Contacts of the helix formed by residues 83 - 94 (chain A) in PDB entry 4UML
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 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A THR* 2.9 34.8 + - - +
81A ASP* 3.0 25.5 + - - +
82A LYS* 1.3 73.7 - - - +
84A PRO* 1.3 76.9 - - + +
85A VAL* 2.8 35.9 + - - +
86A SER* 3.1 14.4 + - - -
87A GLU* 2.9 29.0 + - - +
171A SER* 4.8 10.5 - - - -
173A LYS* 4.1 11.4 - - + -
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Residues in contact with PRO 84 (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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83A ASN* 1.3 90.3 - - + +
85A VAL* 1.3 66.8 + - + +
87A GLU* 3.6 14.5 + - + +
88A SER* 3.3 22.7 + - - -
171A SER* 6.1 1.1 - - - -
173A LYS* 6.0 0.2 - - + -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASP* 5.2 1.9 - - - +
63A VAL* 4.3 7.8 - - + +
72A VAL 4.1 0.7 - - - +
73A ASN* 4.0 6.3 - - - +
74A THR* 4.2 8.5 - - + +
83A ASN* 2.8 17.4 + - - +
84A PRO* 1.3 78.6 - - + +
86A SER* 1.3 63.5 + - - +
88A SER* 3.2 3.6 + - - -
89A ILE* 3.1 45.6 + - + +
167A CYS* 3.9 38.8 - - + -
168A VAL* 4.9 4.9 - - + +
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Residues in contact with SER 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 2.6 31.5 + - - +
74A THR 2.9 18.5 + - - -
75A SER* 4.5 2.4 + - - -
81A ASP 3.6 22.7 + - - -
83A ASN* 3.1 12.1 + - - -
85A VAL* 1.3 74.0 - - - +
87A GLU* 1.3 60.6 + - - +
89A ILE* 4.4 1.8 - - - -
90A PHE* 2.9 45.9 + - - -
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Residues in contact with GLU 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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82A LYS* 4.7 11.1 - - + +
83A ASN* 2.9 36.9 + - - +
84A PRO* 3.8 11.8 - - + +
86A SER* 1.3 78.2 - - - +
88A SER* 1.3 62.4 + - - +
90A PHE* 4.1 3.5 - - - +
91A MET* 3.2 25.7 + - - +
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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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62A ASP* 2.9 40.1 + - - -
64A ALA* 3.9 5.6 - - - -
84A PRO 3.3 11.3 + - - -
85A VAL 3.2 7.4 + - - -
87A GLU* 1.3 74.5 - - - +
89A ILE* 1.3 69.0 + - - +
91A MET* 3.3 6.0 + - - +
92A LEU* 2.9 32.0 + - - +
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Residues in contact with ILE 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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63A VAL* 4.1 5.4 - - + -
64A ALA* 4.0 12.8 - - + -
71A ILE* 3.6 24.0 - - + -
72A VAL 3.6 17.9 - - - +
73A ASN* 3.6 30.1 - - + +
85A VAL* 3.1 22.5 + - + +
86A SER* 4.0 5.2 - - - +
88A SER* 1.3 80.2 - - - +
90A PHE* 1.3 67.1 + - + +
92A LEU 3.8 0.3 - - - -
93A ALA* 2.9 28.9 + - - +
97A LEU* 5.0 0.2 - - + -
120A LEU* 4.0 8.6 - - + +
125A ILE* 3.9 30.1 - - + -
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Residues in contact with PHE 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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73A ASN* 3.9 26.7 - - - -
75A SER* 5.3 1.1 - - - -
79A LEU* 4.2 15.7 - - + -
80A THR* 5.2 4.3 - - - -
81A ASP 4.6 8.7 - - - -
86A SER* 2.9 34.4 + - - +
87A GLU* 4.2 2.9 - - - +
89A ILE* 1.3 73.4 - - + +
91A MET* 1.3 67.1 + - - +
93A ALA* 4.1 0.2 - - - -
94A GLY* 3.1 24.3 + - - +
97A LEU* 3.5 30.5 - - + -
101A LEU* 3.9 22.7 - - + -
127A HIS* 4.6 3.4 - + - -
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Residues in contact with MET 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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87A GLU 3.2 18.4 + - - +
88A SER* 3.6 6.5 - - - +
90A PHE* 1.3 81.1 - - - +
92A LEU* 1.3 75.6 + - + +
94A GLY* 3.5 9.2 + - - -
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Residues in contact with LEU 92 (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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62A ASP* 5.3 2.0 - - - +
64A ALA* 3.8 25.8 - - + +
65A LEU* 4.1 22.9 - - + -
88A SER* 2.9 17.7 + - - +
91A MET* 1.3 88.4 - - + +
93A ALA* 1.3 65.5 + - - +
119A ASN* 3.2 34.8 + - - +
120A LEU* 3.4 17.9 - - + -
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Residues in contact with ALA 93 (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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89A ILE 2.9 17.5 + - - +
90A PHE 4.2 0.7 - - - +
92A LEU* 1.3 79.5 - - - +
94A GLY* 1.3 58.0 + - - +
96A ASP* 5.2 0.5 + - - +
97A LEU* 3.9 28.7 - - + -
117A GLY 3.5 23.1 - - - +
118A PHE* 3.2 9.9 - - + +
119A ASN* 2.9 23.8 + - - +
120A LEU* 3.6 10.6 - - + +
125A ILE* 4.4 2.5 - - + -
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Residues in contact with GLY 94 (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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90A PHE 3.1 16.2 + - - +
91A MET 3.5 6.9 + - - -
92A LEU 3.3 3.2 - - - -
93A ALA* 1.3 76.6 - - - +
95A PRO* 1.3 77.2 - - - +
96A ASP 3.2 4.5 + - - -
97A LEU* 3.3 19.6 + - - +
119A ASN* 5.3 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