Contacts of the strand formed by residues 154 - 161 (chain A) in PDB entry 1QRW
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 ALA 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A PHE* 3.5 25.6 - - + -
88A VAL* 4.4 3.1 - - + -
90A GLY 2.8 17.1 + - - +
91A SER* 3.5 18.7 - - - +
92A THR 4.9 0.2 - - - -
93A GLU* 5.5 0.2 - - - -
147A TRP 3.8 5.4 - - - -
148A ILE* 4.1 4.0 - - + -
152A GLY 3.5 2.8 + - - -
153A GLN* 1.3 71.3 - - - +
155A GLN* 1.3 64.8 + - - +
184A LEU* 3.4 28.1 - - + +
195A LEU* 3.9 9.4 - - + -
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Residues in contact with GLN 155 (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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92A THR 2.8 26.0 + - - -
93A GLU* 3.6 13.2 - - - +
94A ALA* 2.8 34.0 + - + +
100A VAL* 4.0 22.7 - - + -
114A ILE* 4.6 3.9 - - + +
147A TRP* 2.8 19.0 + - + +
148A ILE* 4.3 0.4 - - - -
149A THR* 3.8 8.3 - - + +
153A GLN* 2.9 29.3 + - - +
154A ALA* 1.3 74.2 + - - +
156A GLY* 1.3 56.5 + - - +
181A PHE* 3.6 29.7 - - + -
183A ARG* 3.7 3.5 - - - +
184A LEU* 3.0 19.7 + - - +
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Residues in contact with GLY 156 (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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21A PHE* 3.3 11.8 - - - -
147A TRP* 3.0 28.7 + - - +
154A ALA 3.9 0.2 - - - -
155A GLN* 1.3 81.1 - - - +
157A VAL* 1.3 64.6 + - - -
181A PHE* 3.9 4.3 - - - -
182A GLU 3.0 13.2 - - - -
184A LEU* 3.5 15.9 - - - +
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Residues in contact with VAL 157 (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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20A GLY* 4.1 14.6 - - - -
21A PHE* 4.5 2.7 - - + -
32A VAL* 4.1 18.6 - - + -
33A THR* 3.7 24.2 - - - +
34A ALA* 4.2 3.6 - - - +
63A ASP 4.2 4.3 - - - +
144A GLY 3.6 22.2 - - - +
145A GLY 3.2 3.1 - - - -
147A TRP* 3.9 0.2 - - - -
156A GLY* 1.3 80.2 - - - +
158A MET* 1.3 65.0 + - - +
181A PHE* 3.3 4.6 - - - +
182A GLU* 2.8 41.5 + - + +
184A LEU* 5.2 0.7 - - + -
187A ILE* 3.9 20.6 - - + -
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Residues in contact with MET 158 (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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34A ALA* 3.5 10.2 - - - +
102A HIS* 3.8 9.4 - - - +
138A MET* 3.7 35.7 - - + -
142A ASP* 3.3 33.9 - - - +
143A SER* 3.6 5.5 - - - +
144A GLY 2.8 23.2 + - - +
145A GLY* 2.9 14.0 + - - +
147A TRP* 3.4 48.1 - - + +
157A VAL* 1.3 71.2 - - - +
159A SER* 1.3 58.8 + - - +
160A GLY 3.4 17.9 - - - +
180A LEU 3.0 32.1 - - - +
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Residues in contact with SER 159 (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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34A ALA* 5.0 0.2 - - - -
36A HIS* 3.0 16.7 - - - -
63A ASP* 2.7 31.6 + - - +
123A TYR* 2.8 24.4 + - - -
131A LEU* 4.0 22.6 - - - +
143A SER* 3.7 3.9 + - - -
157A VAL 3.3 1.0 + - - -
158A MET* 1.3 74.4 - - - +
160A GLY* 1.3 50.4 + - - +
180A LEU 2.9 18.3 + - - -
182A GLU* 4.3 6.1 - - - -
201A GOL 2.6 23.4 + - - -
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Residues in contact with GLY 160 (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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123A TYR* 3.2 11.7 + - - -
138A MET* 3.6 15.0 - - - +
143A SER* 5.2 0.2 - - - -
158A MET* 3.4 7.6 - - - +
159A SER* 1.3 82.8 - - - +
161A GLY* 1.3 58.0 + - - -
179A SER 3.7 0.3 - - - -
180A LEU* 2.8 29.2 + - - +
201A GOL 3.3 12.8 - - - -
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Residues in contact with GLY 161 (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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123A TYR* 4.7 4.6 + - - -
138A MET* 3.9 14.0 - - - +
160A GLY* 1.3 74.2 - - - -
162A ASN* 1.3 57.7 + - - -
163A VAL* 2.9 22.3 + - - +
178A SER 3.0 15.3 - - - -
179A SER* 4.2 0.4 - - - -
180A LEU* 4.5 5.3 - - - +
201A GOL 4.8 0.2 + - - -
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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