Contacts of the strand formed by residues 376 - 379 (chain A) in PDB entry 4JF7
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 376 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A PRO* 4.5 0.4 - - - -
278A PRO* 4.3 18.4 - - + -
300A TRP* 4.4 3.6 - - + -
362A ILE 3.7 0.9 - - - +
363A LEU* 3.3 7.9 - - - +
364A ALA* 2.8 46.3 + - + +
373A ASN 5.0 0.4 - - - +
374A GLU* 3.3 21.1 - - - +
375A CYS* 1.3 78.6 - - - +
377A VAL* 1.3 60.3 + - - +
378A LEU* 4.0 10.4 + - + +
426A GLN* 3.7 28.5 - - + +
427A PRO* 3.5 41.1 - - + +
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Residues in contact with VAL 377 (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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277A PRO* 3.7 25.5 - - + +
278A PRO 4.8 8.4 + - - +
279A GLY 5.7 0.9 - - - +
280A VAL* 3.8 17.3 - - + -
284A TRP* 4.0 29.4 - - + +
287A LEU* 4.4 5.8 - - + -
305A ILE* 3.7 24.2 - - + -
362A ILE 3.8 2.5 - - - -
363A LEU* 3.8 14.1 - - + -
375A CYS 4.3 0.2 + - - -
376A LEU* 1.3 72.8 - - - +
378A LEU* 1.3 69.6 + - - +
379A PRO* 3.8 8.4 - - + +
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Residues in contact with LEU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 6.2 0.4 - - + -
361A GLY* 4.3 0.2 - - - -
362A ILE* 2.9 43.4 + - + +
364A ALA* 4.6 11.4 - - + -
376A LEU* 4.6 10.5 - - + +
377A VAL* 1.3 81.6 - - - +
379A PRO* 1.3 68.5 - - + +
420A ILE* 5.3 0.7 - - + -
427A PRO* 3.9 34.3 - - + +
428A SER* 3.9 27.6 - - - +
429A ALA* 4.8 2.7 - - - +
430A ILE* 3.3 34.6 - - + +
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Residues in contact with PRO 379 (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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284A TRP* 4.5 5.8 - - + -
315A LEU* 3.6 43.3 - - + -
319A GLN* 5.1 0.9 - - - +
359A GLN* 4.2 9.0 - - + -
360A SER 3.6 11.9 - - - +
361A GLY* 4.0 1.8 - - - -
377A VAL* 3.8 13.0 - - + +
378A LEU* 1.3 87.1 - - + +
380A PHE* 1.3 67.4 + - - +
381A SER 3.8 0.5 + - - -
430A ILE* 3.8 11.4 - - - +
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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