Contacts of the strand formed by residues 303 - 309 (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 LEU 303 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B LYS* 3.6 4.2 - - - +
295B LEU* 2.7 33.6 + - + -
296B ASN* 3.0 38.7 + - + +
301B ARG* 4.2 26.9 - - + +
302B HIS* 1.3 75.7 - - - +
304B MET* 1.3 54.5 + - - +
475B CYS* 6.1 0.7 - - - -
476B ALA 3.6 6.1 - - - +
477B VAL* 4.0 24.5 - - + +
537B GLY* 5.6 1.3 - - - -
538B THR* 4.2 10.3 - - + +
575B ASP* 4.2 13.7 - - + +
577B LEU* 3.6 42.6 - - + -
753B NAP 4.8 0.9 - - - +
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Residues in contact with MET 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ASN* 3.3 32.3 - - - +
293B ARG 3.7 8.5 - - - +
295B LEU* 3.8 6.0 - - - +
302B HIS* 4.2 13.2 - - - +
303B LEU* 1.3 74.8 - - - +
305B HIS* 1.3 60.7 + - - +
306B LEU* 3.2 28.2 - - + +
474B ILE 3.3 4.2 - - - +
475B CYS* 3.6 3.1 - - - -
476B ALA* 2.9 43.2 + - + +
478B VAL* 3.8 21.8 - - + -
494B THR* 4.0 4.5 - - - +
497B LEU* 3.3 8.5 - - + +
498B ARG* 3.3 31.2 - - + +
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Residues in contact with HIS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B THR* 3.7 3.2 - - - +
292B ASN* 3.2 4.0 + - - -
293B ARG* 2.9 54.9 + - + +
295B LEU* 3.4 24.0 - - + -
304B MET* 1.3 73.3 - - - +
306B LEU* 1.3 64.4 + - - +
307B GLU* 3.0 42.5 - - + +
462B ALA 5.5 1.8 + - - -
473B HIS* 4.1 17.9 + - + +
474B ILE 3.3 7.4 - - - -
544B ILE* 5.9 1.2 - - - +
578B TYR* 2.6 40.3 - + - -
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Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B VAL* 4.5 11.4 - - + -
291B THR 3.0 8.3 - - - +
292B ASN* 4.0 19.3 - - - +
304B MET* 3.2 40.8 - - + +
305B HIS* 1.3 76.3 - - - +
307B GLU* 1.3 68.8 + - - +
308B LEU* 4.7 13.5 - - + -
472B VAL 4.6 0.4 - - - -
473B HIS* 3.3 5.4 - - - +
474B ILE* 2.9 54.3 + - + +
476B ALA* 5.6 1.3 - - + +
497B LEU* 3.9 36.8 - - + +
500B LYS* 5.0 1.8 - - + -
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Residues in contact with GLU 307 (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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289B VAL* 3.7 3.5 - - - -
290B THR* 3.0 38.6 + - - +
291B THR* 3.0 31.6 + - - +
293B ARG* 5.5 0.9 + - - -
305B HIS* 3.0 34.5 - - + -
306B LEU* 1.3 73.1 - - - +
308B LEU* 1.3 63.4 + - - +
468B HIS* 5.4 1.4 - - - -
471B SER* 3.9 2.8 + - - +
472B VAL 3.7 0.2 - - - -
473B HIS* 3.2 39.2 + - + +
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Residues in contact with LEU 308 (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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287B ALA* 3.8 11.2 - - + +
288B ALA 3.7 1.8 - - - -
289B VAL* 4.0 28.3 - - + +
290B THR* 4.6 0.7 - - - -
306B LEU* 4.7 13.0 - - + -
307B GLU* 1.3 81.7 - - - +
309B ASP* 1.3 61.1 + - - +
310B ILE* 3.4 2.8 + - + +
323B VAL* 4.5 9.2 - - + -
325B VAL* 4.5 0.7 - - + -
471B SER* 3.2 8.5 + - - -
472B VAL* 2.9 41.3 + - + +
474B ILE* 3.9 23.1 - - + -
497B LEU* 5.8 0.2 - - + -
512B VAL* 4.1 21.3 - - + -
514B MET* 3.9 28.0 - - + -
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Residues in contact with ASP 309 (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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484A LYS* 5.2 3.8 + - - -
285B PHE* 3.7 14.2 - - - -
287B ALA* 3.9 0.7 - - - +
288B ALA* 2.9 28.7 + - + +
290B THR* 3.4 29.0 - - + +
307B GLU 4.1 0.8 + - - -
308B LEU* 1.3 70.7 - - - +
310B ILE* 1.3 57.7 + - - +
311B SER* 2.9 31.6 + - - -
470B ASN* 2.9 14.1 - - - +
471B SER* 4.8 2.7 - - - +
509B ARG* 4.7 9.5 + - - -
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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
------------------------------------------------------------
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