Contacts of the strand formed by residues 41 - 48 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39G THR 3.3 0.6 + - - -
40G GLU* 1.3 79.3 - - - +
42G LEU* 1.3 67.3 + - - -
43G HIS* 3.4 8.3 - - - -
88G THR* 3.4 6.3 - - - -
89G ALA 2.7 41.3 + - - -
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Residues in contact with LEU 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G GLY* 1.3 71.1 - - - -
43G HIS* 1.3 69.8 + - - +
86G ASN* 3.9 24.7 - - + +
87G VAL 3.5 2.0 - - - +
88G THR* 3.2 32.1 - - + +
121G GLU 4.4 0.3 - - - +
122G LYS* 4.6 0.2 - - - -
123G ALA* 3.4 37.1 + - + +
124G ASP 5.4 1.1 - - - +
126G LEU* 6.4 0.4 - - + -
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Residues in contact with HIS 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G LEU* 3.5 20.2 - - + +
39G THR* 2.8 47.4 + - + -
41G GLY 3.4 23.8 + - - -
42G LEU* 1.3 76.3 + - - +
44G GLY* 1.3 65.7 + - - +
86G ASN* 3.1 6.2 + - - -
87G VAL* 2.9 47.9 + - + +
89G ALA* 4.3 2.2 - - + -
119G VAL* 4.0 6.5 - - + -
120G HIS 2.9 14.4 + - - +
121G GLU* 2.8 30.1 + - + -
122G LYS 3.9 2.2 - - - -
144G LEU* 4.3 12.4 - - + +
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Residues in contact with GLY 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G HIS* 1.3 73.5 - - - +
45G PHE* 1.3 58.6 + - - +
46G ARG* 4.9 4.9 - - - -
85G GLY 3.6 3.6 - - - -
86G ASN* 3.4 12.0 + - - -
119G VAL* 3.3 5.0 - - - +
120G HIS* 2.7 41.6 + - - -
122G LYS 2.9 20.3 + - - -
123G ALA 4.6 0.2 - - - -
124G ASP* 4.1 7.6 - - - -
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Residues in contact with PHE 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G LEU* 5.6 1.6 - - + -
18G ILE* 4.2 19.3 - - + -
31G VAL* 4.2 8.7 - - + -
35G ILE* 4.1 14.8 - - + -
43G HIS 4.1 1.8 - - - +
44G GLY* 1.3 73.8 - - - -
46G ARG* 1.3 62.9 + - - +
84G LEU* 3.1 54.5 + - + +
85G GLY 3.0 14.9 + - - +
86G ASN 4.2 2.7 - - - -
87G VAL* 3.5 33.9 - - + -
97G VAL* 4.2 2.2 - - + -
99G ILE* 4.0 21.3 - - + -
117G LEU* 3.8 34.1 - - + -
118G VAL 3.5 9.6 - - - -
119G VAL* 4.5 11.0 - - + -
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Residues in contact with ARG 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G GLY* 4.1 4.3 - - - -
45G PHE* 1.3 84.3 - - - +
47G VAL* 1.3 64.7 + - - +
48G HIS* 3.6 16.4 + - + +
63G HIS* 4.1 18.2 + - + +
82G GLY 3.2 9.9 - - - +
83G ASP* 3.1 27.9 + - - +
84G LEU* 4.4 0.9 - - - +
117G LEU* 3.4 5.2 - - - +
118G VAL 2.7 41.3 + - - +
120G HIS* 3.3 38.4 + - - +
122G LYS 5.7 0.6 + - - -
123G ALA 5.2 1.4 + - - -
124G ASP* 3.5 37.6 + - - +
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Residues in contact with VAL 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G PHE* 5.4 0.2 - - + -
46G ARG* 1.3 76.4 - - - +
48G HIS* 1.3 62.3 + - - +
63G HIS* 3.6 4.3 - - - +
64G PHE* 2.7 36.2 + - + +
82G GLY* 2.8 22.9 + - - +
84G LEU* 4.1 22.9 - - + -
104G ILE* 4.7 2.0 - - + -
112G ILE* 4.0 39.7 - - + -
115G ARG* 4.0 15.3 - - + -
116G THR 3.2 10.5 - - - +
117G LEU* 4.1 9.6 - - + -
149G ILE* 4.4 5.4 - - + -
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Residues in contact with HIS 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G ARG* 3.6 13.6 - - + +
47G VAL* 1.3 81.6 - - - +
49G GLU* 1.3 65.7 + - - +
50G PHE 3.4 0.4 - - - -
60G ALA* 3.5 22.7 - - + +
61G GLY 2.8 18.4 + - - -
62G PRO 3.3 10.2 - - - +
63G HIS* 4.1 11.2 - - + -
64G PHE* 4.0 2.2 - - - -
115G ARG* 3.4 8.3 - - - +
116G THR 2.7 27.2 + - - +
118G VAL* 3.2 25.0 - - + +
120G HIS* 3.0 34.2 + + - -
143G ARG* 3.4 25.7 + - - -
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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