Contacts of the strand formed by residues 155 - 159 (chain T) in PDB entry 6O81
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 155 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45T GLY* 3.5 8.7 - - - +
47T ILE* 6.2 1.1 - - + +
152T MET* 4.5 10.0 + - + +
153T ASP 3.9 2.0 - - - -
154T ALA* 1.3 71.9 - - - +
156T LEU* 1.3 54.0 + - - +
157T LEU* 4.0 0.7 - - + -
175T ALA* 5.2 15.3 - - + +
178T GLU* 6.2 3.8 - - + -
179T ILE* 6.3 3.1 - - + -
184T HIS 3.3 12.1 + - - +
185T ILE* 3.4 9.7 - - + -
186T LEU* 2.8 34.3 + - - +
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Residues in contact with LEU 156 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44T ILE* 5.9 2.7 - - + -
45T GLY 2.7 18.0 + - - +
46T THR* 3.6 11.4 - - - +
47T ILE 3.1 25.2 + - - +
154T ALA 4.7 1.3 - - - +
155T ALA* 1.3 73.1 - - - +
157T LEU* 1.3 60.8 + - - +
158T LEU* 3.3 7.0 + - + +
186T LEU* 3.4 14.8 - - + +
188T LEU* 6.4 1.1 - - + -
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Residues in contact with LEU 157 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47T ILE 3.7 11.2 - - - +
48T GLY* 4.8 1.1 - - - -
155T ALA* 4.0 1.6 + - + -
156T LEU* 1.3 67.9 - - - +
158T LEU* 1.3 60.0 + - - +
159T ILE* 3.0 9.3 + - + +
171T SER* 6.2 2.2 - - - -
175T ALA* 5.9 7.0 - - + -
185T ILE* 5.5 5.8 - - + -
186T LEU 2.6 17.2 + - - +
187T ILE* 3.4 12.0 - - + +
188T LEU* 2.9 26.1 + - - -
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Residues in contact with LEU 158 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46T THR* 6.2 3.1 - - - -
47T ILE 6.0 0.2 - - - +
48T GLY* 4.0 12.8 - - - +
49T HIS* 3.0 28.9 + - - +
50T VAL* 5.1 10.7 - - + -
54T LYS* 5.5 9.0 - - + -
156T LEU* 3.3 8.8 + - + +
157T LEU* 1.3 69.0 - - - +
159T ILE* 1.3 62.1 + - - +
188T LEU* 3.6 11.2 - - + +
190T ASN* 5.8 6.5 - - + -
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Residues in contact with ILE 159 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48T GLY* 5.7 0.2 - - - -
49T HIS* 5.0 4.9 - - - +
157T LEU* 3.0 10.6 + - + +
158T LEU* 1.3 74.3 - - - +
160T ALA* 1.3 64.3 + - - +
168T PRO* 5.4 11.9 - - + -
187T ILE* 5.9 3.6 - - + -
188T LEU 2.9 22.9 + - - +
189T GLN* 3.4 3.5 - - + -
190T ASN* 3.2 18.5 + - - +
206T GLN* 6.4 2.2 - - + -
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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