Contacts of the strand formed by residues 146 - 150 (chain H) in PDB entry 6B0B
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 SER 146 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144H GLU* 3.4 11.0 + - - +
145H ALA* 1.3 77.5 + - - +
147H SER* 1.3 60.7 + - - +
148H GLU* 3.5 5.0 + - - +
161H ILE* 4.0 23.8 - - - -
162H LYS 4.4 4.1 + - - -
163H GLN* 3.8 23.6 - - - +
164H ARG* 4.4 4.2 + - - +
195H VAL 4.4 0.3 - - - +
196H ASN* 5.8 0.2 - - - -
197H ILE* 4.3 25.2 + - - +
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Residues in contact with SER 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H SER* 1.3 71.7 - - - +
148H GLU* 1.3 60.0 + - - +
149H ARG* 3.7 10.9 + - - +
160H GLU 5.3 1.2 - - - +
161H ILE* 5.5 3.1 - - - +
194H ASN* 4.0 21.8 + - - +
195H VAL 3.9 7.7 + - - -
196H ASN* 3.6 21.0 + - - +
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Residues in contact with GLU 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70H LYS* 4.2 14.0 + - - +
146H SER 3.5 5.1 + - - +
147H SER* 1.3 70.3 - - - +
149H ARG* 1.3 62.5 + - - +
150H MET* 3.5 27.2 + - - +
159H GLY* 3.5 22.2 - - - +
160H GLU 4.1 10.3 - - - +
161H ILE* 3.5 39.8 - - + +
179H THR* 4.8 2.1 + - - -
181H TYR* 3.7 18.4 + - - -
195H VAL* 3.2 33.0 + - + +
197H ILE* 4.3 12.7 - - + +
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Residues in contact with ARG 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H SER* 3.7 11.3 + - - +
148H GLU* 1.3 73.4 - - - +
150H MET* 1.3 67.3 + - - +
151H TYR* 3.8 18.0 - - + -
158H LYS 4.2 2.3 - - - +
159H GLY* 4.3 5.2 - - - -
160H GLU 4.4 8.6 + - - +
193H TYR 4.0 6.3 - - - +
194H ASN* 4.0 21.2 - - + +
222H SER* 5.4 4.5 + - - +
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Residues in contact with MET 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H GLU* 3.5 40.2 - - - +
149H ARG* 1.3 75.6 - - - +
151H TYR* 1.3 64.5 + - - +
157H LEU* 3.7 21.3 - - + -
158H LYS 3.4 18.6 - - - +
159H GLY* 3.8 3.1 - - - -
181H TYR* 3.6 31.2 - - + -
192H ALA* 4.4 3.3 - - - +
193H TYR* 3.3 64.7 + - + +
195H VAL* 4.4 8.5 - - + -
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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