Contacts of the strand formed by residues 143 - 148 (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 ARG 143 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G HIS* 3.4 24.0 + - - -
57G CYS* 2.9 54.1 + - + +
58G THR* 3.6 17.2 + - - +
60G ALA* 3.9 2.2 - - - +
61G GLY 2.8 35.1 + - - +
62G PRO* 4.3 4.0 - - - +
118G VAL* 3.8 18.4 - - + -
119G VAL 4.1 4.3 - - - -
120G HIS* 4.1 10.9 - - + +
142G SER* 1.3 76.4 + - - +
144G LEU* 1.3 64.1 + - - +
145G ALA 3.6 1.1 - - - -
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Residues in contact with LEU 144 (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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10G GLY* 3.5 15.1 - - - -
11G ASP 4.3 3.3 + - - -
12G GLY* 4.7 4.3 + - - -
14G VAL* 3.8 25.6 - - + +
38G LEU* 3.6 28.7 - - + -
39G THR* 5.7 1.8 - - + +
43G HIS* 4.3 7.6 - - + +
57G CYS* 5.0 0.7 - - - -
119G VAL* 3.0 12.2 + - + +
120G HIS 3.9 5.6 - - - +
121G GLU* 3.5 43.5 - - + +
142G SER* 3.9 9.0 - - - +
143G ARG* 1.3 74.2 - - - +
145G ALA* 1.3 62.8 + - - +
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Residues in contact with ALA 145 (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* 4.1 7.3 - - + +
9G LYS 3.1 27.4 - - - +
14G VAL* 3.5 31.2 - - + +
57G CYS* 3.6 5.6 - - - -
118G VAL* 3.5 3.3 - - - +
119G VAL* 3.1 29.8 + - + +
143G ARG 3.6 0.8 - - - -
144G LEU* 1.3 81.9 - - - +
146G CYS* 1.3 64.5 + - - +
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Residues in contact with CYS 146 (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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7G VAL 3.5 0.9 - - - +
8G LEU* 3.4 9.7 - - - +
9G LYS* 2.8 31.5 + - - +
53G ASN* 3.9 16.4 - - - -
57G CYS* 2.0 54.5 - - + -
116G THR* 3.6 15.7 - - + -
117G LEU 3.1 16.4 - - - +
118G VAL* 3.9 4.9 - - + -
145G ALA* 1.3 73.9 - - - +
147G GLY* 1.3 59.9 + - - +
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Residues in contact with GLY 147 (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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6G CYS* 3.3 7.4 - - - -
7G VAL 3.3 17.7 - - - -
8G LEU* 3.7 2.2 - - - +
53G ASN* 6.3 2.2 - - - -
116G THR* 3.3 6.2 - - - -
117G LEU 3.0 27.1 + - - -
146G CYS* 1.3 80.4 - - - +
148G VAL* 1.3 66.8 + - - -
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Residues in contact with VAL 148 (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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5G VAL 3.9 3.5 - - - +
6G CYS* 3.7 9.8 - - - -
7G VAL 4.7 1.6 + - - -
51G GLY* 3.6 26.2 - - - +
53G ASN* 5.0 13.5 - - + -
114G GLY* 4.0 17.0 - - - +
115G ARG 3.4 10.5 - - - +
116G THR* 4.2 3.4 - - - +
147G GLY* 1.3 76.0 - - - -
149G ILE* 1.3 66.5 + - - +
150G GLY 3.4 3.3 + - - -
51H GLY 5.0 0.5 - - - +
148H VAL* 3.6 44.2 - - + +
150H GLY* 4.1 11.4 - - - -
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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