Contacts of the strand formed by residues 334 - 338 (chain L) 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 VAL 334 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328L LEU* 3.1 45.8 - - + +
329L GLU* 4.5 5.7 - - - +
331L HIS* 3.3 25.6 + - + +
332L PRO 3.2 4.6 - - - +
333L LYS* 1.3 80.8 - - - +
335L ARG* 1.3 64.1 + - - +
336L HIS 3.7 10.8 - - - +
337L VAL* 3.5 25.1 - - + -
364L PHE* 4.1 13.0 - - + -
365L GLU 3.7 7.4 - - - +
366L VAL* 4.6 1.3 - - - +
367L ASP* 5.1 0.2 - - - -
442L LEU* 4.3 11.4 - - + -
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Residues in contact with ARG 335 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333L LYS 3.9 2.8 + - - -
334L VAL* 1.3 73.5 - - - +
336L HIS* 1.3 63.2 + - + +
365L GLU* 2.8 28.3 + - + +
366L VAL 4.4 4.3 - - - +
367L ASP* 2.8 34.9 + - + +
368L GLY* 3.3 23.8 + - - +
420L ASN* 3.6 20.1 + - - -
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Residues in contact with HIS 336 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329L GLU* 5.8 1.1 - - - -
334L VAL* 3.6 1.7 - - - +
335L ARG* 1.3 83.6 - - + +
337L VAL* 1.3 94.8 + - - +
338L TYR* 3.8 31.0 - + - -
344L SER* 5.0 16.7 + - - -
346L PRO* 6.1 2.5 - - + -
364L PHE* 3.1 7.0 - - - +
365L GLU* 2.8 49.7 + - + +
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Residues in contact with VAL 337 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325L ALA* 3.9 15.7 - - + +
328L LEU* 3.8 5.8 - - + -
329L GLU* 3.6 32.8 + - + +
334L VAL* 3.5 20.9 - - + -
336L HIS* 1.3 100.8 + - - +
338L TYR* 1.3 67.7 + - - +
339L TYR 3.9 0.5 + - - -
342L LEU* 3.3 35.0 - - + +
344L SER* 4.7 4.2 + - - +
345L HIS* 6.1 0.7 - - - -
362L VAL* 4.3 6.3 - - + -
363L SER 3.6 6.5 - - - +
364L PHE* 3.6 8.7 - - + -
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Residues in contact with TYR 338 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213L PHE* 3.6 57.5 - + + +
214L LEU* 3.6 6.3 - - + +
336L HIS* 3.8 31.4 + + + -
337L VAL* 1.3 72.0 - - - +
339L TYR* 1.3 65.3 + - - +
345L HIS* 4.8 6.7 - + + -
346L PRO* 6.0 3.6 - - + -
362L VAL* 3.9 2.4 - - - +
363L SER* 2.5 58.8 + - - +
364L PHE* 4.2 0.9 - - - -
365L GLU* 3.1 43.4 + - + -
421L LEU* 4.1 2.5 - - + -
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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