Contacts of the strand formed by residues 332 - 336 (chain A) in PDB entry 2Y3I
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 GLN 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A ALA* 3.2 32.9 + - - +
200A LEU* 3.9 5.1 - - - +
202A SER 4.8 0.2 - - - +
203A PRO* 3.5 6.1 - - - +
204A GLU* 2.9 42.0 + - - +
206A PRO 3.2 4.1 + - - +
207A PHE* 3.5 30.3 - - + -
208A LEU 2.9 25.1 + - - -
330A ALA* 3.9 1.0 - - - +
331A LYS* 1.3 80.0 - - - +
333A ILE* 1.3 71.1 + - - +
334A VAL* 5.3 0.4 - - + -
366A CYS* 4.2 0.2 - - - -
367A ILE* 3.2 29.0 - - + +
369A ILE* 4.7 6.0 - - + +
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Residues in contact with ILE 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LEU* 3.3 27.1 - - + +
210A ILE* 3.9 24.7 - - + -
327A VAL* 3.8 34.1 - - + +
330A ALA* 4.1 5.8 - - + -
332A GLN* 1.3 83.3 - - - +
334A VAL* 1.3 72.9 + - - +
335A TRP* 4.4 3.8 - - + +
358A VAL* 4.5 15.3 - - + -
361A ALA* 4.8 2.5 - - + -
366A CYS* 4.1 15.0 - - - -
367A ILE 2.8 12.6 + - - +
368A THR* 3.5 8.8 - - + -
369A ILE* 2.8 29.6 + - - +
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Residues in contact with VAL 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PHE* 5.7 4.3 - - + -
200A LEU* 5.3 4.0 - - + -
207A PHE* 3.5 31.9 - - + -
208A LEU 3.0 8.3 + - - +
209A ALA* 3.4 5.5 - - + +
210A ILE* 2.7 33.8 + - - +
332A GLN* 5.0 1.1 - - - +
333A ILE* 1.3 77.0 - - - +
335A TRP* 1.3 60.0 + - - +
336A ASN* 4.2 0.9 - - + -
369A ILE* 3.3 28.9 - - + +
371A GLY 6.1 0.7 - - - +
398A SER* 5.4 11.0 - - - +
399A LEU* 4.3 24.1 - - + +
402A LEU* 4.8 9.4 - - + -
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Residues in contact with TRP 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ILE* 3.5 37.9 - - + +
333A ILE* 4.6 3.6 - - + -
334A VAL* 1.3 77.6 - - - +
336A ASN* 1.3 72.4 + - - +
337A GLY 2.7 26.9 + - - -
338A PRO* 4.3 6.9 - - + +
339A VAL* 4.8 2.2 - - - +
351A THR* 4.1 32.3 - - + -
354A LEU* 3.8 27.7 - - + +
355A MET* 3.8 41.3 - - + -
358A VAL* 4.3 13.7 - - + -
369A ILE 2.8 13.4 + - - +
370A ILE* 3.4 25.4 - - + +
371A GLY 3.0 26.7 + - - +
375A THR* 4.3 9.2 - - + -
378A CYS* 5.4 0.9 - - - -
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Residues in contact with ASN 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ILE 3.1 12.5 + - - +
211A LEU* 3.7 2.6 - - - +
212A GLY 3.1 21.7 + - - +
219A LYS* 2.4 33.5 - - - +
334A VAL* 4.2 1.3 - - + +
335A TRP* 1.3 76.4 - - - +
337A GLY* 1.3 61.7 + - - +
371A GLY* 2.6 23.4 - - - +
375A THR* 4.1 0.4 - - - -
395A GLY* 3.2 21.7 - - - +
399A LEU* 3.5 35.8 - - + +
1418A LA8 3.0 17.5 + - - -
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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