Contacts of the helix formed by residues 88 - 99 (chain D) in PDB entry 4U2M
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 ASN 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68D ALA* 5.2 10.3 - - + -
72D GLN* 3.6 18.8 - - - +
83D SER 3.0 23.4 + - - -
84D LEU* 3.5 6.6 - - - +
85D SER* 3.0 32.5 + - - +
87D GLU* 1.3 76.7 - - - +
89D VAL* 1.3 72.2 + - - +
90D ASP 3.2 3.2 + - - -
91D ASP* 3.3 13.8 + - + +
92D VAL* 2.9 26.3 + - + +
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Residues in contact with VAL 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D LEU* 4.7 3.8 - - + -
85D SER 2.7 26.7 - - - +
86D PRO* 4.0 10.4 + - + +
87D GLU 3.7 1.0 - - - -
88D ASN* 1.3 84.5 + - - +
90D ASP* 1.3 59.4 + - - +
92D VAL* 3.4 4.9 + - - +
93D LEU* 2.9 25.7 + - + +
108D CYS* 3.7 38.5 - - + +
111D LEU* 3.2 26.7 - - + -
112D LYS* 4.0 23.1 - - + -
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Residues in contact with ASP 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D PRO 5.3 4.7 + - - +
87D GLU 5.5 0.4 - - - -
88D ASN 3.3 0.4 - - - -
89D VAL* 1.3 75.8 - - - +
91D ASP* 1.3 63.7 + - - +
93D LEU* 3.3 8.6 + - - +
94D ALA* 2.9 31.4 + - - +
112D LYS* 2.9 40.1 + - - -
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Residues in contact with ASP 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D ASN* 2.8 34.3 + - - +
68D ALA* 4.2 12.3 - - + +
69D GLY* 3.5 14.4 - - - +
87D GLU 4.1 13.9 - - - +
88D ASN* 3.3 9.0 + - + +
90D ASP* 1.3 79.8 - - - +
92D VAL* 1.3 62.4 + - - +
94D ALA* 3.4 6.5 + - - +
95D VAL* 3.2 20.6 + - - +
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Residues in contact with VAL 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D GLY* 3.8 12.8 - - - -
72D GLN* 3.7 27.8 - - + -
73D VAL* 4.5 8.0 - - + +
82D LEU* 4.4 6.5 - - + -
84D LEU* 4.0 13.7 - - + -
88D ASN* 2.9 35.2 + - + +
89D VAL 3.8 3.6 - - - +
91D ASP* 1.3 75.1 - - - +
93D LEU* 1.3 59.7 + - - +
95D VAL* 3.3 2.8 + - - +
96D ALA* 2.9 26.9 + - - +
104D ILE* 3.5 27.4 - - + -
108D CYS* 3.7 9.4 - - - -
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Residues in contact with LEU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D VAL 2.9 17.8 + - - +
90D ASP* 3.6 7.2 - - - +
91D ASP 3.3 0.2 - - - -
92D VAL* 1.3 79.0 - - - +
94D ALA* 1.3 53.0 + - - +
96D ALA* 3.8 1.7 - - - -
97D THR* 2.6 49.1 + - - +
105D ILE* 4.0 38.1 - - + +
108D CYS* 3.8 14.6 - - + -
109D HIS* 3.9 25.8 - - + +
112D LYS* 4.5 18.2 - - - +
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Residues in contact with ALA 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D SER* 4.8 15.1 + - - +
66D ASN* 6.0 1.1 - - + -
90D ASP 2.9 17.0 + - - +
91D ASP* 3.8 7.4 - - - +
92D VAL 3.2 0.4 - - - -
93D LEU* 1.3 76.6 - - - +
95D VAL* 1.3 65.3 + - + +
97D THR* 3.3 6.8 + - - -
98D PHE* 3.1 23.2 + - - +
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Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D ILE* 4.2 15.7 - - + -
65D SER* 4.7 5.2 - - - +
66D ASN* 3.9 19.7 - - + +
69D GLY* 3.9 5.6 - - - -
70D LEU* 3.8 30.3 - - + +
73D VAL* 3.7 19.1 - - + -
91D ASP 3.2 13.5 + - - +
92D VAL 3.9 5.6 - - - +
94D ALA* 1.3 76.5 - - + +
96D ALA* 1.3 65.7 + - - +
98D PHE* 3.3 8.3 + - + +
99D LEU* 3.0 38.5 + - + +
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Residues in contact with ALA 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D VAL* 4.7 4.0 - - + +
92D VAL 2.9 18.1 + - - +
93D LEU* 3.8 4.5 - - - +
95D VAL* 1.3 79.8 - - - +
97D THR* 1.3 57.2 + - - +
99D LEU* 3.4 2.4 + - - +
100D GLN* 3.0 7.3 + - - -
101D MET* 2.8 36.7 + - + +
104D ILE* 3.5 35.0 - - + -
105D ILE* 3.8 14.2 - - + +
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Residues in contact with THR 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D LEU* 2.6 36.0 + - - +
94D ALA* 3.5 7.4 - - - -
96D ALA* 1.3 74.0 - - - +
98D PHE* 1.3 66.8 + - - +
100D GLN* 3.0 20.3 + - - +
105D ILE* 4.0 14.5 - - + +
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Residues in contact with PHE 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D TYR* 3.6 22.8 + + - -
62D LEU* 5.1 10.1 - - + -
63D ASP 3.4 28.3 - - - -
64D ILE* 4.4 20.4 - - + -
65D SER* 5.2 9.6 - - - +
94D ALA 3.1 9.9 + - - +
95D VAL* 3.5 11.2 - - - +
97D THR* 1.3 79.9 - - - +
99D LEU* 1.3 81.5 + - + +
100D GLN* 3.3 3.5 + - - +
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Residues in contact with LEU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D SER* 3.7 8.1 + - - +
48D TYR* 3.3 31.9 - - + +
49D PHE* 3.7 40.6 - - + -
52D LEU* 5.9 0.7 - - + -
64D ILE* 5.0 5.2 - - + -
70D LEU* 4.8 7.6 - - + -
73D VAL* 4.2 9.9 - - + -
95D VAL* 3.0 37.1 + - + +
96D ALA 4.1 2.9 - - - +
97D THR 3.2 0.4 - - - -
98D PHE* 1.3 100.0 - - + +
100D GLN* 1.3 70.5 + - - +
101D MET* 3.3 23.1 + - + +
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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