Contacts of the helix formed by residues 89 - 101 (chain A) in PDB entry 3DC6
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 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A GLU 3.6 1.6 + - - -
88A PRO* 1.3 75.8 - - - +
90A ALA* 1.3 64.2 + - - +
91A GLU* 3.7 14.0 + - - +
92A LEU* 3.1 24.6 + - - +
93A LEU* 2.9 21.9 + - - +
189A SER* 2.9 26.6 + - - -
192A PHE* 5.1 1.0 - - - -
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Residues in contact with ALA 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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89A SER* 1.3 73.1 - - - +
91A GLU* 1.3 68.1 + - - +
93A LEU* 3.3 6.2 + - - +
94A THR* 3.0 34.1 + - - +
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Residues in contact with GLU 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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89A SER* 3.2 12.1 - - - +
90A ALA* 1.3 89.3 + - - +
92A LEU* 1.3 61.9 + - - +
94A THR* 3.4 7.4 + - - -
95A ALA* 3.1 21.8 + - - +
192A PHE* 3.8 16.7 - - + -
196A GLN* 5.4 2.9 - - - +
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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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88A PRO* 4.0 4.3 - - + -
89A SER* 3.1 21.9 + - - +
91A GLU* 1.3 73.5 - - - +
93A LEU* 1.3 61.3 + - - +
95A ALA* 3.2 2.4 + - - +
96A ILE* 2.8 49.8 + - + +
125A LEU* 5.1 2.2 - - + -
134A LEU* 4.2 12.1 - - + -
154A LEU* 4.8 5.2 - - + -
185A TRP* 3.8 29.2 - - + -
188A VAL* 3.8 15.5 - - + -
189A SER* 3.5 22.7 - - - +
192A PHE* 3.9 36.3 - - + -
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Residues in contact with LEU 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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88A PRO* 4.2 21.9 - - + +
89A SER 2.9 17.8 + - - +
90A ALA* 3.8 5.8 - - - +
92A LEU* 1.3 76.7 - - - +
94A THR* 1.3 56.8 + - - +
96A ILE* 3.6 8.6 - - + +
97A LYS* 2.9 66.2 + - + +
103A LEU* 4.5 24.0 - - + +
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Residues in contact with THR 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 ALA* 3.0 19.1 + - - +
91A GLU* 3.6 8.0 - - - -
92A LEU 3.3 0.2 - - - -
93A LEU* 1.3 76.5 - - - +
95A ALA* 1.3 56.7 + - - +
97A LYS* 3.5 7.7 + - - +
98A SER* 2.9 30.3 + - - -
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Residues in contact with ALA 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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91A GLU 3.1 7.2 + - - +
92A LEU 3.2 6.9 + - - +
94A THR* 1.3 73.1 - - - +
96A ILE* 1.3 61.7 + - - +
98A SER* 3.3 6.1 + - - -
99A ASP* 2.9 38.5 + - - +
134A LEU* 3.6 15.7 - - + -
192A PHE* 3.6 31.4 - - + -
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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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88A PRO* 4.5 6.7 - - + -
92A LEU* 2.8 43.5 + - + +
93A LEU* 3.6 9.2 - - + +
95A ALA* 1.3 73.0 - - - +
97A LYS* 1.3 55.6 + - - +
100A PHE* 2.7 36.1 + - - +
101A GLY 3.4 0.3 + - - -
102A SER 3.7 20.0 - - - +
103A LEU* 3.8 30.5 - - + +
106A LEU* 3.8 33.7 - - + -
125A LEU* 5.2 0.7 - - + -
134A LEU* 3.8 15.0 - - + -
185A TRP* 4.1 10.3 - - + -
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Residues in contact with LYS 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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93A LEU* 2.9 54.9 + - + +
94A THR* 3.8 6.3 - - - +
96A ILE* 1.3 75.5 - - - +
98A SER* 1.3 59.7 + - - +
101A GLY* 2.8 45.9 + - - +
102A SER* 4.5 8.7 - - - +
103A LEU 5.8 0.7 - - - +
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Residues in contact with SER 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 THR* 2.9 19.7 + - - -
95A ALA* 3.6 7.6 - - - -
96A ILE 3.2 0.2 - - - -
97A LYS* 1.3 79.6 - - - +
99A ASP* 1.3 68.0 + - - +
101A GLY 4.7 0.3 + - - -
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Residues in contact with ASP 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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95A ALA* 2.9 22.4 + - - +
98A SER* 1.3 85.9 + - - +
100A PHE* 1.3 83.9 + - + +
101A GLY 3.8 0.2 - - - -
132A LYS 5.0 0.2 - - - +
133A ILE* 3.6 25.9 - - + +
134A LEU* 2.8 36.7 + - + +
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Residues in contact with PHE 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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96A ILE* 2.7 25.9 + - - +
99A ASP* 1.3 84.0 - - + +
101A GLY* 1.3 56.5 + - - +
102A SER 3.2 14.6 - - - +
105A ASN* 3.0 28.1 + - + +
106A LEU* 3.7 41.7 - - + +
109A GLN* 3.7 36.6 - - - -
125A LEU* 4.2 2.5 - - + -
134A LEU* 3.6 42.8 - - + -
135A LYS* 4.1 4.9 - - - -
136A VAL* 3.8 17.9 - - + -
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Residues in contact with GLY 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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96A ILE 3.4 0.4 + - - -
97A LYS* 2.8 35.3 + - - +
98A SER 4.7 0.4 + - - -
99A ASP 3.8 0.6 - - - -
100A PHE* 1.3 75.5 - - - +
102A SER* 1.3 60.9 + - - +
105A ASN* 4.2 6.1 - - - -
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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