Contacts of the strand formed by residues 164 - 172 (chain D) in PDB entry 3QUM
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 VAL 164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155D TRP* 4.0 6.7 - - + -
161D SER* 3.7 39.0 - - - -
162D SER 3.8 1.0 - - - -
163D GLY* 1.3 75.6 - - - +
165D HIS* 1.3 90.1 + - - +
166D THR* 3.7 10.8 - - - +
180D SER* 3.9 7.6 - - - +
181D SER 3.2 11.2 - - - +
182D VAL* 3.5 19.3 - - + +
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Residues in contact with HIS 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ASN* 3.4 22.6 + - + -
138C ASN* 3.3 35.5 + - - -
164C THR* 4.4 10.5 - - + -
167C ASP* 5.8 5.1 + - + +
172C THR* 5.3 1.8 - - - +
174C SER* 3.0 27.4 + - - -
164D VAL* 1.3 81.4 - - - +
166D THR* 1.3 62.3 + - - +
167D PHE* 3.6 22.9 - - + -
180D SER* 3.1 4.9 + - - -
181D SER* 2.6 44.5 + - - +
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Residues in contact with THR 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C THR* 4.1 7.5 - - - +
153D LEU* 3.3 41.8 - - + +
155D TRP* 5.7 0.2 - - - -
164D VAL* 3.7 12.3 - - - +
165D HIS* 1.3 77.6 + - - +
167D PHE* 1.3 65.7 + - - +
168D PRO* 3.2 12.5 - - - +
178D LEU* 4.5 11.7 - - + -
179D SER 3.6 7.6 - - - +
180D SER* 3.7 3.8 + - - -
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Residues in contact with PHE 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C PHE* 3.4 35.2 - + - -
137C ASN* 3.1 22.7 - - - -
162C SER* 3.2 21.0 + - - +
164C THR* 3.4 20.6 - - + -
174C SER* 3.7 1.3 - - - -
175C MET 3.5 28.3 - - - -
176C SER* 3.4 22.2 - - - -
165D HIS* 3.6 22.7 - - + -
166D THR* 1.3 73.8 - - - +
168D PRO* 1.3 74.8 - - - +
169D ALA* 3.3 1.9 + - - -
178D LEU* 4.0 5.0 - - - +
179D SER* 2.8 37.1 + - - +
181D SER* 4.0 4.7 - - - -
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Residues in contact with PRO 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C SER* 3.4 22.2 + - - +
163C TRP 3.9 20.6 - - - +
164C THR* 4.2 15.5 - - - +
165C ASP* 5.1 8.5 - - - +
166D THR* 3.2 11.6 - - - +
167D PHE* 1.3 86.8 - - + +
169D ALA* 1.3 68.2 + - - +
170D VAL* 3.6 1.6 - - - +
178D LEU* 5.4 1.0 - - + -
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Residues in contact with ALA 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D TYR* 3.9 10.8 - - - +
149D GLU* 4.4 8.1 - - - +
167D PHE 3.3 4.1 + - - -
168D PRO* 1.3 77.4 - - - +
170D VAL* 1.3 60.6 + - - +
176D TYR* 4.2 19.6 - - + -
177D THR 3.5 13.7 - - - +
178D LEU* 3.9 21.3 - - + +
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Residues in contact with VAL 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C LEU* 3.8 35.2 - - + -
161C ASN 4.5 7.9 - - - +
162C SER* 3.6 20.6 - - - -
168D PRO 3.6 11.4 - - - +
169D ALA* 1.3 80.7 - - - +
171D LEU* 1.3 61.3 + - - +
172D GLN* 3.9 1.2 + - + +
175D LEU 3.9 1.0 - - - +
176D TYR* 3.7 5.0 - - - -
177D THR* 3.1 38.7 + - - +
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Residues in contact with LEU 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D PHE* 5.5 4.7 - - + -
170D VAL* 1.3 74.0 - - - +
172D GLN* 1.3 70.5 + - - +
173D SER 4.2 7.0 - - - +
174D ASP* 4.3 12.8 - - - +
175D LEU 3.7 6.1 - - - +
176D TYR* 3.0 49.1 - - + +
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Residues in contact with GLN 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C GLY 6.4 0.2 - - - -
160C LEU* 3.4 35.2 - - + +
144D LYS* 5.3 2.1 + - - -
170D VAL* 3.9 1.8 + - + +
171D LEU* 1.3 77.2 - - - +
173D SER* 1.3 87.0 + - - +
174D ASP 3.2 1.9 + - - -
175D LEU* 3.3 18.1 + - - +
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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