Contacts of the helix formed by residues 97 - 108 (chain A) in PDB entry 3DEW
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 GLN 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A THR* 4.2 9.7 + - + +
16A GLU* 2.7 41.2 + - - +
19A ALA* 3.6 17.5 - - + +
60A GLN* 3.9 10.1 - - - +
95A ASN* 2.9 14.4 + - - +
96A PRO* 1.3 80.3 - - + +
98A LEU* 1.3 66.4 + - - +
99A LEU 3.3 0.4 - - - -
100A ARG* 2.5 59.3 + - - +
101A PHE* 3.4 15.6 - - + -
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Residues in contact with LEU 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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60A GLN* 3.4 36.6 - - + +
61A PHE* 4.1 30.5 - - + -
64A PHE* 4.4 5.8 - - + -
91A ARG* 3.3 41.7 - - + +
92A HIS* 4.5 14.6 - - + +
95A ASN* 3.0 28.6 + - + +
96A PRO 3.3 0.2 - - - -
97A GLN* 1.3 78.2 - - - +
99A LEU* 1.3 59.5 + - - +
100A ARG 3.1 0.7 + - - -
101A PHE* 3.1 3.4 + - + -
102A TYR* 2.8 35.7 + - + +
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Residues in contact with LEU 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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92A HIS* 3.6 26.9 + - + +
95A ASN 4.8 0.2 + - - -
96A PRO 4.5 4.4 + - - +
97A GLN 3.3 0.4 - - - -
98A LEU* 1.3 77.3 - - - +
100A ARG* 1.3 60.7 + - - +
102A TYR* 3.9 25.1 - - + -
103A THR* 2.8 41.3 + - + +
159A ASN* 4.1 15.0 - - + +
162A PHE* 3.8 17.9 - - + +
163A LEU* 3.4 44.0 - - + +
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Residues in contact with ARG 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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16A GLU 5.7 0.4 + - - -
19A ALA* 3.5 36.7 - - + +
20A GLN* 5.2 4.6 - - - +
96A PRO 5.0 5.5 + - - +
97A GLN* 2.5 53.5 + - - +
99A LEU* 1.3 78.2 - - - +
101A PHE* 1.3 57.3 + - - +
103A THR* 3.4 4.6 + - - -
104A SER* 3.0 32.3 + - - -
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Residues in contact with PHE 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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15A THR* 3.5 23.3 - - + -
18A PHE* 3.7 23.1 - - + -
19A ALA* 3.5 23.3 - - + -
53A TYR* 4.2 13.0 - + - -
56A VAL* 3.6 25.6 - - + -
57A LEU* 3.9 26.2 - - + -
60A GLN* 3.6 34.1 - - + -
61A PHE* 4.7 5.4 - - + -
97A GLN* 3.4 24.2 - - + -
98A LEU 3.1 5.4 + - - +
100A ARG* 1.3 80.0 - - + +
102A TYR* 1.3 58.5 + - - +
104A SER* 4.5 3.4 - - - -
105A GLU* 2.9 36.7 + - - +
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Residues in contact with TYR 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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61A PHE* 3.7 29.6 - + + -
64A PHE* 4.0 10.8 - + - -
91A ARG* 5.3 1.3 - - - -
92A HIS* 6.1 0.9 - + - -
98A LEU* 2.8 26.6 + - + +
99A LEU* 3.9 24.7 - - + +
101A PHE* 1.3 77.3 - - - +
103A THR* 1.3 67.2 + - + +
105A GLU* 4.0 2.5 - - - +
106A LEU* 3.1 48.8 + - + +
117A VAL* 4.9 0.9 - - - +
121A ILE* 3.7 30.8 - - + +
159A ASN* 4.6 14.6 + - + -
209A ACY 2.5 38.7 + - - +
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Residues in contact with THR 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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99A LEU* 2.8 36.8 + - + +
100A ARG* 3.4 5.2 + - - -
102A TYR* 1.3 78.9 - - + +
104A SER* 1.3 65.6 + - - +
106A LEU* 3.3 6.4 + - + +
107A THR* 2.9 36.9 + - - +
163A LEU* 4.1 30.6 - - + +
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Residues in contact with SER 104 (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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22A GLY* 4.5 18.5 - - - -
23A PHE 5.3 0.5 + - - -
24A TYR* 6.2 0.2 - - - -
53A TYR* 5.6 2.6 + - - -
100A ARG 3.0 21.4 + - - -
101A PHE* 3.9 5.2 - - - -
103A THR* 1.3 76.0 + - - +
105A GLU* 1.3 57.6 + - - +
107A THR* 3.9 4.9 - - - -
108A ASN* 2.7 46.5 + - - +
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Residues in contact with GLU 105 (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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53A TYR* 2.5 33.2 + - - +
57A LEU* 3.5 12.6 - - + +
101A PHE 2.9 20.0 + - - +
102A TYR 4.0 2.9 - - - +
104A SER* 1.3 77.6 - - - +
106A LEU* 1.3 61.0 + - - +
108A ASN 4.3 2.0 - - - -
109A PRO* 3.1 28.5 - - - +
110A THR* 2.6 48.4 + - - +
113A PHE* 3.3 25.8 - - + +
117A VAL* 3.9 25.6 - - + -
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Residues in contact with LEU 106 (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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102A TYR* 3.1 51.4 + - + +
103A THR* 3.3 7.2 + - + +
105A GLU* 1.3 76.7 - - - +
107A THR* 1.3 63.2 + - + +
109A PRO* 4.6 4.2 - - - +
113A PHE* 3.6 29.6 - - + -
117A VAL* 4.8 1.1 - - + -
121A ILE* 3.9 20.0 - - + -
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Residues in contact with THR 107 (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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103A THR* 2.9 26.4 + - - +
104A SER* 3.5 5.7 + - - -
106A LEU* 1.3 85.8 - - + +
108A ASN* 1.3 74.8 + - - +
109A PRO* 3.7 5.3 - - - +
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Residues in contact with ASN 108 (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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24A TYR* 3.5 24.7 - - + -
104A SER* 2.7 29.3 + - - +
105A GLU* 4.3 1.2 - - - -
107A THR* 1.3 85.8 + - - +
109A PRO* 1.4 70.0 - - - +
110A THR* 3.7 2.9 + - - +
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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