Contacts of the strand formed by residues 35 - 41 (chain A) in PDB entry 1DIZ
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 TYR 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.1 9.4 - - + -
19A LEU* 4.1 23.6 - - + +
28A GLU* 2.8 32.6 + - + -
29A THR 3.7 2.9 - - - -
30A VAL* 4.2 27.8 - - + +
34A TYR* 1.3 76.2 - - - +
36A ALA* 1.3 63.6 + - - +
37A ARG* 3.1 45.7 + - + -
48A VAL 5.3 0.7 - - - -
49A THR* 3.3 2.8 - - - +
50A ALA* 2.6 41.9 + - + +
78A MET* 4.8 6.1 - - - -
81A LEU* 3.8 21.2 - - + +
82A PHE* 3.8 27.8 - + + -
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Residues in contact with ALA 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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28A GLU* 3.3 2.1 - - - +
29A THR 2.6 40.7 + - - +
34A TYR* 4.0 17.0 - - + -
35A TYR* 1.3 78.5 - - - +
37A ARG* 1.3 63.7 + - - +
47A VAL* 4.6 4.5 - - + -
48A VAL 3.1 13.5 - - - +
49A THR* 3.9 12.3 - - - +
152A TYR* 3.7 18.6 - - - +
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Residues in contact with ARG 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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27A VAL* 3.0 38.3 - - - +
28A GLU* 3.7 18.1 + - + +
35A TYR* 3.1 34.3 + - + +
36A ALA* 1.3 77.7 - - - +
38A SER* 1.3 83.1 + - - +
39A LEU* 5.0 1.9 - - + +
47A VAL* 3.6 3.1 - - - +
48A VAL* 3.0 31.2 + - + +
78A MET* 4.8 7.6 - - + -
81A LEU* 6.4 0.2 - - - +
111A VAL* 4.0 33.8 - - - +
115A GLU* 2.9 39.7 + - - -
119A ARG* 4.9 0.2 - - - +
152A TYR* 3.8 7.7 - - - -
155A PHE* 4.4 5.5 - - - +
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Residues in contact with SER 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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27A VAL* 3.0 16.7 + - - +
37A ARG* 1.3 101.6 + - - +
39A LEU* 1.3 58.3 + - - +
46A GLY 3.2 9.9 - - - -
47A VAL* 4.4 1.3 - - - +
146A LEU* 4.1 16.4 - - - -
152A TYR* 3.7 9.9 - - - -
153A ILE 2.7 34.2 + - - -
154A CYS* 3.5 12.3 - - - -
155A PHE 4.4 1.0 + - - -
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Residues in contact with LEU 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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37A ARG* 4.4 4.0 - - + +
38A SER* 1.3 80.1 - - - +
40A ALA* 1.3 67.1 + - - +
41A VAL* 4.2 6.3 - - + -
45A ARG* 3.1 3.5 - - - +
46A GLY 2.6 37.2 + - - +
48A VAL* 3.2 36.1 - - + -
67A LEU* 3.7 7.4 - - + +
74A CYS* 3.5 26.5 - - + -
77A LYS* 4.2 19.3 - - + +
78A MET* 4.5 8.3 - - + -
111A VAL* 3.4 38.8 - - + -
154A CYS* 4.8 3.3 - - - -
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Residues in contact with ALA 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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39A LEU* 1.3 80.5 - - - +
41A VAL* 1.3 62.0 + - - +
42A GLY 3.6 9.7 + - - +
44A TYR 3.1 4.9 - - - +
45A ARG* 3.6 25.8 - - + -
77A LYS* 5.0 6.4 + - - -
154A CYS* 4.4 9.0 - - + -
157A THR* 5.9 6.7 - - + -
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Residues in contact with VAL 41 (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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39A LEU* 4.2 3.3 - - + -
40A ALA* 1.3 74.4 - - - +
42A GLY* 1.3 61.9 + - - +
43A GLU 3.5 0.3 + - - -
44A TYR* 2.7 29.1 + - - +
67A LEU* 4.4 3.5 - - + +
70A VAL* 3.6 28.2 - - + +
73A GLU* 3.8 29.8 - - + +
74A CYS* 3.8 27.4 - - - -
77A LYS* 3.8 26.7 - - + +
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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