Contacts of the strand formed by residues 14 - 21 (chain A) in PDB entry 2DMZ
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 PHE 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A SER* 3.2 12.2 - - - +
13A LEU* 1.3 93.4 - - + +
15A GLU* 1.3 61.6 + - - +
103A VAL* 3.1 27.6 - - + -
104A ARG* 3.2 10.8 - - - +
105A ARG* 3.2 46.9 - - + -
106A LYS* 3.1 15.7 + - - +
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Residues in contact with GLU 15 (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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14A PHE* 1.3 76.8 - - - +
16A THR* 1.3 64.6 + - - +
17A TYR* 3.7 22.5 - - - +
103A VAL* 3.3 3.3 - - - -
104A ARG* 2.9 45.9 + - + +
106A LYS* 3.6 31.9 - - + +
110A SER* 5.4 8.5 - - - -
111A THR 4.6 7.7 - - - +
112A SER* 5.5 0.2 - - - -
113A PRO* 4.4 28.0 - - + +
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Residues in contact with THR 16 (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 GLU* 1.3 75.3 - - - +
17A TYR* 1.3 67.2 - - - +
18A ASN* 4.9 3.8 - - - +
72A VAL* 4.5 5.2 - - + +
101A THR* 3.3 32.5 - - + -
102A LEU 3.1 9.9 - - - +
103A VAL* 3.5 17.0 - - - +
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Residues in contact with TYR 17 (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 GLU* 3.7 22.2 - - - +
16A THR* 1.3 76.0 - - - +
18A ASN* 1.3 68.1 + - - +
19A VAL* 3.6 26.7 - - + -
64A HIS* 4.0 15.7 + - + -
69A ASP* 3.3 13.5 + - - -
100A LEU 3.3 2.8 - - - +
101A THR* 3.7 1.0 - - - -
102A LEU* 3.0 57.4 + - + +
103A VAL 4.5 0.2 - - - -
104A ARG* 3.3 45.3 + - + -
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Residues in contact with ASN 18 (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 THR* 4.9 3.2 - - - +
17A TYR* 1.3 80.6 - - - +
19A VAL* 1.3 63.3 + - - +
20A GLU 4.2 0.9 + - - -
64A HIS* 5.5 1.4 + - - -
76A GLY* 5.5 2.1 + - - -
99A HIS* 3.7 31.3 - - + +
100A LEU 3.3 2.7 - - - -
101A THR* 3.8 26.5 + - - +
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Residues in contact with VAL 19 (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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17A TYR* 3.6 19.1 - - + -
18A ASN* 1.3 78.0 - - - +
20A GLU* 1.3 52.6 + - - +
21A LEU* 3.3 8.1 + - + +
62A ASN* 2.9 33.7 - - - +
64A HIS* 3.1 25.4 - - + +
65A ILE* 4.0 13.2 - - + -
98A VAL 2.5 25.5 - - - +
99A HIS* 3.9 2.2 - - - -
100A LEU* 2.8 21.6 + - - +
102A LEU* 3.4 29.8 - - + -
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Residues in contact with GLU 20 (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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18A ASN 4.2 1.0 + - - -
19A VAL* 1.3 69.5 - - - +
21A LEU* 1.3 66.0 + - - +
22A VAL* 4.0 4.9 + - - +
62A ASN* 4.0 12.2 + - - +
97A VAL* 3.6 39.8 - - + +
98A VAL 3.4 3.6 - - - -
99A HIS* 3.3 23.4 + - + +
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Residues in contact with LEU 21 (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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19A VAL* 3.9 1.8 - - + +
20A GLU* 1.3 75.2 - - - +
22A VAL* 1.3 61.2 + - - +
23A ARG* 5.4 0.4 - - + -
29A LEU* 4.0 15.5 - - + -
31A ILE* 3.8 18.6 - - + -
58A ALA* 4.2 10.1 - - + +
59A ALA* 4.1 13.9 - - - +
62A ASN* 3.0 48.7 - - + +
64A HIS* 5.3 0.2 - - + -
65A ILE* 3.2 36.6 - - + -
96A GLN 2.8 20.0 - - - +
97A VAL* 3.8 3.3 - - - -
98A VAL* 2.9 32.2 + - + +
100A LEU* 5.0 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