Contacts of the strand formed by residues 372 - 378 (chain A) in PDB entry 3QEL
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 372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A ARG* 4.2 10.3 + - - -
142A PRO* 3.2 25.9 - - + +
143A PRO 5.0 0.9 + - - -
146A HIS* 4.3 15.1 + - - +
147A GLN* 4.0 21.7 + - + +
149A LEU* 5.8 2.8 - - + +
150A VAL* 3.6 25.8 - - + -
272A GLU* 5.6 0.2 - - - -
290A LEU* 4.2 24.2 - - + -
291A GLN 3.4 5.2 - - - +
292A LEU* 4.0 25.1 - - + -
293A ILE* 3.9 4.7 - - - -
370A ALA* 3.9 27.9 - - + +
371A GLN* 1.3 75.2 - - - +
373A SER* 1.3 65.3 + - - +
387A ILE* 3.0 9.0 - - - +
388A PHE* 2.8 50.3 + + + -
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Residues in contact with SER 373 (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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290A LEU* 3.4 9.4 - - - +
291A GLN* 2.8 40.5 + - - +
293A ILE* 3.6 17.8 - - - +
372A TYR* 1.3 72.3 - - - +
374A ILE* 1.3 60.7 + - - +
375A MET* 3.6 24.0 + - - +
384A GLN* 3.4 20.7 + - - -
386A GLY 3.6 5.2 - - - -
387A ILE* 4.5 2.0 - - - -
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Residues in contact with ILE 374 (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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150A VAL* 4.8 3.8 - - + -
154A MET* 4.1 24.7 - - + -
288A ILE* 3.8 26.0 - - + -
289A GLY 3.7 3.6 - - - +
290A LEU* 4.2 11.4 - - + -
372A TYR 4.3 0.4 - - - +
373A SER* 1.3 73.9 - - - +
375A MET* 1.3 55.3 + - - +
384A GLN* 3.5 3.1 - - - -
385A VAL* 2.7 45.5 + - + +
386A GLY* 2.6 28.4 + - - +
387A ILE 4.1 11.4 - - - -
388A PHE 4.2 9.2 - - - +
393A ILE* 4.1 29.8 - - + -
400A ILE* 6.0 1.3 - - + -
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Residues in contact with MET 375 (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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275A ILE* 4.3 4.0 - - + -
287A ILE 3.8 0.5 - - - +
288A ILE* 3.3 6.8 - - - +
289A GLY 2.7 41.8 + - - +
291A GLN* 3.9 34.8 - - + +
373A SER* 3.6 31.9 - - - +
374A ILE* 1.3 73.8 - - - +
376A ASN* 1.3 60.9 + - - +
382A LEU* 3.9 40.8 - - + +
383A VAL 3.3 13.9 - - - -
384A GLN* 3.8 20.0 - - + +
385A VAL* 4.7 0.9 - - - -
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Residues in contact with ASN 376 (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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286A GLY* 3.3 15.8 - - - +
287A ILE 3.0 16.0 - - - +
288A ILE* 3.8 14.2 - - + +
375A MET* 1.3 73.9 - - - +
377A LEU* 1.3 62.4 + - - +
378A GLN* 3.2 18.5 + - - +
381A LYS 3.3 2.1 - - - +
382A LEU* 4.1 2.2 - - - -
383A VAL* 2.8 31.1 + - - +
385A VAL* 3.6 20.0 - - + -
400A ILE* 3.3 9.1 - - - +
401A ILE 2.8 41.9 + - - +
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Residues in contact with LEU 377 (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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280A LEU* 4.4 15.9 - - + +
283A ALA* 3.3 28.3 - - + +
284A PRO 3.1 25.4 - - - +
285A ASP* 3.6 11.6 - - - +
286A GLY* 2.7 30.4 + - - +
287A ILE* 3.0 27.0 + - + -
376A ASN* 1.3 68.9 + - - +
378A GLN* 1.3 60.6 + - - +
380A ARG* 3.5 36.3 - - - +
381A LYS 3.3 11.0 - - - -
382A LEU* 3.9 17.5 - - + +
401A ILE* 4.8 0.7 - - - +
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Residues in contact with GLN 378 (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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285A ASP* 4.0 0.2 - - - -
376A ASN* 3.2 29.2 - - - +
377A LEU* 1.3 76.3 - - - +
379A ASN* 1.3 74.3 + - + +
380A ARG 3.1 0.4 - - - -
381A LYS* 2.8 30.3 + - - +
383A VAL* 3.8 25.9 - - + +
385A VAL* 3.8 12.5 - - - +
398A ARG* 5.4 0.6 - - - +
399A LYS 2.9 27.6 + - - +
401A ILE* 3.7 31.6 - - + +
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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