Contacts of the strand formed by residues 40 - 45 (chain A) in PDB entry 1ZTU
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 ALA 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ILE* 3.9 0.2 - - - -
39A GLY* 1.3 75.6 - - - -
41A LEU* 1.3 62.0 + - - +
42A LEU* 5.9 0.4 - - + -
55A SER* 3.6 4.7 - - - +
57A ASN* 4.2 0.7 - - - +
58A ALA* 3.9 25.8 - - + +
61A PHE* 3.8 26.6 - - + -
62A LEU* 5.1 2.9 - - + -
125A GLU* 3.6 0.2 - - - -
126A PHE* 2.9 44.5 + - + -
253A LEU* 3.4 5.5 - - - +
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Residues in contact with LEU 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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35A ILE* 3.7 32.8 - - + -
40A ALA* 1.3 76.0 - - - +
42A LEU* 1.3 75.0 + - - +
43A THR* 3.7 20.2 - - + -
54A MET* 3.4 2.6 - - - -
55A SER* 2.9 38.9 + - - +
123A ILE* 3.9 20.2 - - + -
124A LEU 3.2 11.0 - - - +
125A GLU* 4.3 8.3 - - + +
234A LEU* 3.8 15.5 - - + -
248A LEU* 4.2 9.4 - - + -
251A ALA* 4.0 18.4 - - + -
253A LEU* 4.7 3.6 - - + -
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Residues in contact with LEU 42 (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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40A ALA* 5.8 0.4 - - + -
41A LEU* 1.3 82.1 - - - +
43A THR* 1.3 66.4 + - - +
51A VAL* 3.9 26.0 - - + -
53A GLN 3.4 5.4 - - - +
54A MET* 3.1 33.0 - - + -
58A ALA* 4.4 3.8 - - + -
62A LEU* 3.9 27.8 - - + -
69A LEU* 4.9 2.5 - - + -
74A LEU* 4.8 6.7 - - + -
77A LEU* 4.6 13.2 - - + -
124A LEU* 2.8 42.9 + - + +
126A PHE* 3.8 21.7 - - + -
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Residues in contact with THR 43 (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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41A LEU* 3.7 17.7 - - + -
42A LEU* 1.3 79.3 - - - +
44A ALA* 1.3 56.0 + - - +
51A VAL* 3.4 4.2 - - - +
52A LEU* 2.7 32.6 + - - +
53A GLN* 2.9 56.9 + - + +
121A LEU* 3.6 21.3 - - + +
122A LEU 3.2 4.7 - - - -
123A ILE* 3.9 18.4 - - + -
234A LEU* 5.2 0.7 - - + -
246A THR* 4.4 5.6 - - + -
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Residues in contact with ALA 44 (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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43A THR* 1.3 76.1 - - - +
45A ASP* 1.3 62.5 + - - +
49A GLY 3.7 9.2 - - - +
50A GLU 3.2 13.7 - - - +
51A VAL* 4.0 3.6 - - + -
52A LEU* 4.2 1.6 - - - +
74A LEU* 3.7 34.8 - - + -
121A LEU* 3.2 9.0 - - - +
122A LEU* 2.7 35.4 + - + -
124A LEU* 4.4 4.4 - - + +
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Residues in contact with ASP 45 (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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44A ALA* 1.3 71.1 - - - +
46A GLY* 1.3 59.9 + - - +
47A HIS* 2.9 20.2 + - - +
48A SER* 2.8 44.3 + - - +
49A GLY* 3.0 26.0 + - - +
50A GLU* 2.9 15.6 + - + +
52A LEU* 4.2 11.8 - - + +
82A TRP* 4.5 0.2 - - - -
120A GLU 4.1 2.7 - - - -
122A LEU* 4.1 5.2 - - - +
241A GLN* 3.0 28.1 + - - +
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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