - - +
234B CYS* 5.2 1.2 - - - -
266B GLU* 4.3 5.9 + - - -
301B FAD 3.3 35.8 + - - +
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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