Contacts of the strand formed by residues 36 - 41 (chain A) in PDB entry 1YRT
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 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ALA* 3.1 26.5 + - - +
34A LYS* 4.1 5.6 - - + +
35A ASN* 1.3 78.8 - - - +
37A THR* 1.3 61.9 + - - +
38A LEU* 3.7 16.0 + - + +
194A ILE* 4.6 0.4 - - + -
195A MET 3.4 13.0 - - - +
196A PRO* 3.9 10.8 - - + -
275A PHE* 4.0 21.3 - - + -
279A VAL* 5.2 0.4 - - + -
318A ALA* 3.5 14.2 - - - +
342A TYR* 4.3 0.7 - - - -
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Residues in contact with THR 37 (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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36A ALA* 1.3 71.7 - - - +
38A LEU* 1.3 61.7 + - - +
39A MET* 4.0 14.9 - - + +
193A ALA 4.2 0.5 - - - +
194A ILE* 3.6 3.6 - - - -
195A MET* 2.9 44.8 + - + +
315A VAL* 3.7 9.4 - - + -
316A VAL 3.4 10.5 - - - +
317A SER* 3.4 2.8 - - - -
318A ALA* 3.3 18.6 + - - +
333A TYR* 3.6 31.3 + - + +
337A GLN* 3.3 20.8 + - - -
342A TYR* 4.5 1.9 - - - -
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Residues in contact with LEU 38 (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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27A ILE* 3.6 32.3 - - + +
30A VAL* 4.6 1.3 - - + -
31A ALA* 3.8 17.0 - - + +
36A ALA* 3.8 23.3 - - + +
37A THR* 1.3 80.9 - - - +
39A MET* 1.3 61.2 + - - +
40A PHE* 3.6 22.3 - - + -
191A MET* 4.1 2.7 - - + -
193A ALA 4.0 2.9 - - - -
194A ILE* 4.2 13.9 - - + -
279A VAL* 4.1 24.9 - - + -
283A LEU* 4.3 14.1 - - + -
315A VAL* 3.7 1.2 - - - -
316A VAL* 2.8 35.9 + - + +
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Residues in contact with MET 39 (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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37A THR* 4.0 15.7 - - + +
38A LEU* 1.3 78.4 - - - +
40A PHE* 1.3 59.3 + - - +
191A MET* 3.5 7.1 - - - +
192A PHE* 2.6 34.1 + - + -
193A ALA* 3.0 36.1 + - + +
195A MET* 3.5 35.7 - - + -
313A ILE* 3.8 11.2 - - + -
314A PHE 3.4 4.7 - - - -
315A VAL* 3.6 17.7 - - + -
330A LEU* 3.9 30.1 - - + -
333A TYR* 4.2 8.7 - - + -
334A ILE* 4.2 4.9 - - + -
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Residues in contact with PHE 40 (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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19A ILE* 4.2 9.2 - - + -
27A ILE* 3.8 44.2 - - + -
38A LEU* 3.6 32.5 - - + -
39A MET* 1.3 79.5 - - - +
41A ARG* 1.3 70.5 + - - +
189A ILE* 3.6 25.8 - - + -
190A ASP 3.5 4.9 - - - +
191A MET* 3.9 30.3 - - + -
192A PHE* 3.7 5.2 - - - +
283A LEU* 4.5 7.6 - - + -
296A VAL* 5.1 1.1 - - + -
313A ILE* 3.5 6.4 - - - +
314A PHE* 2.8 58.3 + + + +
316A VAL* 4.3 4.5 - - + -
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Residues in contact with ARG 41 (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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17A SER 4.9 0.3 - - - +
19A ILE* 5.9 0.3 - - - +
40A PHE* 1.3 83.9 - - - +
42A LEU* 1.3 70.2 + - - +
43A VAL* 3.5 7.1 + - - +
189A ILE* 5.4 0.2 - - - +
190A ASP* 2.9 55.3 + - + +
192A PHE* 4.4 14.6 - - + -
301A GLU* 4.3 20.4 + - - -
308A GLU* 3.9 31.3 + - - +
310A ASP* 2.9 55.5 + - - +
312A LYS 5.0 0.9 - - - -
313A ILE* 5.4 0.2 - - - +
314A PHE* 5.4 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