Contacts of the strand formed by residues 361 - 365 (chain A) in PDB entry 5FN4
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 361 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A VAL 3.6 2.2 + - - +
276A VAL* 3.3 28.5 - - - +
277A VAL* 2.8 33.7 + - - +
359A VAL* 4.3 2.6 - - - +
360A ASP* 1.3 82.0 - - - +
362A PHE* 1.3 58.0 + - - +
363A VAL* 5.7 0.7 - - - -
397A LEU* 4.4 11.7 - - - -
437A SER* 3.5 9.0 - - - -
501A LEU* 3.4 31.1 - - - +
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Residues in contact with PHE 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A VAL* 3.3 34.1 - - + -
279A ALA* 3.3 32.8 - - + -
359A VAL* 4.4 5.6 - - + -
361A SER* 1.3 76.6 - - - +
363A VAL* 1.3 79.6 + - - +
364A GLU* 3.8 7.9 - - + -
397A LEU* 4.5 1.1 - - - +
426A SER* 4.1 2.2 - - - -
427A LEU* 3.2 41.5 - - + -
430A PHE* 3.2 51.6 - + + -
436A ILE* 4.2 7.2 - - + -
437A SER 2.8 17.0 + - - +
438A GLY 3.7 0.2 - - - -
439A VAL* 2.8 30.5 + - - +
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Residues in contact with VAL 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A VAL* 5.2 4.0 - - + -
277A VAL 2.8 15.5 + - - +
278A ALA* 3.5 5.6 - - - -
279A ALA 2.8 26.8 + - - +
361A SER* 5.5 0.4 - - - +
362A PHE* 1.3 83.9 - - - +
364A GLU* 1.3 63.3 + - - +
365A LEU* 3.5 4.6 - - + +
397A LEU* 5.1 10.3 - - + -
401A LEU* 5.8 6.3 - - + -
439A VAL* 3.5 15.0 - - + -
441A LEU* 4.6 9.4 - - + -
494A LEU* 3.3 34.8 - - + -
497A ALA* 6.1 3.8 - - + -
498A LEU* 4.7 15.7 - - + +
501A LEU* 5.8 3.6 - - + -
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Residues in contact with GLU 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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279A ALA* 3.2 25.4 - - - +
280A THR 3.8 3.6 + - - -
281A ARG* 3.6 15.8 + - - +
333A GLU* 2.9 26.7 - - - +
362A PHE* 3.8 4.4 - - + -
363A VAL* 1.3 77.3 - - - +
365A LEU* 1.3 66.9 + - - +
366A GLY* 3.8 10.5 - - - +
425A SER* 3.2 30.1 + - - +
426A SER* 3.4 11.6 + - - -
427A LEU* 4.3 7.2 - - + -
439A VAL 2.8 14.3 + - - +
440A VAL* 3.5 13.0 - - + -
441A LEU* 2.8 30.3 + - - +
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Residues in contact with LEU 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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279A ALA 3.5 21.5 + - - +
280A THR* 4.7 6.4 - - - +
281A ARG* 4.8 5.2 + - - +
301A SER* 3.3 32.3 + - - +
304A THR* 2.9 32.5 - - - +
305A GLN* 3.5 16.6 - - - +
363A VAL 3.5 4.9 - - - +
364A GLU* 1.3 86.6 - - - +
366A GLY* 1.3 60.0 + - - +
367A GLN 3.5 1.2 + - - -
368A VAL* 4.1 14.1 - - + -
441A LEU* 3.7 9.9 - - + -
490A VAL* 5.6 3.8 - - + -
494A LEU* 3.4 36.6 - - + -
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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