Contacts of the strand formed by residues 73 - 79 (chain F) in PDB entry 5LF4
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 VAL 73 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68F ASN* 3.7 3.0 - - - +
69F VAL* 3.0 49.6 + - + -
70F ASP* 3.1 15.0 + - + +
71F ARG 3.6 0.6 + - - -
72F HIS* 1.3 113.5 - - + +
74F GLY* 1.3 70.2 + - - +
106F ILE 5.0 1.1 - - - +
108F LEU* 3.5 33.0 - - + -
111F LEU* 3.9 14.1 - - + -
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Residues in contact with GLY 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F PHE* 3.8 26.2 - - - -
67F PHE 3.4 8.1 - - - -
68F ASN* 4.6 3.8 - - - -
69F VAL* 4.7 0.2 - - - -
72F HIS 4.2 0.8 + - - -
73F VAL* 1.3 86.9 - - - +
75F MET* 1.3 61.9 + - - +
108F LEU* 5.7 0.2 - - - +
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Residues in contact with MET 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F PHE* 4.4 2.8 - - - -
65F ARG 3.7 0.7 - - - +
66F LEU* 3.3 6.0 - - - +
67F PHE* 2.7 44.3 + - + +
69F VAL* 3.6 31.6 - - + -
74F GLY* 1.3 76.7 - - - +
76F ALA* 1.3 65.0 + - - +
77F VAL* 3.9 22.9 - - + -
84F ALA* 3.6 12.8 - - - +
87F LEU* 3.9 14.6 - - + +
88F ALA* 3.5 32.8 - - + +
91F ALA* 4.7 4.5 - - - -
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Residues in contact with ALA 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F ALA* 4.8 9.9 - - + -
37F ILE 5.4 1.3 - - - +
47F PHE* 3.8 30.0 - - + -
49F VAL* 4.8 5.4 - - + -
65F ARG 3.5 4.0 - - - -
66F LEU* 3.3 23.3 - - + -
75F MET* 1.3 75.6 - - - +
77F VAL* 1.3 63.6 + - - +
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Residues in contact with VAL 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F ALA* 3.9 7.9 - - - +
65F ARG* 2.8 68.4 + - + +
67F PHE* 3.8 19.7 - - + -
75F MET* 3.9 25.1 - - + -
76F ALA* 1.3 78.8 - - - +
78F ALA* 1.3 58.4 + - - +
79F GLY 6.0 0.9 - - - +
81F LEU* 4.1 6.1 - - + -
84F ALA* 3.6 34.8 - - + -
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Residues in contact with ALA 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F VAL* 4.0 30.0 - - + +
33F SER* 3.9 8.3 - - - +
34F SER 4.2 3.4 - - - +
36F ALA* 4.9 6.5 - - + +
65F ARG* 3.4 21.5 - - - +
77F VAL* 1.3 79.7 - - - +
79F GLY* 1.3 58.3 + - - +
84F ALA* 5.4 3.1 - - - +
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Residues in contact with GLY 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F ALA 3.9 9.0 - - - -
30F VAL* 3.9 23.6 - - - -
33F SER* 3.1 18.3 + - - -
65F ARG* 5.3 0.9 + - - +
77F VAL* 6.0 0.7 - - - +
78F ALA* 1.3 75.0 - - - +
80F LEU* 1.3 66.0 + - - -
81F LEU* 3.2 7.4 + - - +
84F ALA* 5.9 0.7 - - - -
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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