Contacts of the strand formed by residues 35 - 41 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B LEU* 4.2 9.0 - - + -
19B LEU* 4.3 23.8 - - + +
28B GLU* 2.8 34.2 + - + +
29B THR 3.7 5.6 - - - -
30B VAL* 4.2 25.1 - - + -
34B TYR* 1.3 78.3 - - - +
36B ALA* 1.3 61.3 + - - +
37B ARG* 3.4 40.2 + - + -
48B VAL 5.5 0.7 - - - -
49B THR* 3.3 3.6 - - - +
50B ALA* 2.7 40.9 + - + +
52B PRO* 6.3 0.2 - - + -
78B MET* 4.9 4.9 - - - -
81B LEU* 3.6 23.7 - - + +
82B PHE* 3.6 28.3 - + + -
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Residues in contact with ALA 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B GLU* 3.2 1.7 - - - +
29B THR* 2.5 42.4 + - - +
34B TYR* 4.1 17.7 - - + -
35B TYR* 1.3 78.3 - - - +
37B ARG* 1.3 61.8 + - - +
47B VAL* 4.6 3.6 - - + -
48B VAL 3.2 11.2 - - - +
49B THR* 4.0 12.1 - - + +
152B TYR* 3.5 20.2 - - + +
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Residues in contact with ARG 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B VAL* 3.1 35.7 - - - +
28B GLU* 3.6 17.3 + - + +
35B TYR* 3.4 34.9 + - + +
36B ALA* 1.3 76.8 - - - +
38B SER* 1.3 83.5 + - - +
39B LEU* 4.9 2.2 - - + +
47B VAL* 3.5 3.3 - - - +
48B VAL* 3.1 33.1 + - + +
78B MET* 4.9 7.6 - - + -
81B LEU* 6.1 0.2 - - - +
111B VAL* 4.0 34.5 - - - +
115B GLU* 2.9 40.0 + - - -
119B ARG* 4.7 2.6 - - - +
152B TYR* 4.0 8.2 - - - -
155B PHE* 4.3 5.3 - - - +
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Residues in contact with SER 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B VAL* 2.9 19.4 + - - +
37B ARG* 1.3 100.5 + - - +
39B LEU* 1.3 60.6 + - - +
46B GLY 3.2 9.4 - - - -
47B VAL* 4.5 1.3 - - - +
146B LEU* 4.1 14.8 - - - -
152B TYR* 3.9 10.7 - - - -
153B ILE 2.7 33.6 + - - -
154B CYS* 3.6 11.2 - - - -
155B PHE 4.3 0.7 + - - -
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ARG* 4.5 3.8 - - + +
38B SER* 1.3 78.6 - - - +
40B ALA* 1.3 66.1 + - - +
41B VAL* 4.2 4.7 - - + -
45B ARG* 3.1 5.0 - - - +
46B GLY 2.7 33.3 + - - -
48B VAL* 3.3 35.2 - - + -
67B LEU* 3.7 7.8 - - + +
74B CYS* 3.7 24.7 - - + -
77B LYS* 4.1 22.0 - - + -
78B MET* 4.3 9.2 - - + -
111B VAL* 3.3 37.0 - - + -
154B CYS* 4.8 3.1 - - - -
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 1.3 80.7 - - - +
41B VAL* 1.3 63.5 + - - +
42B GLY 3.6 8.9 + - - +
44B TYR 3.1 4.9 - - - +
45B ARG* 3.4 24.2 - - + -
77B LYS* 4.8 6.9 + - - -
144B GLU* 5.3 2.0 - - - +
154B CYS* 4.4 9.6 - - + -
157B THR* 5.9 6.5 - - + -
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU* 4.2 3.3 - - + -
40B ALA* 1.3 74.0 - - - +
42B GLY* 1.3 60.9 + - - +
44B TYR* 2.8 27.2 + - - +
67B LEU* 4.5 3.4 - - + -
70B VAL* 3.6 33.1 - - + +
73B GLU* 4.0 31.4 - - + +
74B CYS* 4.0 18.2 - - - -
77B LYS* 3.7 25.1 - - + +
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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