Contacts of the strand formed by residues 167 - 175 (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 THR 167 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165H LEU 4.9 1.8 - - - -
166H TYR* 1.4 72.9 - - - +
168H LEU* 1.4 60.2 + - - +
169H ARG* 5.0 3.6 - - - -
188H SER* 4.0 3.1 - - - -
189H VAL* 2.9 42.2 + - - +
235H ASN* 3.0 15.4 + - - -
237H LEU* 3.5 8.0 - - - +
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Residues in contact with LEU 168 (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* 1.4 76.5 - - - +
169H ARG* 1.3 60.9 + - - +
170H ARG 3.6 2.3 + - - -
187H GLU 3.7 0.9 - - - +
188H SER* 3.9 11.4 - - - -
192H PRO* 4.7 0.2 - - + -
233H ALA* 4.3 22.7 - - + +
235H ASN* 3.4 26.9 - - + +
237H LEU* 3.9 17.3 - - + +
238H GLY* 3.4 37.7 - - - +
239H ARG 3.9 3.4 - - - +
240H GLU* 4.0 21.7 - - + +
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Residues in contact with ARG 169 (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* 5.0 3.5 - - - -
168H LEU* 1.3 72.4 - - - +
170H ARG* 1.4 68.4 + - - +
171H PRO* 3.9 0.5 - - - +
186H SER* 4.0 2.9 - - - -
187H GLU* 2.8 51.2 + - + +
188H SER* 4.6 0.2 - - - +
233H ALA* 5.1 2.3 - - - +
240H GLU* 5.2 0.4 - - - -
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Residues in contact with ARG 170 (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 3.6 4.9 + - - -
169H ARG* 1.4 76.0 - - - +
171H PRO* 1.4 78.5 - - + +
172H TYR* 3.7 2.6 + - - +
185H ILE 4.4 2.8 - - - +
186H SER* 4.5 0.2 - - - -
187H GLU 4.8 0.5 + - - -
233H ALA* 5.7 0.2 - - - -
240H GLU* 4.1 16.6 - - + -
241H CYS 5.1 4.7 - - - +
242H THR* 5.1 4.0 - - - -
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Residues in contact with PRO 171 (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* 1.4 89.9 - - + +
172H TYR* 1.4 58.1 + - - +
173H PHE* 4.8 1.6 - - + -
184H CYS* 3.4 27.4 - - - -
185H ILE 3.9 0.2 - - - +
186H SER* 3.8 16.6 - - - -
231H CYS* 3.5 23.3 - - + +
233H ALA* 4.1 10.3 - - + +
240H GLU 3.5 21.1 - - - +
242H THR* 3.2 35.6 - - - +
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Residues in contact with TYR 172 (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 4.9 1.8 - - - +
171H PRO* 1.4 72.3 - - - +
173H PHE* 1.3 73.2 + - - +
184H CYS* 3.6 1.2 - - - -
185H ILE* 2.9 48.3 + - + +
267H PRO* 4.3 20.2 - - + -
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Residues in contact with PHE 173 (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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171H PRO* 4.8 2.9 - - + -
172H TYR* 1.3 86.1 - - - +
174H ARG* 1.4 61.1 + - - +
182H LEU* 4.0 14.6 - - + -
183H VAL 3.5 4.3 - - - +
184H CYS* 4.1 3.1 - - - -
185H ILE* 5.2 1.6 - - - -
196H TRP* 3.1 41.1 - + - -
231H CYS* 3.7 13.5 - - + -
242H THR* 3.7 29.2 - - - -
243H ARG 4.5 2.7 - - - -
244H LEU* 3.9 29.4 - - + -
267H PRO* 4.2 13.6 - - - +
269H TRP* 3.1 54.9 + + + +
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Residues in contact with ARG 174 (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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173H PHE* 1.4 75.3 - - - +
175H LYS* 1.4 63.9 + - - +
182H LEU* 4.1 2.7 - - - -
183H VAL* 2.9 36.3 + - + +
185H ILE* 3.6 28.0 - - + -
269H TRP* 4.2 3.6 - - - -
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Residues in contact with LYS 175 (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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174H ARG* 1.4 72.5 - - - +
176H MET* 1.4 67.1 + - - +
177H GLU* 3.2 5.2 + - - +
181H ALA 3.7 11.4 - - - +
182H LEU* 4.0 7.0 - - + -
269H TRP* 3.9 25.4 - - + -
298H PHE* 6.4 0.4 - - + -
314H PHE* 4.8 12.3 - - + -
316H PHE* 5.8 6.7 - - + -
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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