Contacts of the strand formed by residues 359 - 367 (chain A) in PDB entry 3N56
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 359 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A ILE 3.5 21.8 - - - +
339A GLY* 3.8 21.6 - - - +
341A GLU* 4.1 14.6 + - - +
346A LEU* 3.9 31.2 - - + -
347A LEU* 3.9 33.3 - - + +
350A LEU* 4.5 5.6 - - + -
358A THR* 1.3 77.2 - - - +
360A VAL* 1.3 75.0 + - - +
361A GLY 4.1 0.4 - - - +
375A ILE* 4.0 13.2 - - + -
376A ASN 3.2 9.2 - - - +
377A VAL* 3.7 17.7 - - + -
394A MET* 5.3 0.2 - - + -
1C SER 5.4 1.0 + - - -
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Residues in contact with VAL 360 (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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358A THR* 6.1 2.7 - - - -
359A LEU* 1.3 81.3 - - - +
361A GLY* 1.3 60.9 + - - +
374A ILE* 3.8 10.9 - - + +
375A ILE* 3.3 1.9 - - - +
376A ASN* 2.7 51.5 + - + +
1C SER 4.3 6.5 - - - +
2C PRO* 4.2 33.9 - - + -
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Residues in contact with GLY 361 (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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335A GLY* 3.9 10.1 - - - +
338A ILE* 4.9 6.1 - - - -
339A GLY* 4.5 10.9 - - - -
359A LEU* 4.1 7.1 - - - +
360A VAL* 1.3 76.3 - - - +
362A GLY* 1.3 56.6 + - - -
373A PHE* 5.0 0.2 - - - -
374A ILE* 3.1 10.3 - - - -
375A ILE* 4.3 2.9 - - - -
1C SER* 2.8 32.3 + - - +
2C PRO* 3.2 5.5 - - - +
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Residues in contact with GLY 362 (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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335A GLY* 3.7 20.2 - - - -
361A GLY* 1.3 73.8 - - - -
363A GLN* 1.3 63.0 + - - -
373A PHE* 3.4 18.4 - - - -
374A ILE* 2.9 35.1 + - - +
1C SER* 5.1 0.2 - - - -
2C PRO* 3.9 7.4 - - - -
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Residues in contact with GLN 363 (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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319A ILE* 4.8 2.7 - - + -
322A LEU* 3.7 9.2 - - - +
329A ASN* 3.1 26.4 + - - +
331A GLY* 3.5 21.9 + - - -
332A HIS* 3.2 18.8 + - - +
362A GLY* 1.3 73.1 - - - -
364A LYS* 1.3 59.2 + - - +
365A GLU 4.3 0.3 + - - -
371A MET* 3.4 29.9 - - + +
372A PHE 3.3 7.0 - - - +
373A PHE* 4.0 9.7 - - + -
2C PRO* 3.8 18.7 - - + +
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Residues in contact with LYS 364 (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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205A GLU* 2.8 37.5 + - - -
215A PHE* 6.3 0.2 - - - -
316A THR* 5.4 0.2 + - - -
362A GLY 3.8 0.8 + - - -
363A GLN* 1.3 74.1 - - - +
365A GLU* 1.3 70.6 + - - +
371A MET* 3.7 7.4 - - - +
372A PHE* 2.8 58.2 + - + +
374A ILE* 4.2 32.0 - - + +
2C PRO* 5.3 5.8 - - + -
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Residues in contact with GLU 365 (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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323A GLN* 5.7 0.7 - - - +
363A GLN 4.2 0.4 + - - -
364A LYS* 1.3 86.3 - - - +
366A GLY* 1.3 62.3 + - - +
371A MET* 4.2 13.0 - - + -
372A PHE* 3.6 10.5 - - - -
453A GLU* 5.5 2.3 - - - +
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Residues in contact with GLY 366 (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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97A LEU* 4.8 3.8 - - - +
144A GLY* 5.8 2.1 - - - -
145A GLU* 4.5 2.9 - - - +
215A PHE* 5.4 4.3 - - - -
364A LYS 3.8 1.0 + - - -
365A GLU* 1.3 80.2 - - - +
367A ALA* 1.3 63.6 + - - +
370A PHE* 3.4 31.5 + - - -
371A MET* 4.1 2.0 - - - +
372A PHE* 3.8 8.1 - - - -
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Residues in contact with ALA 367 (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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97A LEU* 3.7 18.4 - - + -
145A GLU* 3.2 22.7 - - - +
288A PHE* 3.7 7.6 - - + -
321A ASP* 3.4 6.7 - - - +
366A GLY* 1.3 76.9 + - - +
368A ARG* 1.3 61.7 + - - +
369A GLY 2.9 8.3 + - - -
370A PHE* 2.9 42.5 + - + +
371A MET* 5.1 0.5 - - - +
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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
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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