Contacts of the strand formed by residues 182 - 189 (chain H) in PDB entry 3QS7
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 182 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173H PHE* 4.0 15.7 - - + -
174H ARG 4.0 2.2 - - - +
175H LYS* 4.0 12.8 - - + +
181H ALA* 1.4 70.7 - - - +
183H VAL* 1.4 68.2 + - - +
196H TRP* 3.8 27.8 - - + -
220H VAL* 3.6 1.4 - - - +
221H LEU* 2.9 35.3 + - + +
224H LEU* 3.6 25.1 - - + +
244H LEU* 3.9 27.1 - - + -
269H TRP* 3.6 39.5 - - + -
314H PHE* 5.3 3.8 - - + -
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Residues in contact with VAL 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H PHE* 3.5 5.9 - - - -
174H ARG* 2.9 42.8 + - + +
176H MET* 4.0 20.2 - - + +
182H LEU* 1.4 80.4 - - - +
184H CYS* 1.3 67.5 + - - +
185H ILE* 3.8 13.8 + - + +
196H TRP* 4.0 5.2 - - - -
219H LYS* 3.4 13.5 - - + +
220H VAL* 3.8 26.9 - - + -
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Residues in contact with CYS 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171H PRO* 3.4 23.3 - - - -
172H TYR 3.6 3.4 - - - -
173H PHE* 4.1 3.8 - - - -
183H VAL* 1.3 71.9 - - - +
185H ILE* 1.3 61.5 + - - +
186H SER* 3.8 4.5 + - - -
194H VAL* 3.6 23.0 - - + +
196H TRP* 3.6 19.4 - - + +
219H LYS* 2.9 18.0 + - - +
231H CYS* 2.0 48.9 - - - -
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Residues in contact with ILE 185 (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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170H ARG 4.4 0.9 - - - +
171H PRO 3.8 0.2 - - - -
172H TYR* 2.9 47.0 + - + +
173H PHE 5.2 0.9 - - - -
174H ARG* 3.6 29.8 - - + +
183H VAL* 3.8 13.9 + - + +
184H CYS* 1.3 72.7 - - - +
186H SER* 1.3 59.0 + - - +
187H GLU* 4.2 2.0 + - + -
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Residues in contact with SER 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169H ARG 4.1 2.5 - - - -
170H ARG 4.5 0.2 - - - -
171H PRO* 3.8 22.7 - - - -
184H CYS* 3.8 4.5 + - - -
185H ILE* 1.3 74.5 - - - +
187H GLU* 1.3 60.8 + - - +
188H SER 4.2 0.3 + - - -
192H PRO* 4.4 10.9 - - - +
194H VAL* 4.1 19.1 - - - +
233H ALA* 3.7 30.7 - - - -
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Residues in contact with GLU 187 (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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168H LEU* 3.7 0.9 - - - +
169H ARG* 2.8 48.2 + - + +
170H ARG 4.8 0.6 + - - -
185H ILE* 4.2 2.3 + - + +
186H SER* 1.3 72.8 - - - +
188H SER* 1.4 64.1 + - - +
192H PRO* 4.9 0.3 - - - +
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Residues in contact with SER 188 (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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167H THR* 3.4 18.6 - - - -
168H LEU* 3.9 7.9 - - - -
186H SER 4.2 0.6 + - - -
187H GLU* 1.4 78.4 - - - +
189H VAL* 1.3 66.9 + - - +
190H PRO 3.2 22.9 - - - +
191H GLU* 3.4 9.4 + - - +
192H PRO* 3.6 21.2 - - - +
235H ASN* 3.4 8.1 - - - -
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Residues in contact with VAL 189 (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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164F LEU* 4.7 20.0 - - + +
164H LEU 4.8 4.9 - - - +
165H LEU 4.6 7.6 - - - +
166H TYR* 3.4 10.7 - - - +
167H THR* 2.9 49.0 + - - +
188H SER* 1.3 76.9 - - - +
190H PRO* 1.4 63.6 - - + +
191H GLU 4.2 0.2 - - - +
237H LEU* 3.3 4.7 - - - +
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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