Contacts of the strand formed by residues 167 - 173 (chain B) in PDB entry 3QK3
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 ARG 167 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B ASN* 4.0 14.8 - - - +
161B TYR* 3.4 7.4 - - - +
163B PHE* 3.0 38.6 + - + +
164B PRO* 3.0 35.7 + - - +
165B GLY* 3.8 13.8 + - - +
166B TYR* 1.3 82.0 - - - +
168B GLY* 1.3 66.6 + - - +
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Residues in contact with GLY 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ASN* 3.2 31.9 + - - +
95B SER* 3.6 12.5 - - - -
161B TYR* 3.9 5.7 - - - -
162B GLU* 3.6 3.8 - - - -
163B PHE* 3.5 22.0 - - - -
167B ARG* 1.3 77.8 - - - +
169B ARG* 1.3 64.9 + - - -
170B GLN* 3.7 3.3 + - - +
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Residues in contact with ARG 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A GLU 5.1 4.9 + - - -
179A ARG* 5.8 4.5 - - - +
183A GLU* 2.7 34.5 + - - +
70B GLU* 5.1 2.2 + - - -
76B GLY* 3.9 7.9 + - - -
77B GLU* 3.5 61.5 - - + +
95B SER* 3.7 4.3 - - - +
97B ASP* 3.8 18.0 + - - +
160B GLY 3.8 0.2 - - - +
161B TYR* 3.3 6.2 - - - -
162B GLU* 2.9 52.0 + - + +
168B GLY* 1.3 70.5 - - - -
170B GLN* 1.3 64.2 + - - +
171B TYR* 3.2 33.7 + - + +
185B ASP 4.0 17.6 + - - -
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Residues in contact with GLN 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B GLU* 4.8 0.4 + - - -
78B GLN* 3.7 34.8 + - + +
79B PHE* 4.3 6.7 - - - +
80B VAL* 2.9 41.2 + - + +
92B TRP 3.7 20.6 + - - -
94B ASN* 4.4 15.0 - - - +
159B VAL* 3.6 11.4 - - + +
160B GLY 3.3 5.4 - - - -
161B TYR* 3.4 33.5 + - + -
168B GLY 4.2 2.7 - - - +
169B ARG* 1.3 77.7 - - - +
171B TYR* 1.3 72.1 + - - +
172B VAL 4.4 0.2 - - - -
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Residues in contact with TYR 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ARG* 5.0 7.3 - - - -
183A GLU* 5.3 0.9 + - - -
78B GLN* 3.6 8.1 - - - -
159B VAL* 3.4 1.6 - - - -
160B GLY 2.8 31.7 + - - +
162B GLU* 4.5 12.6 + - + -
169B ARG* 3.2 57.5 + - + +
170B GLN* 1.3 76.6 - - - +
172B VAL* 1.3 64.2 - - - +
173B PHE* 3.6 8.9 - - + -
184B TRP* 3.5 44.6 - + + +
185B ASP 3.5 19.3 - - - -
186B ALA* 3.7 17.9 - - + +
187B SER* 4.9 2.4 + - - -
188B GLN 5.8 0.4 - - - -
190B GLN 4.9 3.1 - - - -
191B LEU* 3.8 24.9 - - + -
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LEU* 3.6 27.8 - - + -
78B GLN* 2.8 26.2 + - + +
80B VAL* 3.4 33.0 - - + -
107B LEU* 4.4 4.0 - - + -
157B THR* 4.0 10.3 - - + -
158B TRP 3.4 9.0 - - - +
159B VAL* 4.6 1.8 - - + -
170B GLN 5.8 0.2 - - - -
171B TYR* 1.3 74.7 - - - +
173B PHE* 1.3 67.7 + - - +
174B GLU* 4.0 24.7 + - + +
178B TYR* 4.4 4.9 + - - -
184B TRP* 4.5 10.4 - - - +
197B ILE* 4.3 4.9 - - + -
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Residues in contact with PHE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 4.6 4.5 - - + -
118B LEU* 5.8 1.1 - - + -
151B VAL* 3.7 28.7 - - + -
153B ALA* 4.4 8.9 - - + +
156B GLY 4.0 1.4 - - - +
157B THR* 3.4 2.6 - - - -
158B TRP* 2.8 54.3 + - + +
160B GLY* 4.0 15.5 - - - -
171B TYR* 3.6 17.9 - - + -
172B VAL* 1.3 71.1 - - - +
174B GLU* 1.3 64.2 + - - +
178B TYR* 3.7 19.1 - + + -
184B TRP* 3.4 57.7 - + + -
191B LEU* 3.9 22.9 - - + -
194B VAL* 4.8 6.1 - - + -
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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