Contacts of the strand formed by residues 421 - 425 (chain D) in PDB entry 1I43
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 421 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D PRO* 3.6 23.3 - - + -
213D PHE* 3.6 38.1 - - + -
338D TYR* 4.1 11.2 - - + -
363D SER* 4.0 23.6 - - - -
364D PHE 3.8 8.5 - - - +
365D GLU* 4.4 6.6 - - + +
398D GLN* 3.5 21.5 - - - +
399D PRO* 3.7 25.1 - - + +
400D ALA 5.2 0.4 + - - +
417D ILE* 4.4 11.7 - - + -
418D MET* 3.2 21.5 + - + +
420D ASN* 1.3 79.3 - - - +
422D VAL* 1.3 64.9 + - - +
423D ARG 4.3 0.2 - - - -
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Residues in contact with VAL 422 (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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363D SER* 3.3 2.2 - - - -
364D PHE* 2.8 65.9 + - + +
366D VAL* 4.5 8.3 - - + -
373D THR* 3.3 34.3 - - + -
376D PHE* 4.4 5.2 - - + -
377D VAL* 4.3 10.5 - - + -
396D VAL* 4.1 23.1 - - + -
397D ASP 3.7 6.1 - - - +
398D GLN* 4.1 6.7 - - + -
420D ASN 3.8 2.2 - - - +
421D LEU* 1.3 77.9 - - - +
423D ARG* 1.3 61.8 + - - +
424D PHE 3.7 0.9 + - - -
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Residues in contact with ARG 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D ASN* 3.4 26.2 + - - +
212D PRO* 4.5 7.9 - - + +
239D PHE* 4.6 3.2 - - + -
361D ALA* 5.0 13.0 - - + -
362D VAL 4.7 2.2 - - - +
363D SER* 3.2 23.1 - - - +
386D ALA 5.1 0.8 + - - -
387D PRO* 4.8 0.6 - - - +
388D SER 3.6 25.7 + - - +
389D PHE* 3.9 20.9 - - - +
395D ILE* 4.0 1.5 - - - +
396D VAL* 3.6 4.2 - - - +
397D ASP* 3.1 61.5 + - - +
399D PRO* 4.0 15.3 - - + +
421D LEU* 5.8 0.2 - - + -
422D VAL* 1.3 72.3 - - - +
424D PHE* 1.3 66.6 + - - +
425D SER* 3.9 3.0 + - - +
603D PMC 3.6 38.2 + - - -
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Residues in contact with PHE 424 (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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360D GLY 3.8 0.3 - - - +
361D ALA* 3.5 2.8 - - - +
362D VAL 2.8 44.2 + - - +
364D PHE* 3.9 22.9 - + + -
376D PHE* 5.5 0.2 - + - -
380D LEU* 4.1 10.3 - - + -
383D PRO* 3.6 28.5 - - + -
394D SER* 4.2 9.0 - - - -
395D ILE 3.8 2.7 - - - -
396D VAL* 3.2 25.6 - - + -
422D VAL 3.7 1.0 + - - -
423D ARG* 1.3 74.5 - - - +
425D SER* 1.3 72.4 + - - +
426D PHE* 3.4 47.3 + + + -
434D LEU* 4.5 6.5 - - + -
438D ILE* 4.0 29.6 - - + -
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Residues in contact with SER 425 (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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262D PHE* 5.8 0.7 - - - -
360D GLY 4.1 4.3 + - - -
361D ALA* 4.7 3.4 - - - +
388D SER 4.5 0.9 - - - -
389D PHE* 3.0 39.2 - - - +
390D GLY 3.2 12.3 + - - -
391D GLY 4.8 1.2 + - - -
393D GLU 5.0 1.9 + - - -
394D SER* 3.3 4.0 - - - -
395D ILE* 2.8 46.7 + - - +
423D ARG* 3.9 5.7 + - - -
424D PHE* 1.3 72.2 - - - +
426D PHE* 1.3 65.1 + - - +
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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