Contacts of the helix formed by residues 152 - 158 (chain c) in PDB entry 4B2Q
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 LEU 152 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150c THR* 2.9 20.4 + - - +
151c GLY* 1.3 78.5 - - - +
153c LYS* 1.3 61.4 + - - +
154c ALA* 3.3 3.8 - - + +
155c VAL* 2.9 18.0 + - + +
156c ASP* 2.8 29.0 + - - +
180c VAL* 3.5 51.6 - - + +
183c ASP* 4.1 22.9 - - + +
365c PRO* 5.1 17.9 - - + -
432c GLN* 3.9 21.8 - - + +
433c ASN 5.6 2.9 - - - +
436c SER 6.2 0.2 - - - -
437c PRO* 5.9 0.7 - - + -
443c GLN* 3.6 1.8 - - - -
1511c ATP 6.4 0.2 - - - +
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Residues in contact with LYS 153 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152c LEU* 1.3 71.4 - - - +
154c ALA* 1.3 64.7 + - - +
155c VAL 3.0 1.0 + - - -
157c ALA* 3.0 30.5 + - - +
429c LEU* 2.5 34.7 + - - +
430c LEU* 4.4 15.7 - - + +
431c LYS 4.4 1.6 + - - -
432c GLN* 3.4 28.3 + - - +
438c LEU* 3.8 8.1 - - + -
443c GLN* 3.4 36.0 - - + +
446c LEU* 3.7 27.0 - - + +
447c ILE* 5.1 11.0 - - + -
467c GLU* 2.9 28.5 + - - -
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Residues in contact with ALA 154 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152c LEU* 3.3 1.7 - - + -
153c LYS* 1.3 78.6 - - - +
155c VAL* 1.3 57.8 + - + +
158c LEU* 3.3 34.8 - - + +
159c VAL* 4.2 1.9 + - - +
365c PRO* 4.7 9.4 - - + +
367c ILE* 3.7 27.5 - - + +
430c LEU* 4.0 42.0 + - + +
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Residues in contact with VAL 155 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150c THR* 3.4 28.9 - - + +
152c LEU* 2.9 30.5 + - + +
154c ALA* 1.3 75.8 - - - +
156c ASP* 1.3 63.2 + - - +
157c ALA 3.0 4.7 + - - -
159c VAL* 2.9 54.8 + - + +
160c PRO* 5.0 0.2 - - + -
161c ILE* 4.4 3.4 - - + -
180c VAL* 4.4 3.1 - - + -
352c ILE* 4.2 22.4 - - + -
367c ILE* 3.7 23.8 - - + -
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Residues in contact with ASP 156 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148c VAL 3.6 8.5 - - - +
149c GLN* 3.9 13.9 + - - +
150c THR* 3.1 27.5 + - - +
151c GLY* 2.9 28.1 + - - -
152c LEU 2.8 17.2 + - - +
155c VAL* 1.3 74.3 - - - +
157c ALA* 1.3 56.0 + - - +
160c PRO* 4.2 8.6 - - - +
161c ILE 4.9 4.5 + - - -
381c GLN* 3.5 19.4 - - - +
382c VAL* 6.3 0.7 - - + -
385c LEU* 3.1 20.3 - - + +
443c GLN* 3.6 22.9 + - - +
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Residues in contact with ALA 157 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153c LYS* 3.0 20.2 + - - +
154c ALA* 5.1 0.4 - - - -
155c VAL 3.0 0.8 - - - -
156c ASP* 1.3 80.2 - - - +
158c LEU* 1.3 68.4 + - + +
381c GLN* 3.0 18.6 + - - +
385c LEU* 3.7 18.6 - - + +
389c ALA* 4.9 10.1 - - + +
392c LEU* 4.7 11.1 - - + +
430c LEU* 5.3 1.8 - - + -
447c ILE* 4.7 20.4 - - + -
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Residues in contact with LEU 158 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154c ALA* 3.3 22.5 + - + +
155c VAL 3.3 1.2 + - - -
157c ALA* 1.3 86.7 - - + +
159c VAL* 1.3 67.7 + - + +
160c PRO* 3.0 12.2 - - - +
367c ILE* 5.7 3.8 - - + -
369c VAL* 3.5 37.5 - - + -
374c SER* 5.3 0.7 - - - -
381c GLN* 4.4 0.7 - - - +
392c LEU* 4.3 17.5 - - + -
393c LYS* 4.0 46.5 - - + +
396c LEU* 4.3 6.7 - - + -
430c LEU* 4.1 20.6 - - + -
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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