Contacts of the strand formed by residues 77 - 82 (chain Y) 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 THR 77 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Y SER* 4.2 5.6 - - - -
22Y CYS 3.1 24.9 - - - +
23Y ALA* 3.9 10.8 - - + +
29Y PHE* 3.4 7.7 - - - -
71Y SER* 3.3 2.1 - - - -
72Y ASP 2.8 33.2 + - - -
75Y LYS* 2.8 25.7 + - - +
76Y ASN* 1.3 78.4 + - - +
78Y ALA* 1.3 70.9 + - - +
79Y TYR* 3.8 32.3 + - + -
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Residues in contact with ALA 78 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Y SER* 3.6 0.5 - - - -
22Y CYS* 2.8 38.6 + - + -
29Y PHE* 4.0 2.3 - - + -
34Y ILE* 4.0 35.0 - - + +
36Y TRP* 3.9 11.8 - - + +
51Y ASN* 5.1 2.2 - - + +
69Y ILE* 5.5 1.1 - - + -
70Y SER 3.1 10.3 - - - +
71Y SER* 4.2 8.7 - - - +
77Y THR* 1.3 79.3 - - - +
79Y TYR* 1.3 61.4 + - - +
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Residues in contact with TYR 79 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Y ARG* 3.3 48.5 + - - +
20Y LEU 3.1 8.1 - - - +
21Y SER* 3.4 27.6 - - - -
36Y TRP* 3.7 4.0 - - - -
68Y THR 4.0 0.2 - - - +
69Y ILE* 3.4 9.9 - - - +
70Y SER* 2.6 52.4 + - - +
71Y SER 4.4 3.1 - - - -
72Y ASP* 3.7 24.6 + - + +
75Y LYS* 3.7 26.5 - - - +
77Y THR* 3.8 25.1 + - + +
78Y ALA* 1.3 78.1 - - - +
80Y LEU* 1.3 59.7 + - - +
81Y GLN* 4.0 0.9 - - + +
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Residues in contact with LEU 80 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Y LEU 3.9 0.5 - - - +
19Y ARG* 3.3 4.2 - - - -
20Y LEU* 2.7 41.0 + - + +
36Y TRP* 3.6 47.9 - - + -
48Y VAL* 4.4 8.1 - - + -
67Y PHE* 4.0 16.8 - - + -
68Y THR 3.6 10.3 - - - +
69Y ILE* 3.7 20.0 - - + -
79Y TYR* 1.3 72.3 - - - +
81Y GLN* 1.3 69.4 + - - +
82Y MET* 3.8 17.1 + - + +
90Y TYR* 4.0 23.8 - - + -
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Residues in contact with GLN 81 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Y SER* 2.7 30.5 + - - -
18Y LEU 3.6 13.1 + - - +
19Y ARG* 3.3 32.8 - - + +
66Y ARG 3.9 0.7 - - - +
67Y PHE* 3.3 4.9 - - - -
68Y THR* 2.8 48.5 + - + +
79Y TYR* 4.0 1.4 - - + -
80Y LEU* 1.3 72.4 - - - +
82Y MET* 1.3 89.6 + - + +
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Residues in contact with MET 82 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Y SER* 3.3 5.0 - - - -
18Y LEU* 2.8 39.4 + - - +
20Y LEU* 4.4 14.4 - - - -
67Y PHE* 3.4 26.7 - - + -
80Y LEU* 3.9 21.1 - - + +
81Y GLN* 1.3 77.8 - - - +
82Y ASN* 1.3 96.8 + - - +
86Y ASP 4.7 0.2 - - - +
90Y TYR* 3.0 51.6 - - + +
109Y VAL* 4.9 7.4 - - + -
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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