Contacts of the strand formed by residues 385 - 390 (chain A) in PDB entry 1EFT
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 ARG 385 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ARG* 3.9 43.9 + - - +
125A GLN* 3.1 50.9 + - - +
126A VAL* 5.3 0.4 - - - -
127A GLY* 5.4 6.3 - - - +
343A TYR 4.3 1.7 - - - +
344A PHE* 4.2 4.7 - - - -
345A ARG 5.1 1.6 + - - -
383A GLY 3.4 10.3 + - - -
384A LEU* 1.3 92.2 - - - +
386A PHE* 1.3 60.1 + - - +
398A GLY 3.5 9.0 - - - +
399A VAL* 4.1 20.6 - - + +
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Residues in contact with PHE 386 (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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125A GLN* 2.8 30.0 + - - -
316A PHE* 3.9 8.1 - + - -
318A ALA* 3.8 26.9 - - + -
320A VAL* 4.2 5.6 - - + -
342A PHE* 3.7 18.6 - + - -
343A TYR 3.2 17.5 - - - +
344A PHE* 3.4 26.7 - + + -
372A VAL* 5.3 0.4 - - + -
384A LEU 4.0 2.2 - - - -
385A ARG* 1.3 76.1 - - - +
387A ALA* 1.3 72.4 + - - +
388A ILE* 3.7 24.2 - - + -
397A ALA* 3.9 0.2 - - - -
398A GLY* 3.1 39.1 + - - -
399A VAL 3.9 0.7 - - - -
400A VAL* 3.7 22.7 - - + -
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Residues in contact with ALA 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 5.1 1.8 - - + -
122A LEU* 3.8 28.7 - - + -
125A GLN* 4.5 11.0 - - + -
342A PHE* 3.5 3.8 - - - -
343A TYR* 2.9 45.3 + - + +
386A PHE* 1.3 80.7 - - - +
388A ILE* 1.3 65.3 + - - +
389A ARG* 5.0 0.4 - - + -
396A GLY 3.8 9.6 - - - +
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Residues in contact with ILE 388 (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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320A VAL* 3.9 26.7 - - + -
322A VAL* 6.3 0.2 - - + -
334A PHE* 6.0 2.7 - - + -
338A TYR* 5.1 1.1 - - + -
340A PRO* 3.4 35.0 - - + -
341A GLN 3.3 6.1 - - - +
342A PHE* 4.0 13.5 - - + -
353A VAL* 5.7 0.4 - - + -
370A PHE* 4.2 13.2 - - + -
386A PHE* 3.7 22.7 - - + -
387A ALA* 1.3 75.2 - - - +
389A ARG* 1.3 69.6 + - - +
394A THR* 3.6 2.9 - - - +
395A VAL* 3.1 37.4 + - + -
396A GLY* 3.2 20.1 + - - +
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Residues in contact with ARG 389 (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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86A ALA 4.5 6.1 + - - -
89A ILE* 3.9 35.6 - - - +
90A LYS* 5.6 1.2 - - - +
93A ILE* 4.5 7.4 - - + -
118A GLU* 2.6 32.0 + - - -
122A LEU* 4.5 1.6 - - - -
340A PRO* 3.6 1.2 - - - +
341A GLN* 2.9 37.1 + - + +
343A TYR* 3.5 35.3 + - + +
387A ALA* 5.0 2.2 - - + -
388A ILE* 1.3 80.8 - - - +
390A GLU* 1.3 63.4 + - - +
392A GLY* 3.9 23.0 + - - +
393A ARG* 3.3 15.8 - - - +
394A THR* 3.2 28.1 - - + +
395A VAL* 4.4 1.3 - - - +
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Residues in contact with GLU 390 (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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330A ARG* 3.9 11.7 + - - -
338A TYR* 2.6 44.1 + - + +
339A ARG 4.9 3.6 - - - +
340A PRO* 3.7 17.0 - - + -
341A GLN* 5.0 2.0 - - - +
389A ARG* 1.3 78.7 - - - +
391A GLY* 1.3 73.5 + - - +
392A GLY 2.9 5.6 + - - +
393A ARG* 2.9 45.7 + - - +
395A VAL* 4.1 4.9 - - + +
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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