Contacts of the strand formed by residues 471 - 477 (chain B) in PDB entry 3QFR
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 SER 471 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290B THR* 4.8 2.1 + - - -
307B GLU* 3.9 5.0 + - - +
308B LEU 3.2 17.2 + - - -
309B ASP* 5.1 1.8 - - - -
310B ILE* 3.8 1.1 - - - +
317B TYR* 2.7 31.9 + - - -
463B SER* 3.7 1.4 + - - -
468B HIS* 2.8 18.3 + - - +
469B PRO 3.3 2.0 + - - -
470B ASN* 1.3 79.8 - - - +
472B VAL* 1.3 57.7 + - - +
473B HIS* 2.9 33.9 + - - -
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Residues in contact with VAL 472 (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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306B LEU 4.1 0.2 - - - +
307B GLU* 3.7 0.5 - - - -
308B LEU* 2.9 37.8 + - + +
310B ILE* 3.4 30.1 - - + -
317B TYR* 3.7 13.2 - - + -
323B VAL* 3.7 23.1 - - + -
461B ILE* 3.7 33.2 - - + -
463B SER* 4.0 3.1 - - - -
471B SER* 1.3 74.6 + - - +
473B HIS* 1.3 66.8 + - - +
474B ILE* 4.1 1.5 + - + +
514B MET* 4.1 17.7 - - + -
516B VAL* 4.7 4.3 - - + -
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Residues in contact with HIS 473 (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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305B HIS* 4.1 14.9 + - - +
306B LEU 3.3 5.6 - - - +
307B GLU* 3.2 44.8 + - + -
461B ILE* 3.5 7.7 - - - +
462B ALA* 2.7 37.1 + - + +
463B SER* 3.5 25.7 + - - -
468B HIS* 3.6 34.3 - + - -
471B SER* 2.9 32.1 + - - -
472B VAL* 1.3 75.0 - - - +
474B ILE* 1.3 65.2 + - - +
548B GLN* 5.2 3.0 + - - -
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Residues in contact with ILE 474 (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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304B MET 3.3 1.7 - - - +
305B HIS* 3.3 8.9 - - - +
306B LEU* 2.9 49.7 + - + +
308B LEU* 3.9 30.5 - - + -
323B VAL* 3.7 26.9 - - + -
325B VAL* 4.9 8.7 - - + -
459B TYR* 3.5 40.2 - - + -
460B SER 4.8 2.0 - - - +
462B ALA* 5.0 0.2 - - - -
472B VAL 4.6 3.8 - - - +
473B HIS* 1.3 78.4 - - - +
475B CYS* 1.3 66.2 + - - +
476B ALA* 4.4 4.7 - - + -
497B LEU* 5.2 11.9 - - + -
578B TYR* 4.6 2.7 - - - -
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Residues in contact with CYS 475 (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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295B LEU* 3.9 12.8 - - - -
303B LEU* 5.9 0.7 - - - -
304B MET 3.6 4.3 - - - -
460B SER 4.7 4.2 + - - -
462B ALA* 4.5 2.0 - - + +
473B HIS 4.4 0.4 + - - -
474B ILE* 1.3 73.7 - - - +
476B ALA* 1.3 54.7 + - - +
538B THR* 4.0 16.7 - - - -
540B VAL* 4.6 1.1 - - - -
541B ALA* 3.7 21.3 - - + +
577B LEU* 4.2 17.3 - - - -
578B TYR* 3.4 36.3 - - + +
752B FAD 2.7 31.1 + - - +
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Residues in contact with ALA 476 (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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303B LEU* 3.6 1.7 - - - -
304B MET* 2.9 48.8 + - + +
306B LEU* 5.6 1.1 - - + +
459B TYR* 3.6 26.2 - - + -
474B ILE* 4.0 6.2 - - + -
475B CYS* 1.3 76.1 - - - +
477B VAL* 1.3 60.3 + - - +
494B THR* 4.5 11.0 - - + -
497B LEU* 5.5 4.3 - - + -
538B THR* 4.2 3.6 - - - -
752B FAD 3.0 13.5 - - - +
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Residues in contact with VAL 477 (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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301B ARG* 4.3 25.8 - - + +
302B HIS 4.0 5.2 - - - +
303B LEU* 4.0 29.2 - - + +
476B ALA* 1.3 71.4 - - - +
478B VAL* 1.3 74.7 + - - +
479B VAL* 3.5 9.2 + - + +
494B THR* 3.6 11.8 - - - +
538B THR* 3.8 11.1 - - + +
752B FAD 3.2 11.1 + - + +
753B NAP 3.8 18.6 - - - +
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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