Contacts of the strand formed by residues 41 - 48 (chain N) in PDB entry 1OZT
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 GLY 41 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39N THR 3.4 0.6 + - - -
40N GLU* 1.3 80.0 - - - +
42N LEU* 1.3 68.3 + - - -
43N HIS* 3.5 9.3 - - - -
88N THR* 3.3 6.4 - - - -
89N ALA 2.7 41.2 + - - -
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Residues in contact with LEU 42 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41N GLY* 1.3 71.7 - - - -
43N HIS* 1.3 69.5 + - - +
86N ASN* 3.9 23.1 - - + +
87N VAL 3.5 1.6 - - - +
88N THR* 3.1 32.5 - - + +
122N LYS* 3.8 0.7 - - - -
123N ALA* 3.4 36.9 + - + +
124N ASP 5.7 0.2 - - - +
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Residues in contact with HIS 43 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N LEU* 3.5 27.2 - - + +
39N THR* 2.8 42.8 + - + -
40N GLU 4.8 0.2 - - - -
41N GLY 3.5 23.2 + - - -
42N LEU* 1.3 76.1 + - - +
44N GLY* 1.3 66.1 + - - +
86N ASN* 3.1 5.9 + - - -
87N VAL* 2.9 37.5 + - + +
89N ALA* 4.3 2.0 - - + -
119N VAL* 3.9 13.7 - - + -
120N HIS 2.9 24.3 + - - +
121N GLU 3.0 21.5 + - - -
122N LYS 3.7 3.4 - - - -
144N LEU* 4.3 9.1 - - + +
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Residues in contact with GLY 44 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43N HIS* 1.3 73.4 - - - +
45N PHE* 1.3 58.9 + - - -
46N ARG* 5.0 0.9 - - - -
85N GLY 3.6 4.0 - - - -
86N ASN* 3.3 11.8 + - - -
119N VAL* 3.3 6.4 - - - +
120N HIS* 2.7 42.8 + - - +
122N LYS 2.8 19.4 + - - -
124N ASP* 4.0 10.1 - - - -
140N ALA* 4.6 2.0 - - - -
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Residues in contact with PHE 45 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8N LEU* 5.6 0.7 - - + -
18N ILE* 4.1 19.3 - - + -
20N PHE* 6.0 0.2 - + - -
31N VAL* 4.2 9.6 - - + -
35N ILE* 4.1 16.2 - - + -
43N HIS 4.1 1.8 - - - +
44N GLY* 1.3 74.1 - - - -
46N ARG* 1.3 63.3 + - - +
84N LEU* 3.1 58.0 + - + +
85N GLY 3.0 17.2 + - - +
87N VAL* 3.5 33.4 - - + -
97N VAL* 4.3 2.0 - - + -
99N ILE* 3.9 20.2 - - + -
117N LEU* 3.8 34.5 - - + -
118N VAL 3.6 9.9 - - - -
119N VAL* 4.5 10.5 - - + -
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Residues in contact with ARG 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N GLY* 4.1 0.8 - - - -
45N PHE* 1.3 81.6 - - - +
47N VAL* 1.3 65.9 + - - +
48N HIS* 3.6 15.1 - - + +
63N HIS* 3.4 34.2 + - + -
82N GLY 3.2 10.8 - - - +
83N ASP* 3.3 19.9 + - - +
84N LEU* 4.7 0.9 - - - +
85N GLY 5.2 0.2 - - - +
117N LEU* 3.5 5.4 - - - +
118N VAL 2.7 40.4 + - - +
120N HIS* 3.2 31.2 + - - +
124N ASP* 2.9 33.5 + - - +
137N THR* 2.7 30.7 + - - -
140N ALA* 3.0 25.0 - - - +
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Residues in contact with VAL 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20N PHE* 5.4 0.2 - - + -
46N ARG* 1.3 77.0 - - - +
48N HIS* 1.3 72.8 + - - +
63N HIS* 3.9 2.1 - - - -
64N PHE* 3.0 28.8 + - + +
82N GLY* 2.9 23.5 + - - +
84N LEU* 4.1 16.6 - - + -
104N ILE* 4.8 2.2 - - + -
112N ILE* 4.0 43.1 - - + -
115N ARG* 4.1 9.2 - - + -
116N THR 3.2 10.3 - - - +
117N LEU* 4.1 15.3 - - + -
149N ILE* 4.4 6.3 - - + -
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Residues in contact with HIS 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46N ARG* 3.6 14.0 - - + +
47N VAL* 1.3 82.4 - - - +
49N GLU* 1.3 68.0 + - - +
50N PHE 3.4 0.7 - - - -
60N ALA* 3.6 21.8 - - + +
61N GLY 2.9 17.8 + - - -
62N PRO 3.3 11.5 + - - +
63N HIS* 4.2 16.2 - + - -
64N PHE* 3.9 2.7 - - - -
115N ARG* 3.4 8.3 - - - +
116N THR 2.7 29.0 + - - +
118N VAL* 3.2 22.5 - - + +
120N HIS* 3.1 33.8 + + - -
143N ARG* 3.5 25.3 + - - -
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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