Contacts of the strand formed by residues 67 - 71 (chain F) in PDB entry 4MXV
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 67 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38F ARG* 4.0 4.7 - - - -
48F VAL* 4.4 15.3 - - + -
59F TYR* 3.4 23.9 - - + -
63F PHE* 3.1 49.2 + + + +
65F GLY 4.4 7.1 + - - -
66F ARG* 1.3 124.0 - - + +
68F THR* 1.3 60.7 + - - +
80F LEU* 4.0 11.9 - - + -
81F GLN 3.1 4.5 - - - +
82F MET* 3.5 53.4 - - + -
86F ASP* 3.9 8.3 - - - -
90F TYR* 4.6 5.8 - + - -
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Residues in contact with THR 68 (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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59F TYR* 3.3 8.3 - - - +
65F GLY 4.9 3.8 + - - -
66F ARG 4.2 5.0 + - - -
67F PHE* 1.3 74.7 + - - +
69F ILE* 1.3 70.7 + - - +
70F SER* 4.0 9.0 + - - +
79F TYR 3.7 2.1 - - - +
80F LEU* 3.7 0.4 - - - -
81F GLN* 2.7 51.5 + - + +
82F ASN* 4.4 6.4 - - - -
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Residues in contact with ILE 69 (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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34F ILE 4.9 0.7 - - - +
36F TRP* 3.6 26.0 - - + +
48F VAL* 4.2 10.1 - - + -
49F GLY* 3.5 37.7 - - - -
50F TYR 3.9 2.0 - - - +
51F ASN* 3.4 26.9 - - + +
57F THR* 3.1 24.1 - - + +
59F TYR* 2.7 31.3 + - + +
68F THR* 1.3 77.8 - - - +
70F SER* 1.3 68.4 + - - +
78F ALA* 5.8 0.9 - - + -
79F TYR 3.3 8.7 - - - +
80F LEU* 3.8 16.4 - - + -
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Residues in contact with SER 70 (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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51F ASN* 3.8 13.9 + - - -
68F THR* 4.6 10.1 + - - +
69F ILE* 1.3 77.9 - - - +
71F SER* 1.3 67.2 + - - +
78F ALA* 3.4 3.6 - - - +
79F TYR* 2.8 44.0 + - - +
81F GLN* 5.9 1.4 - - - +
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Residues in contact with SER 71 (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 PHE* 4.3 4.3 - - - -
51F ASN* 2.6 29.1 + - - -
52F PRO* 3.3 31.1 + - - +
55F ALA* 5.1 3.3 - - - +
70F SER* 1.3 79.7 - - - +
72F ASP* 1.3 64.4 + - - +
73F LYS* 4.2 2.0 - - - +
77F THR 3.2 13.2 - - - -
78F ALA* 4.2 2.2 - - - +
79F TYR* 4.3 4.9 - - - -
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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