Contacts of the strand formed by residues 137 - 144 (chain A) in PDB entry 1QM4
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 GLY 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A ASP 3.2 4.4 + - - -
136A GLN* 1.3 75.5 + - - +
138A LEU* 1.3 60.0 + - - +
139A MET* 4.2 16.2 - - - -
291A VAL* 5.4 2.7 - - - -
320A SER* 3.5 3.8 - - - -
321A TYR* 2.9 38.0 + - - +
22B THR* 4.2 11.0 + - - -
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Residues in contact with LEU 138 (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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137A GLY* 1.3 74.1 - - - +
139A MET* 1.3 68.9 + - - +
140A PHE* 3.6 21.0 + - + -
279A GLY* 5.0 8.3 - - - -
318A GLN* 3.3 34.8 - - + +
319A VAL 3.5 7.2 - - - +
320A SER* 3.4 19.5 - - - +
20B MET 4.6 1.3 - - - +
21B PHE* 3.6 42.2 - - + -
22B THR* 3.6 30.2 - - - +
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Residues in contact with MET 139 (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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137A GLY* 4.3 7.0 - - - -
138A LEU* 1.3 94.0 - - - +
140A PHE* 1.3 64.2 + - - +
291A VAL* 3.6 18.2 - - + +
292A ASP* 3.1 40.8 - - - +
295A ALA* 3.8 23.8 - - + +
296A ALA* 3.7 27.8 - - + +
318A GLN* 3.6 3.1 - - - -
319A VAL* 2.7 42.9 + - + +
321A TYR* 4.4 8.5 - - - -
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Residues in contact with PHE 140 (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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138A LEU* 3.6 16.8 - - + -
139A MET* 1.3 76.3 - - - +
141A GLY* 1.3 59.1 + - - +
272A TYR* 4.5 8.5 + - + -
277A ALA* 3.5 53.2 - - + +
278A HIS* 3.8 1.8 - - - -
279A GLY* 3.9 24.0 - - - -
296A ALA* 4.1 11.7 - - - +
299A ALA* 3.6 9.8 - - - +
316A LEU* 4.1 17.9 - - + -
317A VAL 3.3 2.9 - - - -
318A GLN* 3.6 37.9 - - + -
381A PHE* 5.9 0.5 - - - -
21B PHE* 3.4 31.0 - + - -
274B GLY 3.8 6.1 - - - -
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Residues in contact with GLY 141 (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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140A PHE* 1.3 75.5 - - - +
142A TYR* 1.3 61.5 + - - -
272A TYR* 3.9 6.3 - - - -
299A ALA* 3.4 25.3 - - - +
303A ALA* 4.0 4.3 - - - -
316A LEU* 3.1 9.6 - - - +
317A VAL* 2.6 35.4 + - - -
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Residues in contact with TYR 142 (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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141A GLY* 1.3 73.5 - - - +
143A ALA* 1.3 54.5 + - - +
144A THR* 3.8 22.5 - - + +
146A GLU* 5.1 0.9 + - - -
152A PRO* 3.8 25.6 - - + -
196A VAL* 5.0 0.5 - - - +
272A TYR* 3.3 45.7 + + + -
275A TRP* 3.3 28.5 + + - -
276A GLY* 4.0 21.5 - - - -
300A ARG* 2.7 30.9 + - - +
303A ALA* 3.7 5.2 - - - +
314A ARG* 3.0 37.6 + - + +
315A VAL 3.2 24.7 - - - -
316A LEU* 4.1 7.4 - - + -
336A TYR* 4.2 13.7 - + - -
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Residues in contact with ALA 143 (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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142A TYR* 1.3 80.1 - - - +
144A THR* 1.3 63.0 + - - +
150A CYS* 3.4 11.2 - - + +
300A ARG* 3.5 9.0 - - - +
303A ALA* 3.5 32.5 - - + +
304A LYS* 3.6 4.9 - - - +
307A VAL* 3.6 11.7 - - + -
314A ARG* 3.4 2.8 - - - +
315A VAL* 2.9 33.1 + - + +
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Residues in contact with THR 144 (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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142A TYR* 3.8 24.8 + - + +
143A ALA* 1.3 78.2 - - - +
145A ASP* 1.3 63.3 + - - +
146A GLU* 2.8 33.1 + - - +
147A THR 4.0 0.2 - - - +
150A CYS* 3.0 25.0 + - - -
151A MET* 3.6 6.6 + - - -
152A PRO* 3.5 25.8 - - + -
196A VAL* 4.6 5.9 + - - +
307A VAL* 4.6 4.7 - - - -
313A ARG 3.5 10.1 + - - -
314A ARG* 4.1 6.8 - - - +
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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