Contacts of the strand formed by residues 85 - 91 (chain A) in PDB entry 4M92
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 LEU 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A SER* 3.4 33.2 - - - +
46A ILE* 4.1 17.7 - - + -
75A TRP* 3.5 33.4 + - + -
82A SER* 3.7 5.2 + - - +
83A ASN 3.5 1.4 + - - -
84A LYS* 1.3 80.3 - - - +
86A PHE* 1.3 74.9 + - - +
87A PHE* 4.3 11.4 - - + -
141A ILE* 4.1 17.3 - - + -
145A THR* 4.3 12.1 - - + +
147A VAL* 3.8 34.3 - - + -
149A ILE* 4.2 12.1 - - + -
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Residues in contact with PHE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 4.7 3.1 - - + -
15A LEU* 3.8 31.2 - - + -
16A MET* 3.6 32.8 - - + -
19A SER* 3.7 10.8 - - - -
25A PHE* 3.7 28.5 - + + -
43A TYR* 3.9 26.5 - + - -
44A SER 3.2 5.7 + - - +
45A MET* 3.5 19.3 - - + +
46A ILE* 2.9 29.1 + - - +
75A TRP* 5.0 2.0 - - - +
81A PHE* 5.8 2.2 - + - -
82A SER 4.7 1.6 - - - -
83A ASN* 3.3 32.5 - - + -
85A LEU* 1.3 78.1 - - - +
87A PHE* 1.3 68.1 + - - +
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Residues in contact with PHE 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A SER 3.9 15.0 + - - +
24A ILE* 3.3 10.4 - - + -
25A PHE* 2.9 26.6 + - - -
45A MET* 4.4 0.2 - - - -
46A ILE* 3.5 14.4 - - + -
68A TYR* 3.5 27.1 - + + +
71A LEU* 3.6 27.6 - - + -
72A ALA* 4.2 13.0 - - + -
75A TRP* 3.6 42.4 - + + -
85A LEU* 4.3 11.7 - - + -
86A PHE* 1.3 74.8 - - - +
88A SER* 1.3 63.8 + - - +
141A ILE* 3.6 14.1 - - + -
149A ILE* 3.5 25.4 - - + -
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Residues in contact with SER 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 3.9 4.3 - - - -
25A PHE* 3.2 16.8 - - - +
27A MET* 3.2 29.3 - - - +
36A ILE* 4.2 7.2 - - - -
45A MET* 3.0 24.2 - - - -
46A ILE 2.8 12.3 + - - -
47A VAL* 3.4 5.7 - - - -
48A MET 3.0 14.0 + - - -
68A TYR* 2.8 18.4 + - - -
87A PHE* 1.3 74.1 + - - +
89A MET* 1.3 60.4 + - - +
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Residues in contact with MET 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 3.8 21.7 - - + +
25A PHE 2.8 6.3 + - - -
26A ARG* 4.0 34.5 - - + +
27A MET* 2.9 26.3 + - - +
47A VAL* 4.5 0.4 - - - -
48A MET* 3.2 25.1 - - + +
50A THR* 4.3 17.7 - - + -
52A LEU* 4.5 9.4 - - + -
65A ASN* 3.7 22.7 - - - +
68A TYR* 4.6 0.2 - - + -
69A GLN* 4.0 11.2 - - - +
88A SER* 1.3 75.4 - - - +
90A VAL* 1.3 69.3 + - - +
91A ASP* 5.0 3.8 - - - +
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A MET* 3.8 24.9 - - + +
32A PHE* 3.9 29.2 - - + -
47A VAL* 4.0 10.5 - - + +
48A MET 2.9 8.3 + - - -
49A PHE* 3.4 14.6 - - + -
50A THR* 2.9 26.4 + - - +
89A MET* 1.3 78.8 - - - +
91A ASP* 1.3 68.0 - - - +
95A GLY* 4.0 18.6 - - - +
98A VAL* 4.2 11.7 - - + -
99A PHE* 3.6 12.9 - - + -
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Residues in contact with ASP 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ARG* 5.4 5.0 + - + +
27A MET 4.5 2.6 + - - -
50A THR* 3.3 13.3 - - + +
51A ALA* 3.8 2.0 - - - -
52A LEU* 2.9 39.6 + - - +
53A GLN* 4.1 10.0 + - - +
89A MET* 4.2 6.9 - - - +
90A VAL* 1.3 73.1 - - - +
92A TYR* 1.3 61.7 + - - +
93A ASP* 2.9 37.2 + - - +
94A GLU* 3.0 30.1 + - - +
95A GLY* 2.8 28.1 + - - -
99A PHE* 4.0 1.1 - - - -
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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