Contacts of the strand formed by residues 372 - 378 (chain B) in PDB entry 3QEK
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B ARG* 3.8 22.0 + - - -
142B PRO* 3.3 28.8 - - + +
143B PRO 4.9 0.3 + - - -
146B HIS* 4.1 18.7 + - - +
147B GLN* 4.1 12.2 + - + -
149B LEU* 5.5 3.8 - - + +
150B VAL* 3.5 29.4 - - + -
290B LEU* 4.4 18.8 - - + -
291B GLN 3.3 7.4 - - - +
292B LEU* 3.9 23.8 - - + -
293B ILE* 3.8 4.7 - - - -
370B ALA* 3.8 21.6 - - + +
371B GLN* 1.3 74.6 - - - +
373B SER* 1.3 64.4 + - - +
374B ILE* 3.6 0.6 + - + +
387B ILE* 3.3 4.9 - - - +
388B PHE* 2.8 51.2 + + + -
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Residues in contact with SER 373 (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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290B LEU* 3.4 6.2 - - - +
291B GLN* 2.8 36.7 + - - -
293B ILE* 3.5 14.3 - - - +
372B TYR* 1.3 70.9 - - - +
374B ILE* 1.3 62.1 + - - +
375B MSE 3.0 33.2 + - - +
384B GLN* 2.9 24.4 + - - -
387B ILE* 3.4 10.4 - - - +
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Residues in contact with ILE 374 (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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150B VAL* 4.6 5.2 - - + -
154B MSE 4.3 17.7 - - + -
288B ILE* 3.8 25.1 - - + -
289B GLY 3.9 3.8 - - - +
290B LEU* 4.2 14.4 - - + -
372B TYR 4.3 0.4 - - - +
373B SER* 1.3 71.2 - - - +
375B MSE 1.3 59.7 + - - +
384B GLN* 3.4 3.8 - - - -
385B VAL* 2.9 43.4 + - + +
386B GLY* 2.9 17.2 + - - +
387B ILE 3.7 28.3 - - - +
388B PHE* 3.9 8.3 - - + +
393B ILE* 3.9 29.4 - - + -
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Residues in contact with MSE 375 (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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275B ILE* 4.1 14.1 - - + -
287B ILE* 3.8 0.3 - - - +
288B ILE* 3.2 8.1 - - - +
289B GLY 2.9 38.0 + - - +
291B GLN* 2.7 48.7 - - + +
373B SER* 3.0 41.3 - - - +
374B ILE* 1.3 73.8 - - - +
376B ASN* 1.3 61.8 + - - +
382B LEU* 4.3 16.8 - - + +
383B VAL 3.5 3.1 - - - -
384B GLN* 3.6 32.5 - - + +
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Residues in contact with ASN 376 (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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286B GLY* 3.2 8.5 + - - -
287B ILE 3.0 17.5 + - - +
288B ILE* 3.8 9.6 - - + +
375B MSE 1.3 75.7 - - - +
377B LEU* 1.3 63.6 + - - +
378B GLN* 2.8 29.1 + - - +
382B LEU* 4.5 2.0 - - - -
383B VAL* 2.7 36.5 + - - +
385B VAL* 3.7 24.5 - - + -
400B ILE* 3.6 8.5 - - - +
401B ILE 2.9 36.6 + - - -
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Residues in contact with LEU 377 (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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280B LEU* 3.9 13.2 - - + +
283B ALA* 3.8 35.9 - - + +
284B PRO 3.8 10.1 - - - +
285B ASP* 3.9 4.8 - - - +
286B GLY* 2.9 31.1 + - - +
287B ILE* 3.0 24.0 + - + +
375B MSE 4.4 0.2 - - - -
376B ASN* 1.3 69.8 - - - +
378B GLN* 1.3 62.8 + - - +
379B ASN 4.2 0.4 - - - -
380B ARG* 3.6 31.4 - - - +
381B LYS 3.4 30.7 - - - +
382B LEU* 3.6 17.6 - - + +
401B ILE* 5.3 0.9 - - - +
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Residues in contact with GLN 378 (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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285B ASP* 4.7 0.2 - - - -
376B ASN* 2.8 33.8 + - - +
377B LEU* 1.3 74.8 - - - +
379B ASN* 1.3 68.7 + - - +
380B ARG 3.2 0.2 - - - -
381B LYS* 2.9 52.2 + - - +
383B VAL* 3.9 20.8 - - + +
385B VAL* 4.1 11.3 - - - +
398B ARG* 5.5 1.2 - - - +
399B LYS 3.1 23.1 + - - +
401B ILE* 3.8 30.2 - - + +
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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