Contacts of the strand formed by residues 165 - 169 (chain C) in PDB entry 3Q3G
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 165 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152C VAL* 6.1 0.7 - - + -
154C TRP* 3.5 35.2 - - + +
161C ARG 4.1 10.3 - - - +
162C GLN* 4.0 26.9 + - - +
163C ASN 3.3 0.2 - - - -
164C GLY* 1.4 77.0 + - - +
166C LEU* 1.3 65.3 + - - +
167C ASN* 3.5 25.8 - - - +
183C SER* 3.7 1.8 - - - +
184C THR 3.3 4.5 - - - +
185C LEU* 3.9 17.0 - - + -
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Residues in contact with LEU 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C GLY* 3.5 22.2 - - - +
165C VAL* 1.3 76.5 - - - +
167C ASN* 1.4 61.7 + - - +
182C SER 3.9 0.7 - - - +
183C SER* 3.6 0.7 - - - -
184C THR* 2.9 36.9 + - - +
186C THR* 5.4 0.2 - - - -
180D VAL* 3.7 31.2 - - + -
181D LEU 4.0 11.2 - - - +
182D GLN* 3.5 49.6 - - + +
605D EDO 4.1 7.9 + - - +
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Residues in contact with ASN 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C VAL* 4.0 16.8 - - - +
165C VAL* 3.5 13.9 - - - +
166C LEU* 1.4 80.2 + - - +
168C SER* 1.3 60.5 + - - +
169C TRP* 3.5 40.5 - - + -
181C MET* 4.8 2.0 - - - -
182C SER 3.3 4.5 - - - +
183C SER* 2.7 35.2 + - - -
180D VAL* 3.6 16.0 - - - +
605D EDO 5.4 0.4 - - - -
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Residues in contact with SER 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C ASN* 1.3 74.7 - - - +
169C TRP* 1.3 64.3 + - - +
181C MET* 3.4 3.3 - - - +
182C SER 2.7 36.8 + - - -
177D PHE* 3.8 8.0 - - - -
178D PRO* 2.6 46.5 + - - +
180D VAL* 4.0 7.4 - - - +
605D EDO 3.7 20.4 - - - -
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Residues in contact with TRP 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C PHE* 5.2 2.5 - + - -
148C LYS 5.1 6.3 + - - -
150C ILE* 4.4 14.1 + - + +
152C VAL* 6.0 0.7 - - + -
167C ASN* 3.5 42.6 - - + -
168C SER* 1.3 79.4 + - - +
170C THR* 1.3 67.4 + - - +
171C ASP* 4.0 0.5 + - - +
180C SER 3.6 6.5 - - - +
181C MET* 3.3 35.9 - - + +
178D PRO* 3.4 20.6 - - - +
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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