Contacts of the strand formed by residues 158 - 163 (chain H) in PDB entry 6CMO
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 CYS 158 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139H VAL* 4.1 14.8 - - + -
140H PHE 3.5 9.2 - - - +
141H PRO* 4.6 4.7 - - + -
142H LEU* 3.8 4.8 - - - +
157H GLY* 1.3 73.4 - - - +
159H LEU* 1.3 60.1 - - - +
160H VAL* 3.6 16.8 + - - +
172H TRP* 5.4 9.0 - - - -
196H LEU* 3.9 6.9 - - - +
197H SER* 4.0 11.6 - - - -
198H SER* 3.9 13.3 + - - -
214H CYS* 2.0 50.0 - - + -
216H VAL* 5.6 0.9 - - - -
227H LYS* 5.9 1.1 - - + -
229H VAL* 5.8 1.3 - - + -
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Residues in contact with LEU 159 (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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138H SER 3.7 1.7 - - - +
139H VAL* 3.4 0.5 - - - -
140H PHE* 2.6 59.0 + - + +
142H LEU* 3.6 11.0 - - + +
158H CYS* 1.3 68.8 - - - +
160H VAL* 1.3 59.3 + - - +
161H LYS* 3.7 34.3 + - + +
195H SER* 4.9 7.9 - - - +
196H LEU 3.3 18.2 - - - +
197H SER* 4.7 9.4 - - - +
125L GLN* 3.9 17.3 - - - +
130L THR 4.9 3.8 - - - +
131L ALA* 5.0 1.6 - - - -
132L SER* 4.2 26.7 - - - +
179L THR* 5.6 5.8 - - + -
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Residues in contact with VAL 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H PRO* 4.1 17.0 - - + -
138H SER 3.7 2.7 - - - -
139H VAL* 3.8 36.3 - - + +
158H CYS* 4.1 16.4 - - - +
159H LEU* 1.3 71.7 - - - +
161H LYS* 1.3 60.7 + - - +
163H TYR* 3.8 17.7 - - + -
172H TRP* 6.2 2.5 - - + -
195H SER* 3.3 3.8 - - - -
196H LEU* 2.8 53.4 + - + -
216H VAL* 3.9 21.5 - - + -
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Residues in contact with LYS 161 (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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137H PRO* 4.0 0.5 - - - +
138H SER* 2.7 48.4 + - - +
140H PHE* 4.0 19.3 - - + -
159H LEU* 3.8 38.2 - - + +
160H VAL* 1.3 74.5 - - - +
162H ASP* 1.3 72.0 + - - +
163H TYR* 3.6 1.3 - - - -
189H GLN* 3.0 32.5 + - - +
195H SER* 4.3 11.4 - - - -
130L THR* 4.4 16.2 - - - +
181L THR* 4.9 9.7 - - - +
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Residues in contact with ASP 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135H LYS* 4.2 7.6 - - + +
136H GLY 2.9 23.2 - - - +
137H PRO* 3.5 0.2 - - - +
138H SER* 4.7 9.7 - - - -
161H LYS* 1.3 83.7 - - - +
163H TYR* 1.3 58.4 + - - +
189H GLN* 3.5 21.0 + - - +
191H SER* 3.8 8.7 + - - -
193H LEU* 3.7 24.0 - - + +
194H TYR 3.5 10.9 + - - -
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Residues in contact with TYR 163 (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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135H LYS 4.4 1.3 - - - -
137H PRO* 3.8 25.1 - - + -
160H VAL* 3.8 20.9 - - + -
162H ASP* 1.3 76.9 - - - +
164H PHE* 1.3 69.4 + - - +
165H PRO 5.0 0.2 - - - -
166H GLU* 3.2 32.5 + - - +
168H VAL* 4.5 7.9 - - + +
186H ALA* 3.3 24.1 - - - +
193H LEU* 3.4 19.4 - - - +
194H TYR* 3.4 30.8 + - + -
195H SER* 3.7 2.0 - - - -
196H LEU* 3.4 30.3 - - + +
218H HIS* 3.7 35.0 - + + +
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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