Contacts of the strand formed by residues 355 - 359 (chain B) in PDB entry 3QN3
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 LYS 355 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B GLN* 3.5 26.2 - - + +
327B ASN 3.0 11.8 + - - +
328B ALA* 3.0 7.3 - - + +
329B VAL* 2.9 26.0 + - - +
350B GLN* 6.0 0.2 - - - -
353B ASN* 3.8 24.9 + - - +
354B TYR* 1.3 74.0 - - - +
356B CYS* 1.3 61.2 + - - +
379B THR 5.4 3.6 - - - +
381B GLN* 3.6 13.9 - - - +
350C GLN 5.3 0.6 + - - -
351C ARG* 2.7 35.5 + - + +
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Residues in contact with CYS 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B VAL* 3.6 11.7 - - - -
331B ILE* 3.9 11.9 - - + -
346B VAL* 3.8 29.2 - - + -
349B ALA* 3.6 31.4 - - - -
350B GLN* 4.1 9.0 - - - +
354B TYR 3.8 3.1 + - - -
355B LYS* 1.3 75.0 - - - +
357B VAL* 1.3 62.8 + - - +
358B MET 3.8 0.4 - - - -
379B THR* 3.5 42.4 + - + +
381B GLN* 3.8 8.8 + - - +
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Residues in contact with VAL 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B MET* 4.2 14.6 - - + -
303B GLN* 4.1 12.8 - - - +
305B VAL* 4.5 14.1 - - + -
329B VAL 3.1 10.0 + - - +
330B LEU* 3.6 24.6 - - + +
331B ILE* 2.7 31.4 + - - +
355B LYS 5.0 2.7 - - - +
356B CYS* 1.3 76.8 - - - +
358B MET* 1.3 58.3 + - - +
359B SER 3.3 0.5 + - - -
381B GLN* 3.8 28.5 - - + +
382B ILE* 4.1 5.4 - - - -
383B LYS* 3.9 27.4 - - + +
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Residues in contact with MET 358 (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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331B ILE* 3.9 34.0 - - + +
333B PRO* 4.2 10.5 - - - -
346B VAL* 5.1 0.2 - - + -
356B CYS 3.8 2.0 - - - -
357B VAL* 1.3 69.7 - - - +
359B SER* 1.3 58.9 + - - +
370B ILE* 3.4 34.1 - - + +
373B PHE* 3.7 47.3 - - + +
374B ALA* 3.7 18.8 - - + +
377B LEU* 4.3 8.7 - - + -
379B THR* 4.2 16.1 + - + +
381B GLN 3.2 10.3 + - - +
382B ILE* 3.3 8.3 - - + +
383B LYS* 2.8 27.5 + - - -
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Residues in contact with SER 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU* 3.5 36.4 - - - +
331B ILE 2.8 24.7 + - - +
332B LYS* 3.8 9.4 - - - -
333B PRO* 4.1 11.6 - - - +
357B VAL 4.0 0.2 - - - -
358B MET* 1.3 76.7 - - - +
360B HIS* 1.3 75.4 + - - +
361B ARG* 5.1 1.0 - - - +
370B ILE* 3.8 13.1 - - - +
383B LYS* 3.6 19.3 - - - -
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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