Contacts of the strand formed by residues 421 - 428 (chain B) in PDB entry 4QDQ
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 ARG 421 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B GLN 3.8 12.6 - - - +
309B SER 3.1 5.4 - - - -
310B ARG 3.6 20.6 - - - +
311B LEU* 4.3 2.0 - - - -
312B HIS* 3.7 11.1 + - - +
313B GLY* 2.9 30.5 + - - +
316B ASN 3.8 15.2 + - - +
317B GLY* 4.2 0.9 - - - -
344B THR* 3.2 4.9 - - - -
345B GLN* 2.8 72.1 + - + +
346B GLY 2.8 26.0 + - - +
347B ALA* 4.2 5.8 - - - +
348B ILE 5.1 1.0 - - - +
390B ALA 3.2 15.2 + - - -
391B THR* 4.2 8.1 - - - +
420B LEU* 1.3 80.9 - - - +
422B LEU* 1.3 62.4 + - - +
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Residues in contact with LEU 422 (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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283B MET* 3.2 19.9 - - + +
309B SER 2.7 13.7 + - - +
311B LEU* 2.9 24.4 + - - +
329B LEU* 3.9 27.6 - - + +
331B VAL* 4.0 23.1 - - + -
342B ILE* 3.5 32.8 - - + -
343B ALA 3.2 10.5 - - - +
344B THR* 4.1 7.6 - - + -
407B VAL* 5.8 0.4 - - + -
409B ILE* 3.9 21.1 - - + -
420B LEU* 4.9 3.8 - - + -
421B ARG* 1.3 76.8 - - - +
423B GLU* 1.3 66.6 + - - +
424B LEU* 4.1 13.5 - - + -
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Residues in contact with GLU 423 (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 PRO* 3.9 17.2 - - + +
281B LEU* 3.7 0.5 + - - +
282B GLY* 3.5 5.0 + - - -
283B MET* 3.0 27.1 + - - +
284B GLU* 3.0 32.6 + - - +
285B SER 4.6 0.7 + - - -
311B LEU* 3.8 23.5 - - + +
342B ILE* 3.6 3.1 - - - -
343B ALA* 2.9 31.6 + - + +
422B LEU* 1.3 75.0 - - - +
424B LEU* 1.3 91.2 + - - +
425B PHE* 3.6 29.2 - - + -
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Residues in contact with LEU 424 (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 PRO* 3.5 3.3 - - - +
281B LEU* 2.8 37.2 + - + -
283B MET* 4.3 3.3 - - + +
288B ILE* 5.1 2.7 - - + -
331B VAL* 3.9 37.9 - - + -
333B LEU* 4.4 7.9 - - + -
339B LEU* 3.8 12.6 - - + -
341B ALA 3.7 1.6 - - - -
342B ILE* 3.9 23.6 - - + -
407B VAL* 4.0 33.0 - - + -
409B ILE* 4.8 0.4 - - + -
422B LEU* 4.1 19.7 - - + -
423B GLU* 1.3 87.5 + - - +
425B PHE* 1.3 64.3 + - - +
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Residues in contact with PHE 425 (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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278B ASN* 3.4 26.0 - - + +
279B VAL 3.3 5.2 - - - +
280B PRO* 3.7 28.5 - - + -
281B LEU* 4.0 4.7 - - - -
311B LEU* 5.4 3.1 - - + -
339B LEU* 3.5 8.0 - - - +
340B THR* 2.8 26.5 + - - +
341B ALA* 3.0 38.5 + - + -
343B ALA* 3.5 29.4 - - + -
395B LEU* 3.7 12.3 - - + -
423B GLU* 3.6 25.1 - - + -
424B LEU* 1.3 76.4 - - - +
426B GLY* 1.3 59.2 + - - +
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Residues in contact with GLY 426 (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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277B CYS* 3.4 19.1 - - - -
278B ASN 3.7 1.0 + - - -
279B VAL* 2.9 37.1 + - - +
281B LEU* 3.9 6.9 - - - +
338B MET 3.2 12.3 - - - -
340B THR* 3.7 2.2 + - - -
425B PHE* 1.3 76.8 - - - +
427B CYS* 1.3 65.2 + - - +
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Residues in contact with CYS 427 (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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276B GLN 5.2 1.1 - - - +
277B CYS* 2.1 52.7 - - + -
279B VAL* 5.1 5.8 - - + -
281B LEU* 4.0 6.5 - - - +
337B THR* 3.3 6.6 - - - +
338B MET* 2.8 40.4 + - - +
426B GLY* 1.3 73.0 - - - +
428B ARG* 1.3 71.5 + - - +
431B ASP* 3.6 17.7 - - + +
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Residues in contact with ARG 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B LEU* 5.5 5.8 - - + +
287B ARG* 2.8 43.2 - - - +
335B PHE* 5.7 12.1 - - + -
336B LEU 4.8 3.1 - - - +
337B THR* 4.5 15.7 - - + +
338B MET* 5.3 0.2 - - - -
427B CYS* 1.3 82.7 - - - +
429B VAL* 1.3 65.7 + - - +
430B THR* 4.0 14.1 + - + +
431B ASP* 2.9 52.9 + - - +
432B ALA 4.6 0.2 + - - -
562B ARG* 5.3 0.3 + - - -
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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