Contacts of the strand formed by residues 391 - 396 (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 GLY 391 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A GLY* 3.0 11.3 + - - +
292A GLY* 2.8 26.2 + - - -
304A PRO* 3.3 11.6 - - - +
390A GLU* 1.3 76.4 - - - +
392A ARG* 1.3 61.5 + - - -
402A TYR* 4.1 8.0 + - - -
403A TYR* 3.1 20.9 - - - -
463A TYR* 3.8 4.3 - - - -
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Residues in contact with ARG 392 (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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167A PHE* 4.0 14.6 + - - +
168A SER* 5.7 0.8 - - - +
169A LEU 6.0 0.6 - - - +
292A GLY* 3.7 3.8 - - - -
293A SER* 3.0 33.1 + - - +
304A PRO* 3.8 4.5 - - - +
391A GLY* 1.3 75.2 - - - +
393A LEU* 1.3 69.8 + - - +
394A TYR* 3.5 33.5 + - + +
401A TYR 3.7 0.2 - - - +
402A TYR* 3.4 8.2 - - - -
403A TYR* 2.9 33.9 + - + -
463A TYR* 3.3 13.5 - - - +
465A ASP* 2.7 37.0 + - - -
467A TRP* 4.3 7.1 - - - -
525A HIS* 4.1 9.3 - - - +
526A THR 2.9 27.6 + - - +
527A THR* 2.9 24.8 + - - +
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Residues in contact with LEU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A SER* 3.0 33.1 + - - +
295A VAL* 3.6 20.9 - - + +
302A LEU* 3.5 29.8 - - + +
303A PHE 3.4 32.3 - - - +
304A PRO* 3.5 7.4 - - + +
362A ILE* 3.8 25.4 - - + -
392A ARG* 1.3 78.3 + - - +
394A TYR* 1.3 63.0 + - - +
400A VAL* 4.1 11.2 - - + -
401A TYR 3.3 11.4 - - - +
402A TYR* 3.9 20.2 - - + -
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Residues in contact with TYR 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A VAL* 3.7 8.6 - - - +
392A ARG* 3.5 35.5 - - + -
393A LEU* 1.3 78.2 - - - +
395A MET* 1.3 62.1 + - - +
396A TYR* 3.7 31.4 - + + -
400A VAL* 3.3 10.7 - - - +
401A TYR* 2.8 44.3 + - + +
402A TYR 4.6 0.4 - - - -
403A TYR* 3.6 24.1 - - + +
415A LEU* 4.7 3.6 - - + -
465A ASP* 3.2 34.8 - - - +
466A ALA 3.4 21.8 + - - -
467A TRP* 3.9 26.7 - + + -
526A THR 4.6 1.1 - - - -
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Residues in contact with MET 395 (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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128A ASN* 3.1 48.2 + - + +
170A THR* 6.0 3.8 - - + -
295A VAL* 3.5 26.4 - - + +
296A TYR 3.0 30.7 - - - +
297A TYR* 3.8 25.6 - - + -
394A TYR* 1.3 75.5 - - - +
396A TYR* 1.3 64.8 + - - +
397A GLY 3.2 24.9 - - - +
398A ASP* 4.9 0.9 - - - -
399A SER 3.4 6.3 - - - +
400A VAL* 4.1 15.0 - - - -
467A TRP* 5.0 1.6 - - - -
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Residues in contact with TYR 396 (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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128A ASN 3.6 2.9 - - - -
129A GLN* 3.7 14.6 - - - -
130A PHE* 3.3 45.4 - + + -
394A TYR* 3.7 35.1 - + + -
395A MET* 1.3 74.7 - - - +
397A GLY* 1.3 62.4 + - - +
398A ASP 3.2 0.7 + - - -
399A SER* 2.9 28.4 + - - +
401A TYR* 3.5 32.8 - + + -
415A LEU* 6.1 0.2 - - - +
466A ALA 4.2 1.6 + - - -
467A TRP* 3.6 29.3 - + - -
468A LEU* 2.9 51.1 + - + +
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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