Contacts of the strand formed by residues 361 - 366 (chain I) 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 ALA 361 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214I LEU* 3.3 17.2 - - + +
239I PHE* 3.9 34.1 - - + -
262I PHE* 4.7 3.5 - - + -
339I TYR* 3.3 21.0 - - - -
358I PHE 4.7 0.5 - - - +
359I GLY 3.4 0.8 - - - -
360I GLY* 1.3 78.8 - - - +
362I VAL* 1.3 59.5 + - - +
363I SER* 6.1 0.2 - - - +
389I PHE* 5.2 6.5 - - + -
423I ARG* 5.1 9.6 - - + -
424I PHE 3.5 6.7 - - - +
425I SER* 4.5 6.7 - - - +
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Residues in contact with VAL 362 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214I LEU* 4.4 0.2 - - - -
321I ALA* 3.7 16.2 - - + +
325I ALA* 4.5 8.7 - - + -
328I LEU* 4.5 9.0 - - + -
337I VAL* 4.3 14.4 - - + -
338I TYR 4.0 11.7 - - - +
339I TYR* 3.5 21.1 - - + -
361I ALA* 1.3 81.4 - - - +
363I SER* 1.3 66.1 + - - +
364I PHE* 4.0 11.2 - - + -
422I VAL 3.9 0.5 - - - +
423I ARG* 5.1 0.2 - - - -
424I PHE* 2.7 44.0 + - + +
426I PHE* 3.6 26.2 - - + -
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Residues in contact with SER 363 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212I PRO* 2.8 29.0 + - - +
214I LEU* 4.5 3.5 - - - +
337I VAL* 3.6 2.4 - - - +
338I TYR* 2.6 49.8 + - - +
361I ALA* 6.1 0.2 - - - +
362I VAL* 1.3 73.7 - - - +
364I PHE* 1.3 58.5 + - - +
421I LEU* 4.0 14.6 - - - -
422I VAL 3.3 8.3 - - - -
423I ARG* 3.3 24.6 - - - +
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Residues in contact with PHE 364 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328I LEU* 3.6 34.3 - - + -
334I VAL* 4.2 17.0 - - + -
336I HIS 3.1 17.7 - - - +
337I VAL* 3.7 15.3 - - + +
338I TYR* 4.3 2.9 - - - -
362I VAL* 4.0 6.7 - - + -
363I SER* 1.3 79.9 - - - +
365I GLU* 1.3 61.5 + - - +
366I VAL* 4.1 16.4 - - + -
376I PHE* 3.7 37.2 - + - -
421I LEU* 4.1 2.1 - - - +
422I VAL* 2.8 47.5 + - + +
424I PHE* 4.0 28.7 - + + -
438I ILE* 5.4 0.9 - - + -
442I LEU* 5.5 0.7 - - + -
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Residues in contact with GLU 365 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213I PHE* 4.7 6.4 - - - -
334I VAL* 3.7 4.9 - - - +
335I ARG* 3.0 38.7 + - + -
336I HIS* 2.8 25.3 + - + +
338I TYR* 3.2 37.8 + - + -
364I PHE* 1.3 72.4 - - - +
366I VAL* 1.3 62.5 + - - +
416I GLY 5.0 0.7 - - - +
418I MET* 4.0 21.2 - - - +
420I ASN* 3.7 26.1 - - + +
421I LEU* 4.4 7.6 - - + +
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Residues in contact with VAL 366 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333I LYS 3.8 9.4 - - - +
334I VAL* 4.7 1.3 - - + +
335I ARG* 4.1 2.9 + - - -
364I PHE* 4.1 16.2 - - + -
365I GLU* 1.3 75.2 - - - +
367I ASP* 1.3 70.3 + - - +
368I GLY 2.9 10.3 + - - +
372I THR* 4.4 6.7 - - + -
373I THR* 3.9 26.0 - - + +
376I PHE* 3.9 27.6 - - + -
420I ASN* 3.2 27.7 + - - +
422I VAL* 4.3 2.7 - - + -
442I LEU* 4.9 6.5 - - + -
445I ILE* 4.0 24.7 - - + -
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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