Contacts of the strand formed by residues 76 - 80 (chain E) in PDB entry 3MX4
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 TYR 76 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49E TYR* 3.7 34.2 + + - -
50E ALA* 3.3 3.3 - - - +
51E LEU* 2.8 51.2 + - + +
74E PRO* 3.4 1.3 - - - +
75E ILE* 1.3 84.4 - - + +
77E VAL* 1.3 80.6 + - - +
78E GLY* 3.9 3.2 - - - -
104E ARG* 4.8 3.5 + - - -
108E HIS* 4.1 6.1 - - - -
151E PRO* 3.6 0.6 - - - +
153E TRP* 3.7 33.9 - - + -
154E ASN* 3.4 23.9 + - - -
160E PHE* 3.9 18.8 - + + -
161E GLY* 3.4 28.0 - - - -
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Residues in contact with VAL 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E VAL* 4.2 8.5 - - + -
49E TYR 3.5 9.6 - - - +
50E ALA* 4.2 8.7 - - + -
74E PRO* 4.1 15.0 - - + -
76E TYR* 1.3 85.9 - - - +
78E GLY* 1.3 62.2 + - - +
142E GLN* 3.8 33.3 + - + +
145E LEU* 4.1 22.9 - - + -
146E ILE* 3.9 11.5 - - + +
151E PRO* 3.6 17.7 - - + -
154E ASN* 2.7 33.8 + - - +
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Residues in contact with GLY 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E VAL* 3.4 8.1 - - - +
49E TYR* 2.9 58.9 + - - +
76E TYR* 3.9 6.7 - - - -
77E VAL* 1.3 74.9 - - - +
79E LYS* 1.3 60.7 + - - -
104E ARG* 5.3 0.4 - - - -
142E GLN* 4.2 9.2 - - - -
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Residues in contact with LYS 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E GLY 3.3 9.9 - - - +
48E VAL* 4.6 0.7 - - - -
49E TYR* 3.4 5.8 + - - -
78E GLY* 1.3 75.9 - - - +
80E ALA* 1.3 64.4 + - - +
81E VAL* 4.5 19.9 - - + +
85E TRP* 5.0 14.8 - - - -
104E ARG* 3.5 18.3 + - - +
138E ILE* 3.7 25.6 - - + -
139E SER* 4.4 16.6 - - - -
142E GLN* 3.5 35.5 - - + +
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Residues in contact with ALA 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E ALA* 3.2 7.4 - - - +
47E GLY* 2.6 37.0 + - - +
49E TYR* 4.5 0.4 - - + -
79E LYS* 1.3 76.8 - - - +
81E VAL* 1.3 61.6 + - - +
100E GLU* 3.6 35.4 - - + +
101E LEU* 3.9 10.3 - - + -
104E ARG* 4.1 14.8 - - + -
138E ILE* 4.0 1.9 - - - +
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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