Contacts of the strand formed by residues 421 - 425 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212K PRO* 3.5 32.1 - - + -
213K PHE* 3.5 29.4 - - + -
338K TYR* 4.2 5.8 - - + -
363K SER* 3.9 23.6 - - - -
364K PHE 3.7 15.7 - - - +
365K GLU* 4.4 7.3 - - + +
398K GLN* 3.5 21.1 - - - +
399K PRO* 3.8 18.9 - - + +
400K ALA 5.2 0.4 + - - +
417K ILE* 4.4 9.9 - - + -
418K MET* 3.0 22.6 + - + +
420K ASN* 1.3 80.0 - - - +
422K VAL* 1.3 71.3 + - - +
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Residues in contact with VAL 422 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363K SER* 3.4 2.9 - - - -
364K PHE* 2.9 65.7 + - + +
366K VAL* 4.5 8.3 - - + -
373K THR* 3.3 33.4 - - + -
376K PHE* 4.4 4.9 - - + -
377K VAL* 4.2 11.0 - - + -
396K VAL* 4.1 22.7 - - + -
397K ASP 3.7 6.1 - - - +
398K GLN* 4.1 7.0 - - + -
420K ASN 3.7 2.7 - - - +
421K LEU* 1.3 78.3 - - - +
423K ARG* 1.3 61.8 + - - +
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Residues in contact with ARG 423 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211K ASN* 3.4 23.7 + - - +
212K PRO* 4.4 9.7 - - + +
239K PHE* 5.1 7.6 - - - -
361K ALA* 5.2 6.3 - - + -
362K VAL 3.9 4.3 - - - +
363K SER* 3.3 20.4 - - - +
386K ALA 5.0 0.8 + - - -
387K PRO 4.7 1.0 - - - -
388K SER 3.6 24.9 + - - +
389K PHE* 3.8 20.2 - - - +
395K ILE* 4.0 1.5 - - - +
396K VAL* 3.5 6.5 - - - +
397K ASP* 3.1 59.1 + - - +
399K PRO* 3.9 14.3 - - + +
421K LEU* 5.7 0.2 - - + -
422K VAL* 1.3 72.5 - - - +
424K PHE* 1.3 67.7 + - - +
425K SER* 4.1 2.2 + - - +
610K PMC 3.2 44.3 + - - -
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Residues in contact with PHE 424 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360K GLY 3.9 0.3 - - - +
361K ALA* 3.6 2.6 - - - +
362K VAL 2.8 42.8 + - - +
364K PHE* 3.9 23.8 - + + -
376K PHE* 5.5 1.1 - + - -
380K LEU* 4.1 9.6 - - + -
383K PRO* 3.6 28.0 - - + -
394K SER* 4.2 8.5 - - - -
395K ILE 3.7 2.7 - - - -
396K VAL* 3.2 25.1 - - + -
422K VAL 3.7 0.8 + - - -
423K ARG* 1.3 76.5 - - - +
425K SER* 1.3 70.7 + - - +
426K PHE* 3.4 47.1 + + + -
434K LEU* 4.6 6.1 - - + -
438K ILE* 4.0 28.9 - - + -
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Residues in contact with SER 425 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262K PHE* 5.7 1.0 - - - -
317K GLN* 5.4 0.2 + - - -
360K GLY 4.2 3.6 + - - -
361K ALA* 4.7 4.6 - - - +
388K SER 4.6 0.4 - - - -
389K PHE* 3.1 37.3 - - - +
390K GLY* 3.1 14.2 + - - -
391K GLY 4.9 1.0 + - - -
393K GLU 5.0 1.6 + - - -
394K SER* 3.1 4.7 - - - -
395K ILE* 2.7 46.7 + - - +
423K ARG* 4.1 4.9 + - - -
424K PHE* 1.3 72.7 - - - +
426K PHE* 1.3 66.6 + - - +
427K GLY* 4.3 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