Contacts of the strand formed by residues 116 - 120 (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 THR 116 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47N VAL* 3.2 4.7 - - - +
48N HIS 2.7 35.5 + - - -
50N PHE 2.7 24.8 + - - -
51N GLY* 3.3 12.8 - - - -
52N ASP 4.0 2.3 + - - -
53N ASN* 5.9 0.9 - - - +
60N ALA* 3.7 16.5 - - + +
115N ARG* 1.3 76.0 + - - +
117N LEU* 1.3 71.2 + - - +
118N VAL* 3.7 10.3 - - + -
146N CYS* 3.6 19.5 - - + -
147N GLY 3.4 13.4 + - - +
148N VAL* 4.2 5.0 - - - +
149N ILE* 4.3 3.8 - - - -
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Residues in contact with LEU 117 (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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6N CYS* 3.7 20.9 - - - -
8N LEU* 3.3 8.1 - - + +
18N ILE* 3.8 36.8 - - + -
20N PHE* 4.0 15.3 - - + -
45N PHE* 3.8 30.1 - - + -
46N ARG 3.5 20.9 - - - +
47N VAL* 4.1 13.0 - - + +
84N LEU* 4.4 7.4 - - + -
116N THR* 1.3 74.5 - - - +
118N VAL* 1.3 60.6 + - - +
146N CYS* 3.0 26.5 - - - +
147N GLY 3.0 7.9 + - - -
149N ILE* 4.0 10.4 - - + +
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Residues in contact with VAL 118 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8N LEU* 4.7 1.3 - - - -
44N GLY 3.9 0.3 - - - +
45N PHE* 3.6 7.8 - - - -
46N ARG 2.7 33.9 + - - -
48N HIS* 3.2 35.2 - - + +
57N CYS* 4.9 0.2 - - + -
60N ALA* 4.6 4.7 - - + -
116N THR* 3.7 17.0 - - + -
117N LEU* 1.3 81.9 - - - +
119N VAL* 1.3 68.0 + - - +
120N HIS* 3.8 14.2 - - + +
143N ARG* 3.7 32.5 - - + -
145N ALA 3.5 11.9 - - - +
146N CYS* 3.9 5.8 - - + -
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Residues in contact with VAL 119 (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* 4.9 5.6 - - + -
14N VAL* 3.9 26.5 - - + -
35N ILE* 4.3 19.1 - - + -
38N LEU* 4.4 10.3 - - + -
43N HIS* 3.9 20.2 - - + -
44N GLY 3.3 9.4 - - - +
45N PHE* 4.5 4.7 - - + -
87N VAL* 4.0 15.7 - - + -
118N VAL* 1.3 75.9 - - - +
120N HIS* 1.3 62.7 + - - +
144N LEU* 3.0 23.7 + - + +
145N ALA* 3.1 19.3 + - + +
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Residues in contact with HIS 120 (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* 2.9 29.3 + - - +
44N GLY 2.7 26.3 + - - +
46N ARG* 3.2 30.8 + - + +
48N HIS* 3.1 36.7 + + - -
63N HIS* 5.6 0.2 - - - -
118N VAL* 3.8 10.0 - - + +
119N VAL* 1.3 78.3 - - - +
121N GLU* 1.3 61.2 + - - +
122N LYS 3.3 3.4 - - - +
140N ALA* 3.3 24.5 - - + +
141N GLY 3.3 18.1 + - - -
142N SER 3.5 5.8 + - - -
143N ARG* 4.0 18.8 - - + +
144N LEU* 3.8 4.8 - - - +
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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