Contacts of the strand formed by residues 35 - 40 (chain A) in PDB entry 2IDZ
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 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLY* 5.3 2.4 - - - +
8A LYS 2.7 13.1 + - - +
9A ARG* 3.2 39.9 + - + +
10A ILE 2.9 25.6 + - - -
33A GLY 3.7 2.1 + - - +
34A ALA* 1.3 72.3 - - - +
36A LEU* 1.3 70.1 + - - +
37A VAL* 4.1 0.9 + - - +
81A ALA 4.7 3.0 + - - -
82A ILE* 3.9 31.8 + - - +
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Residues in contact with LEU 36 (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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10A ILE* 3.2 23.1 - - + +
12A VAL* 4.1 9.2 - - + -
26A ALA* 3.4 46.7 - - + +
29A ALA* 3.9 9.6 - - + -
30A GLN* 3.5 20.5 + - + +
34A ALA* 3.7 25.2 + - + +
35A GLN* 1.3 86.2 - - - +
37A VAL* 1.3 63.6 + - - +
38A LEU* 4.0 9.4 - - + -
54A LEU* 4.9 0.4 - - + -
57A LYS 4.7 2.1 + - - +
58A ALA* 3.4 18.3 - - + +
59A PRO* 3.3 22.2 - - - +
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Residues in contact with VAL 37 (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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10A ILE 3.0 6.1 + - - +
11A LEU* 3.0 23.9 - - + +
12A VAL 2.8 24.3 + - - -
35A GLN* 5.4 0.9 - - - +
36A LEU* 1.3 78.2 - - - +
38A LEU* 1.3 68.2 + - - +
59A PRO* 3.6 14.8 - - + +
61A LEU* 3.7 40.8 - - + -
78A VAL* 4.4 7.6 - - + -
81A ALA* 4.4 4.5 - - + -
82A ILE* 3.3 34.5 - - + -
88A LEU* 4.9 3.6 - - + -
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Residues in contact with LEU 38 (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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12A VAL* 3.2 25.8 - - + +
15A ILE* 4.0 14.4 - - + -
26A ALA* 4.3 1.6 - - + -
36A LEU* 4.0 20.9 - - + -
37A VAL* 1.3 81.9 - - - +
39A THR* 1.3 68.2 + - - +
51A THR* 3.6 40.2 - - + +
54A LEU* 3.8 10.1 - - + -
58A ALA* 3.8 22.9 - - + +
59A PRO 2.8 9.6 + - - +
60A LEU* 3.4 13.2 - - + -
61A LEU* 2.7 27.4 + - - +
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Residues in contact with THR 39 (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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11A LEU* 3.6 32.3 - - + -
12A VAL 3.0 8.3 + - - +
13A SER* 3.1 38.8 - - - -
14A GLY 3.7 7.2 + - - -
15A ILE* 4.3 5.9 + - - +
38A LEU* 1.3 80.7 - - - +
40A GLY* 1.3 59.1 + - - +
47A ILE* 5.3 0.2 - - - +
60A LEU* 3.8 4.8 - - - +
61A LEU* 2.9 14.6 - - + +
63A LEU* 3.7 21.9 + - + +
74A LEU* 4.2 18.4 - - + -
95A ILE* 5.2 0.3 - - - +
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Residues in contact with GLY 40 (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 GLY* 5.4 1.6 - - - -
15A ILE 4.6 2.2 - - - -
39A THR* 1.3 75.5 - - - +
41A PHE* 1.3 62.2 + - - -
44A LEU* 3.9 4.3 - - - +
47A ILE* 3.6 20.4 - - - -
60A LEU* 3.7 8.5 - - - +
61A LEU 2.9 7.9 + - - -
62A GLU* 3.5 9.4 - - - +
63A LEU 2.8 25.0 + - - -
300A ZID 5.5 0.4 - - - -
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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