Contacts of the helix formed by residues 92 - 103 (chain A) in PDB entry 1U78
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 SER 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A ARG* 4.4 3.8 - - - +
91A ALA* 1.3 73.8 - - - +
93A LYS* 1.3 65.5 + - - +
94A ARG* 3.6 9.7 + - - +
95A THR* 2.9 27.5 + - - -
96A ILE* 3.2 10.0 + - - +
20B T 2.7 60.2 + - - -
21B T 4.8 6.1 - - - -
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Residues in contact with LYS 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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80A ALA* 3.8 16.3 - - + +
81A ARG* 3.9 23.1 - - + +
84A ARG* 4.2 11.8 - - - +
91A ALA 3.5 1.6 + - - -
92A SER* 1.3 72.7 - - - +
94A ARG* 1.3 64.5 + - + +
96A ILE* 3.4 13.0 + - - +
97A LEU* 3.3 22.9 + - + +
31C T 3.8 35.9 + - - +
32C G 3.0 55.1 + - - -
33C G 5.5 0.8 + - - -
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Residues in contact with ARG 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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92A SER* 3.6 3.3 + - - +
93A LYS* 1.3 79.5 - - - +
95A THR* 1.3 59.9 + - - +
97A LEU* 3.1 25.9 + - - +
98A ASN* 2.9 49.3 + - - +
20B T 3.9 15.0 - - + +
21B T 3.5 37.4 + - + +
22B C 4.1 4.7 - - - +
33C G 3.3 36.3 + - - +
34C G 2.8 51.4 + - - -
35C A 4.2 3.9 + - - +
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Residues in contact with THR 95 (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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60A ALA* 4.5 4.7 - - + -
61A LEU* 4.6 11.7 - - + -
91A ALA* 4.5 12.3 - - + -
92A SER* 2.9 13.8 + - - -
94A ARG* 1.3 70.7 - - - +
96A ILE* 1.3 67.9 + - - +
98A ASN* 3.0 13.1 + - + +
99A VAL* 2.9 28.0 + - + +
102A ARG* 5.8 0.9 - - - +
19B T 3.1 37.7 + - - +
20B T 2.5 33.3 + - - +
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Residues in contact with ILE 96 (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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61A LEU* 4.7 2.9 - - + -
69A VAL* 4.2 26.0 - - + -
80A ALA* 3.9 22.9 - - + +
83A ILE* 4.4 5.6 - - + -
84A ARG* 3.7 28.0 - - + +
89A LEU* 4.3 11.7 - - + -
91A ALA* 3.4 22.0 - - + +
92A SER 3.2 21.6 + - - +
93A LYS* 3.5 7.0 - - - +
95A THR* 1.3 78.7 - - - +
97A LEU* 1.3 57.4 + - - +
99A VAL* 3.0 11.3 + - - +
100A ILE* 2.9 45.9 + - + +
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Residues in contact with LEU 97 (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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80A ALA* 3.6 21.3 - - + +
93A LYS* 3.3 12.5 + - - +
94A ARG* 3.1 27.2 + - - +
96A ILE* 1.3 78.6 - - - +
98A ASN* 1.3 58.3 + - - +
100A ILE* 3.3 17.6 + - + +
101A LYS* 2.9 32.0 + - - +
32C G 3.5 67.1 - - + +
33C G 4.0 12.3 + - - +
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Residues in contact with ASN 98 (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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94A ARG* 2.9 33.6 + - - +
95A THR* 3.2 11.9 + - - +
97A LEU* 1.3 76.5 - - - +
99A VAL* 1.3 56.5 + - - +
101A LYS* 3.4 10.1 + - - +
102A ARG* 2.9 59.6 + - - +
19B T 4.5 12.7 + - - +
20B T 3.9 25.1 + - - +
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Residues in contact with VAL 99 (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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61A LEU* 4.2 16.4 - - + -
66A GLU* 3.5 44.6 - - + +
69A VAL* 3.9 20.0 - - + -
70A ILE* 4.1 15.3 - - + -
95A THR* 2.9 20.7 + - + +
96A ILE 3.3 7.6 - - - +
98A ASN* 1.3 72.7 - - - +
100A ILE* 1.3 66.9 + - - +
102A ARG* 3.1 26.6 + - - +
103A SER* 3.0 16.9 + - - +
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Residues in contact with ILE 100 (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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69A VAL* 3.8 13.9 - - + +
70A ILE* 5.3 3.6 - - - -
73A ALA* 4.0 30.5 - - + -
78A LYS 6.1 0.2 - - - +
80A ALA* 5.0 3.6 - - - -
83A ILE* 4.1 10.5 - - + -
96A ILE* 2.9 38.1 + - + +
97A LEU* 3.3 21.5 + - + +
99A VAL* 1.3 74.4 - - - +
101A LYS* 1.3 61.3 + - - +
103A SER* 3.3 21.7 + - - -
104A GLY 4.3 2.8 + - - -
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Residues in contact with LYS 101 (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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97A LEU 2.9 17.7 + - - +
98A ASN* 3.7 11.0 - - - +
100A ILE* 1.3 73.7 - - - +
102A ARG* 1.3 63.4 + - + +
103A SER 3.1 3.1 + - - -
104A GLY* 3.3 16.2 + - - -
33C G 4.6 27.1 - - + +
34C G 4.3 19.8 + - - -
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Residues in contact with ARG 102 (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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59A LYS* 3.6 27.6 - - - +
66A GLU* 3.7 10.7 + - - -
95A THR* 5.5 1.4 + - - +
98A ASN* 2.9 44.0 + - - +
99A VAL* 3.1 20.2 + - - +
101A LYS* 1.3 75.6 - - + +
103A SER* 1.3 56.9 + - - +
104A GLY 3.2 4.7 + - - -
18B C 5.0 3.6 - - - +
19B T 3.0 30.1 + - - +
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Residues in contact with SER 103 (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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70A ILE* 3.3 38.7 - - - +
99A VAL 3.0 14.4 + - - -
100A ILE* 3.6 9.8 + - - -
101A LYS 3.1 1.6 - - - -
102A ARG* 1.3 75.9 - - - +
104A GLY* 1.3 59.6 + - - +
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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