Contacts of the strand formed by residues 162 - 168 (chain A) in PDB entry 1QK0
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 TYR 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A VAL* 4.9 2.3 - - - +
97A THR* 3.0 43.5 - - + +
98A PRO 4.0 8.1 - - - -
99A TRP* 3.4 46.2 - + + -
100A ALA 5.8 0.7 - - - -
152A ILE* 3.6 12.7 - - + +
155A ALA* 3.9 9.4 - - + -
156A ASN* 2.9 33.0 + - - +
160A GLY* 4.0 14.4 - - - -
161A ASN* 1.3 80.4 - - - +
163A ALA* 1.3 61.4 + - - +
212A ILE* 4.2 3.8 - - - +
213A ARG* 4.8 3.3 + - - +
504A MAN 4.1 13.6 + - - -
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Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A VAL* 4.0 25.6 - - + -
97A THR 3.0 9.1 + - - +
98A PRO* 3.8 2.4 - - - +
99A TRP* 3.0 24.3 + - - +
152A ILE* 3.9 3.8 - - - -
162A TYR* 1.3 74.1 - - - +
164A GLY* 1.3 61.2 + - - +
165A GLN* 4.0 1.3 + - - +
212A ILE* 4.4 0.9 - - - -
213A ARG* 3.2 26.2 - - + +
215A LEU* 4.3 17.3 - - + -
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Residues in contact with GLY 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A TRP* 4.8 1.6 - - - -
148A THR* 5.5 0.7 - - - -
149A LEU* 4.7 2.5 - - - -
152A ILE* 3.5 23.2 - - - +
163A ALA* 1.3 74.4 - - - +
165A GLN* 1.3 63.3 + - - +
166A PHE* 3.8 18.4 - - - -
212A ILE* 4.1 2.0 - - - +
213A ARG 3.0 9.8 + - - -
214A THR* 3.7 1.0 - - - -
215A LEU* 2.8 27.7 + - - +
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Residues in contact with GLN 165 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A PHE* 3.5 24.1 - - - -
98A PRO* 3.5 29.0 - - + +
99A TRP* 4.6 5.8 + - - +
101A ASN* 5.4 0.2 + - - -
131A PRO* 4.1 5.1 + - - +
132A SER* 3.5 25.4 + - - +
133A PHE* 3.4 40.6 - - + -
134A MET* 2.9 21.8 + - - +
148A THR* 5.9 0.4 - - - +
163A ALA 4.0 6.3 + - - +
164A GLY* 1.3 78.0 - - - +
166A PHE* 1.3 72.0 + - - +
215A LEU* 3.4 13.8 - - + +
379A PRO* 6.1 1.5 - - - +
392A VAL* 4.6 2.3 - - - +
393A TRP 5.8 0.8 - - - +
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Residues in contact with PHE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PHE* 3.5 4.2 - - - -
134A MET* 3.1 28.7 - - + +
136A LEU* 4.0 13.9 - - + -
145A MET* 3.7 59.0 - - + -
148A THR* 3.8 25.8 - - + -
149A LEU* 3.9 12.6 - - + -
164A GLY* 3.8 9.9 - - - -
165A GLN* 1.3 93.4 - - - +
167A VAL* 1.3 64.3 + - - +
214A THR* 3.7 21.5 - - + -
215A LEU 3.1 6.1 + - - -
216A LEU* 3.3 18.6 - - + +
217A VAL 3.2 21.3 + - - -
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PHE* 3.6 21.3 - - + -
134A MET 2.8 9.1 + - - -
135A TRP* 3.5 50.0 - - + +
136A LEU* 2.9 31.2 + - - +
166A PHE* 1.3 73.8 - - - +
168A VAL* 1.3 63.7 + - - +
169A TYR* 3.5 2.2 + - + +
217A VAL* 3.6 10.8 - - + +
220A PRO* 3.6 37.0 - - + -
394A VAL* 3.7 11.9 - - + -
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A LEU* 5.0 2.9 - - + -
167A VAL* 1.3 70.8 - - - +
169A TYR* 1.3 60.2 + - - +
195A TYR* 3.5 13.0 - - - +
198A TYR* 3.6 22.7 - - + +
199A ILE* 3.9 10.5 - - + -
202A ILE* 4.4 10.5 - - + -
216A LEU* 4.5 17.5 - - + -
217A VAL 3.0 9.5 + - - +
218A ILE* 3.8 27.1 - - + -
219A GLU* 2.8 48.9 + - + +
220A PRO* 3.7 1.6 - - - +
249A ALA* 5.2 0.9 - - + -
253A LEU* 4.5 11.4 - - + -
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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