Contacts of the strand formed by residues 385 - 390 (chain D) in PDB entry 1I2M
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 ALA 385 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324D GLY* 3.5 3.6 - - - +
369D TRP* 3.6 10.3 - - - +
370D GLY* 2.8 32.6 + - - -
377D LEU* 3.8 18.2 - - + -
379D THR* 5.5 1.8 - - + -
383D GLU 3.7 1.0 + - - +
384D ASP* 1.3 71.0 - - - +
386D TRP* 1.3 65.5 + - - +
387D SER 3.2 15.8 + - - +
389D VAL* 4.2 19.3 - - + -
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Residues in contact with TRP 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D ALA 3.4 24.5 - - - -
322D GLU* 4.3 3.6 - - - -
323D TYR* 3.7 13.7 - + - -
324D GLY* 3.4 26.9 - - - +
327D GLY* 3.2 15.6 + - - -
328D LEU 3.3 0.3 + - - -
329D GLY 2.9 37.2 + - - +
330D GLU* 3.7 57.4 + - + +
332D ALA* 4.2 17.5 - - + -
384D ASP* 4.0 24.8 + - + +
385D ALA* 1.3 76.4 - - - +
387D SER* 1.3 59.5 + - - +
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Residues in contact with SER 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D GLY 4.0 1.1 - - - -
328D LEU 4.2 1.6 - - - -
329D GLY* 3.4 24.1 + - - -
330D GLU* 4.9 0.3 + - - +
343D ARG* 3.7 37.7 + - - -
369D TRP* 3.9 4.7 - - - +
385D ALA* 3.7 11.1 - - - +
386D TRP* 1.3 74.9 - - - +
388D PRO* 1.3 78.9 - - - +
389D VAL* 3.5 12.0 + - - +
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Residues in contact with PRO 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D GLY 3.3 14.8 - - - +
341D ILE* 3.6 26.5 - - + -
343D ARG* 4.2 21.1 + - + +
344D LEU* 3.7 25.1 - - + -
367D PHE* 4.0 11.4 - - + -
368D ALA 3.5 8.3 - - - +
369D TRP* 3.6 20.8 - - + -
387D SER* 1.3 91.1 - - - +
389D VAL* 1.3 61.8 + - - +
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Residues in contact with VAL 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367D PHE* 3.8 3.4 - - - -
368D ALA* 2.9 44.1 + - + +
377D LEU* 4.8 2.0 - - + +
379D THR* 3.6 30.1 - - + -
385D ALA* 4.2 15.3 - - + -
387D SER* 3.6 9.6 - - - +
388D PRO* 1.3 79.7 - - - +
390D GLU* 1.3 67.5 + - - +
391D MET* 3.4 0.9 + - - +
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Residues in contact with GLU 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365D ARG* 3.1 49.8 + - + +
366D VAL 3.5 12.8 - - - +
367D PHE* 3.5 25.5 - - + -
378D GLY 5.3 1.0 - - - +
379D THR* 5.7 2.4 - - - +
389D VAL* 1.3 77.8 - - - +
391D MET* 1.3 70.6 + - - +
392D MET* 3.6 32.3 + - + +
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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