Contacts of the helix formed by residues 155 - 159 (chain K) in PDB entry 1J0B
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 PRO 155 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61K LEU* 5.5 0.4 - - + -
75K THR* 3.0 7.1 + - - -
134K MET* 3.7 14.6 - - + -
153K VAL* 3.9 8.6 - - + +
154K ILE* 1.3 95.1 - - + +
156K PRO* 1.3 79.8 - - + +
158K GLY 3.1 8.4 + - - -
159K ALA* 4.4 3.4 - - + +
160K SER* 3.9 39.9 - - - +
226K LYS* 6.5 0.4 - - - -
323U SER 5.4 7.6 - - - +
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Residues in contact with PRO 156 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76K VAL* 3.2 32.0 - - + +
77K GLY* 6.0 0.7 - - - -
131K PHE* 3.6 31.4 - - + -
134K MET* 3.4 12.3 - - + -
155K PRO* 1.3 89.3 - - + +
157K GLY* 1.3 65.5 + - - +
159K ALA* 2.9 24.8 + - + +
191K SER* 3.8 12.3 + - - -
226K LYS* 4.9 10.1 - - - +
1111K 5PA 5.6 2.5 - - + -
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Residues in contact with GLY 157 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54K LYS* 3.4 15.7 + - - -
57K LYS* 3.5 12.2 - - - -
76K VAL 4.6 0.4 + - - -
83K HIS* 3.1 24.9 - - - -
156K PRO* 1.3 71.3 - - - +
158K GLY* 1.3 63.3 + - - +
159K ALA* 2.8 3.1 + - - -
191K SER* 4.0 3.9 + - - -
1111K 5PA 3.0 34.8 + - - -
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Residues in contact with GLY 158 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57K LYS* 3.6 6.7 - - - +
61K LEU* 4.0 7.9 - - - -
83K HIS* 3.1 10.1 - - - -
154K ILE* 3.7 21.3 - - - -
155K PRO 3.1 11.8 + - - -
156K PRO 2.9 3.0 + - - -
157K GLY* 1.3 75.8 - - - +
159K ALA* 1.3 51.1 + - - +
160K SER* 2.7 25.0 + - - +
163K GLY* 3.5 17.3 - - - -
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Residues in contact with ALA 159 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57K LYS* 5.2 0.4 - - - -
155K PRO* 4.2 8.5 + - + +
156K PRO* 2.9 17.3 + - + +
157K GLY 2.8 3.6 + - - -
158K GLY* 1.3 71.2 - - - +
160K SER* 1.3 65.5 + - - +
161K PRO* 4.4 0.2 - - - +
164K THR* 5.3 0.9 - - - +
191K SER* 3.5 24.5 - - - +
193K GLY* 4.2 15.5 - - - +
226K LYS* 5.8 8.7 - - + -
230K LEU* 3.2 26.9 - - + +
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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