Contacts of the strand formed by residues 98 - 105 (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 VAL 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A VAL 2.5 24.0 - - - +
20A GLU* 4.1 2.0 - - - -
21A LEU* 2.9 25.5 + - + +
23A ARG* 4.8 5.4 - - + -
29A LEU* 4.1 32.3 - - + -
74A VAL* 4.4 15.5 - - + -
75A ASP* 4.2 13.9 - - + -
91A LEU 5.6 0.4 - - - +
94A ALA* 3.9 16.4 - - + -
95A GLY 2.9 24.5 - - - +
96A GLN 3.0 7.5 + - - +
97A VAL* 1.3 71.3 - - - +
99A HIS* 1.3 52.1 + - - +
100A LEU* 3.3 12.8 + - + +
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Residues in contact with HIS 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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18A ASN* 3.7 26.2 - - + +
19A VAL 3.2 5.6 - - - -
20A GLU* 3.3 37.1 + - + +
75A ASP* 2.5 45.7 + - - +
76A GLY 3.7 2.8 + - - +
97A VAL* 3.7 27.4 + - + +
98A VAL* 1.3 69.3 - - - +
100A LEU* 1.3 61.9 + - - +
101A THR* 3.7 3.8 + - - -
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Residues in contact with LEU 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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17A TYR 3.3 2.8 - - - +
18A ASN* 3.3 6.6 - - - -
19A VAL* 2.8 32.3 + - + +
21A LEU* 5.0 0.9 - - + -
29A LEU* 5.0 0.7 - - + -
31A ILE* 4.8 11.9 - - + -
65A ILE* 3.5 35.9 - - + -
71A ILE* 3.4 32.8 - - + -
73A ALA 3.5 1.6 - - - +
74A VAL* 4.0 28.7 - - + -
75A ASP 4.2 0.2 - - - +
91A LEU* 4.8 7.6 - - + -
98A VAL* 3.3 10.1 + - + +
99A HIS* 1.3 73.3 - - - +
101A THR* 1.3 86.9 + - - +
102A LEU* 3.5 17.6 - - + +
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Residues in contact with THR 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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16A THR* 3.3 30.1 - - + -
17A TYR 3.7 2.7 - - - -
18A ASN* 3.8 20.7 + - - +
71A ILE* 3.5 4.2 - - - -
72A VAL* 2.9 38.4 + - + +
73A ALA* 2.7 39.5 + - + +
76A GLY* 4.7 3.8 + - - -
99A HIS 3.9 3.3 + - - -
100A LEU* 1.3 74.2 - - - +
102A LEU* 1.3 59.9 + - - +
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A THR* 3.1 6.6 - - - +
17A TYR* 3.0 54.1 + - + +
19A VAL* 3.4 33.4 - - + -
65A ILE* 3.6 34.1 - - + -
69A ASP* 3.8 27.6 - - + +
70A LYS 3.5 7.9 - - - +
71A ILE* 4.6 8.1 - - + -
72A VAL* 4.8 0.4 - - - -
100A LEU* 3.5 24.7 - - + +
101A THR* 1.3 76.2 - - - +
103A VAL* 1.3 61.1 + - - +
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Residues in contact with VAL 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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14A PHE* 3.1 37.6 - - + +
15A GLU 3.3 10.1 - - - +
16A THR* 3.5 21.1 - - - +
69A ASP* 5.0 2.2 - - - -
70A LYS* 3.2 58.7 + - + +
72A VAL* 3.8 9.9 - - + -
102A LEU* 1.3 74.7 - - - +
104A ARG* 1.3 59.3 + - - +
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Residues in contact with ARG 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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14A PHE* 3.6 4.0 - - - -
15A GLU* 2.9 42.6 + - + +
17A TYR* 3.3 39.0 + - + -
64A HIS 4.5 2.6 + - - -
66A GLN* 4.1 16.0 + - - -
68A ASN 5.4 4.3 - - - +
69A ASP* 4.0 19.2 + - - +
102A LEU 4.3 0.2 - - - -
103A VAL* 1.3 75.3 - - - +
105A ARG* 1.3 70.9 + - - +
108A SER* 5.5 6.6 + - - -
109A SER* 4.4 12.3 + - - -
110A SER* 3.3 29.8 + - - +
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Residues in contact with ARG 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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13A LEU* 4.4 9.9 - - + +
14A PHE* 3.2 35.8 - - + +
104A ARG* 1.3 76.5 - - - +
106A LYS* 1.3 75.9 + - - +
108A SER* 3.6 18.6 - - - -
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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