Contacts of the strand formed by residues 248 - 252 (chain A) in PDB entry 3QPV
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 ILE 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A ARG* 3.6 39.9 - - - +
247A THR* 1.3 77.3 - - - +
249A TYR* 1.3 63.7 + - - +
250A LEU* 3.7 27.6 - - + -
376A LEU* 4.5 22.7 - - + +
380A GLU 4.6 0.9 - - - +
382A VAL* 3.4 9.4 - - + +
384A VAL* 5.0 0.7 - - + -
398A PHE* 3.6 33.7 - - + -
417A LEU 3.6 1.7 - - - +
418A LYS* 3.7 0.9 - - - -
419A LEU* 2.8 53.2 + - + +
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Residues in contact with TYR 249 (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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247A THR* 3.3 34.4 + - + +
248A ILE* 1.3 75.0 - - - +
250A LEU* 1.3 66.7 + - - +
284A PHE* 3.8 17.0 - + + -
285A VAL* 6.5 1.6 - - + -
288A GLN* 3.1 31.1 + - + +
290A LEU* 3.5 38.9 - - + +
293A LEU* 4.3 9.9 - - + -
381A ASN* 5.3 0.4 - - + -
382A VAL 2.7 19.4 + - - +
383A LEU* 3.5 22.6 - - + -
384A VAL 2.9 24.6 + - - -
416A VAL* 3.7 22.2 - - + -
417A LEU 3.3 4.3 - - - -
418A LYS* 3.8 18.5 + - + -
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Residues in contact with LEU 250 (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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248A ILE* 3.7 18.6 - - + -
249A TYR* 1.3 84.2 - - - +
251A CYS* 1.3 63.9 + - - +
376A LEU* 5.1 0.7 - - + -
383A LEU* 5.0 0.2 - - - -
384A VAL* 3.5 22.9 - - + +
386A CYS* 5.5 0.9 - - - -
391A LEU* 3.6 31.6 - - + -
394A LEU* 4.2 27.1 - - + -
395A LEU* 4.1 16.8 - - + +
398A PHE* 4.5 5.6 - - + -
415A THR 3.7 0.9 - - - +
416A VAL* 3.4 1.9 - - - -
417A LEU* 2.8 40.8 + - + +
419A LEU* 4.0 25.6 - - + -
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Residues in contact with CYS 251 (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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250A LEU* 1.3 78.4 - - - +
252A ARG* 1.3 64.2 + - - +
277A PHE* 4.1 15.9 - - + -
281A LEU* 4.1 13.0 - - - -
383A LEU* 4.2 9.4 - - - -
384A VAL 3.1 7.4 + - - +
385A ILE* 3.3 26.4 - - - -
386A CYS* 2.7 29.3 + - - -
391A LEU* 3.4 15.6 - - - +
415A THR 3.3 20.2 - - - +
416A VAL* 4.1 8.7 - - + -
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Residues in contact with ARG 252 (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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251A CYS* 1.3 80.0 - - - +
253A HIS* 1.3 76.0 + - + +
254A GLY 3.4 1.6 + - - -
277A PHE* 3.5 17.7 - - - -
385A ILE* 4.1 3.3 - - - +
386A CYS 3.4 7.6 - - - +
387A HIS 4.1 9.0 - - - -
388A GLN* 3.0 23.3 + - - +
391A LEU* 3.7 17.3 - - + -
411A CYS 2.8 37.1 + - - -
412A PRO* 3.9 13.3 + - - +
413A LEU* 3.7 34.5 - - + +
414A HIS 5.3 2.7 + - - +
415A THR 4.7 1.6 + - - -
440A THR* 2.9 36.3 + - - +
441A HIS 5.6 0.2 - - - +
710A PHS 2.8 39.2 + - - +
720A F6P 4.1 1.0 - - - -
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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