Contacts of the strand formed by residues 84 - 92 (chain M) in PDB entry 4UJ3
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 ALA 84 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13M LYS* 3.5 16.2 - - + +
15M VAL* 3.8 37.0 - - + -
81M TYR* 3.0 20.9 + - + +
82M ARG 3.1 2.2 + - - -
83M GLY* 1.3 77.2 + - - +
85M VAL* 1.3 60.3 + - - +
86M GLY 3.5 1.3 - - - +
114M ASP* 5.0 10.4 + - - +
117M ILE* 3.7 20.5 - - + +
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Residues in contact with VAL 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M PHE* 3.9 24.0 - - + -
13M LYS 2.9 17.4 + - - +
83M GLY 3.5 14.6 - - - +
84M ALA* 1.3 73.5 - - - +
86M GLY* 1.3 58.1 + - - +
116M ASN 4.6 0.9 - - - +
117M ILE* 3.5 10.8 - - - +
118M VAL* 3.0 21.3 + - - +
172M ILE* 3.6 36.4 - - + +
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Residues in contact with GLY 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M LYS 3.5 2.1 + - - +
14M VAL* 3.2 12.3 - - - -
15M VAL* 3.1 24.4 + - - +
84M ALA* 3.5 1.7 - - - +
85M VAL* 1.3 84.1 - - - +
87M ALA* 1.3 60.5 + - - +
117M ILE* 3.6 4.5 - - - +
118M VAL* 3.0 11.7 - - - -
168M ILE* 4.3 2.5 - - - -
172M ILE* 3.5 17.0 - - - -
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Residues in contact with ALA 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M VAL* 4.2 0.4 - - - -
15M VAL* 3.4 21.8 - - + +
17M ILE* 4.8 4.3 - - + -
86M GLY* 1.3 75.4 - - - +
88M LEU* 1.3 61.0 + - - +
89M LEU 3.7 0.7 + - - -
109M LEU* 4.0 25.6 - - + -
117M ILE* 4.0 13.5 - - + -
118M VAL 2.7 10.7 + - - +
119M ILE* 3.4 3.3 - - + +
120M MET 2.8 28.2 + - - +
168M ILE* 3.5 7.6 - - - +
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Residues in contact with LEU 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M VAL* 4.3 8.0 - - + +
15M VAL 3.0 8.1 + - - -
16M LEU* 3.5 24.2 - - + -
17M ILE* 3.1 26.5 + - - +
27M LEU* 5.6 3.6 - - + -
87M ALA* 1.3 69.8 - - - +
89M LEU* 1.3 61.4 + - - +
90M VAL* 3.4 10.9 + - + +
120M MET* 3.3 48.2 - - + +
122M VAL* 4.4 6.7 - - + -
164M ALA* 5.6 1.3 - - + -
165M PHE* 3.2 44.2 - - + -
168M ILE* 3.7 16.2 - - + -
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Residues in contact with LEU 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M ILE* 3.5 22.2 - - + +
87M ALA 3.7 1.8 + - - -
88M LEU* 1.3 69.3 - - - +
90M VAL* 1.3 67.5 + - - +
102M VAL* 4.1 23.3 - - + -
105M TRP* 3.8 22.4 - - + -
106M LEU* 3.5 46.9 - - + +
109M LEU* 4.6 2.7 - - + -
119M ILE* 4.3 13.5 - - + -
120M MET 2.8 13.5 + - - +
121M LEU* 3.3 21.4 - - + +
122M VAL 2.9 25.8 + - - +
148M LEU* 5.2 1.3 - - + -
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Residues in contact with VAL 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M LEU* 4.5 2.9 - - + -
17M ILE 2.8 14.0 + - - +
18M GLY* 3.4 18.9 - - - -
19M ASP 3.9 0.9 + - - -
22M VAL* 3.2 41.4 - - + +
24M LYS* 4.1 10.5 - - + +
27M LEU* 3.9 24.0 - - + -
88M LEU* 3.5 22.0 - - + +
89M LEU* 1.3 76.6 - - - +
91M TYR* 1.3 68.9 + - - +
98M THR 4.9 1.7 - - - +
105M TRP* 5.4 0.7 - - - -
122M VAL* 2.7 16.6 - - + +
124M ASN* 4.1 11.2 - - + -
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Residues in contact with TYR 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M VAL* 3.7 10.3 - - - -
90M VAL* 1.3 79.7 - - - +
92M ASP* 1.3 70.9 + - - +
93M ILE* 3.3 35.1 - - + +
98M THR* 3.4 23.8 - - - +
99M TYR* 4.0 22.4 - + + -
102M VAL* 4.0 4.7 - - + -
121M LEU* 3.9 32.3 - - + -
122M VAL 2.5 17.1 + - - +
123M GLY* 3.2 24.8 - - - -
124M ASN* 3.2 25.5 + - - +
134M VAL* 3.8 14.3 + - + +
139M ALA* 3.3 24.9 - - + +
150M PHE* 3.4 13.9 - + - -
152M GLU* 4.1 0.5 + - - -
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Residues in contact with ASP 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M GLY 4.1 0.2 - - - +
22M VAL* 3.7 14.4 - - - +
91M TYR* 1.3 77.5 - - - +
93M ILE* 1.3 65.3 + - - +
94M ALA* 3.0 16.8 + - - +
95M LYS* 2.6 56.0 + - + +
98M THR* 2.8 26.3 + - + +
124M ASN 4.0 2.2 - - - -
125M LYS* 3.1 37.2 + - - +
134M VAL* 4.6 1.4 - - - +
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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