Contacts of the strand formed by residues 356 - 361 (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 VAL 356 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D HIS* 3.1 16.0 + - - -
325D ARG* 4.9 0.9 - - - -
352D CYS* 3.4 0.9 - - - -
353D GLY* 2.9 41.2 + - - -
355D SER* 1.3 84.4 - - - +
357D GLY* 1.3 59.8 + - - +
358D TYR* 3.5 25.1 - - + +
369D TRP 3.3 10.8 - - - +
370D GLY* 4.2 1.3 - - - -
371D MET* 3.1 31.6 - - + +
376D GLN* 3.8 22.0 - - + +
377D LEU* 4.2 7.4 - - + -
406D SER* 3.7 6.1 - - - +
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Residues in contact with GLY 357 (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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305D HIS* 4.4 4.7 - - - -
307D VAL* 4.6 2.7 - - - -
351D ALA 3.6 7.2 - - - -
352D CYS* 4.4 0.2 - - - -
356D VAL* 1.3 74.8 - - - +
358D TYR* 1.3 71.0 + - - -
368D ALA* 3.4 1.0 - - - +
369D TRP* 2.9 59.9 + - - +
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Residues in contact with TYR 358 (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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307D VAL* 4.4 0.5 - - - +
350D VAL* 3.3 7.3 - - - +
351D ALA* 2.8 40.0 + - + +
356D VAL* 3.5 18.4 - - + +
357D GLY* 1.3 75.0 - - - -
359D ALA* 1.3 61.7 + - - +
366D VAL* 4.4 2.7 - - + -
367D PHE 3.2 9.2 - - - +
368D ALA* 3.5 30.7 - - + -
369D TRP* 3.6 10.7 - - - -
376D GLN* 2.6 29.4 + - - +
377D LEU* 5.4 0.2 - - + -
391D MET* 4.1 12.1 - - - -
404D VAL* 3.8 32.5 - - + -
406D SER* 3.5 27.6 - - - -
411D THR* 2.6 33.7 + - + -
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Residues in contact with ALA 359 (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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315D ALA* 4.9 0.2 - - + -
344D LEU* 3.9 32.1 - - + -
347D VAL* 4.1 16.2 - - + -
349D SER 3.4 6.7 - - - +
350D VAL* 4.3 5.2 - - + +
358D TYR* 1.3 76.6 - - - +
360D VAL* 1.3 63.4 + - - +
361D THR* 4.0 1.5 + - + -
365D ARG 3.9 0.3 - - - +
366D VAL* 3.4 2.6 - - - +
367D PHE* 2.9 34.5 + - - +
369D TRP* 3.8 9.4 - - + -
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Residues in contact with VAL 360 (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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347D VAL* 3.3 4.2 - - - +
348D SER* 2.7 43.6 + - - +
349D SER* 2.8 31.2 + - - +
359D ALA* 1.3 73.2 - - - +
361D THR* 1.3 61.2 + - - +
364D GLY 4.9 0.2 - - - -
365D ARG 3.3 10.1 - - - +
366D VAL* 4.3 3.8 - - + -
401D VAL* 3.4 42.8 - - + +
402D LEU 4.7 4.5 - - - +
403D SER* 4.4 2.0 - - - -
404D VAL* 3.6 31.4 - - + +
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Residues in contact with THR 361 (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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344D LEU* 5.5 0.7 - - + -
345D PRO* 3.8 22.4 - - + +
346D ALA 3.2 14.1 - - - +
347D VAL* 4.1 3.6 - - + +
348D SER* 3.3 8.8 + - - -
359D ALA 4.9 0.9 - - - +
360D VAL* 1.3 78.4 - - - +
362D LYS* 1.3 65.5 + - - +
363D ASP* 2.5 32.9 + - - +
364D GLY* 3.0 14.0 + - - -
365D ARG* 2.8 27.1 + - + +
367D PHE* 3.7 33.9 - - + -
401D VAL 5.1 0.2 - - - +
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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