Contacts of the strand formed by residues 290 - 297 (chain A) in PDB entry 1Y57
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 THR 290 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A THR* 3.3 6.2 - - - +
286A TRP* 2.8 53.5 + - + -
287A ASN* 5.4 1.2 + - - +
289A THR* 1.3 91.6 + - - +
291A ARG* 1.3 72.4 + - - +
292A VAL* 3.6 4.2 + - + +
326A TYR* 4.1 22.9 - - + +
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Residues in contact with ARG 291 (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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270A GLU* 4.8 3.2 + - - -
283A MET* 3.5 30.6 - - + +
284A GLY 3.5 10.8 - - - +
285A THR* 4.7 2.7 + - - +
289A THR 4.0 2.2 + - - -
290A THR* 1.3 78.1 - - - +
292A VAL* 1.3 66.6 + - - +
326A TYR* 4.2 6.1 + - - -
340A TYR* 3.5 47.8 + - + +
342A SER* 6.0 1.6 - - - -
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Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 4.5 0.4 - - + -
283A MET* 3.5 8.8 - - - +
284A GLY 2.9 46.9 + - - +
285A THR 4.1 8.3 - - - +
286A TRP* 3.7 24.0 - - + -
290A THR* 3.7 2.2 - - + +
291A ARG* 1.3 80.3 - - - +
293A ALA* 1.3 59.3 + - - +
294A ILE* 3.9 22.7 - - + -
326A TYR* 3.6 27.1 - - + -
337A VAL* 3.7 14.1 - - + -
338A THR 3.4 8.1 - - - +
340A TYR* 3.8 7.6 - - - -
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Residues in contact with ALA 293 (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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273A LEU* 5.1 0.4 - - + -
281A VAL* 4.8 4.7 - - + -
282A TRP 3.2 8.3 - - - +
292A VAL* 1.3 73.6 - - - +
294A ILE* 1.3 61.7 + - - +
295A LYS 4.1 0.4 - - - -
336A ILE 3.7 1.0 - - - +
337A VAL* 3.4 5.4 - - - +
338A THR* 2.9 38.4 + - - +
339A GLU 3.9 0.7 - - - +
340A TYR* 3.9 8.1 - - + +
600A MPZ 3.4 46.9 - - + +
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Residues in contact with ILE 294 (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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267A LEU* 4.2 20.9 - - + -
268A ARG 4.5 2.0 - - - +
269A LEU* 3.6 26.5 - - + -
280A GLU 3.9 0.2 - - - +
281A VAL* 3.4 5.1 - - - -
282A TRP* 2.8 40.0 + - + +
284A GLY* 4.4 13.7 - - - +
285A THR 5.1 0.2 - - - +
292A VAL* 3.9 22.9 - - + -
293A ALA* 1.3 77.6 - - - +
295A LYS* 1.3 62.2 + - - +
296A THR* 3.8 9.2 + - + +
335A TYR* 3.7 42.0 - - + -
336A ILE 3.5 3.6 - - - +
337A VAL* 4.3 9.6 - - + -
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Residues in contact with LYS 295 (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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280A GLU 3.5 9.4 - - - +
281A VAL* 4.4 9.6 - - + +
293A ALA* 4.1 0.8 - - - +
294A ILE* 1.3 73.0 - - - +
296A THR* 1.3 61.5 + - - +
307A PHE* 3.8 26.8 - - + -
310A GLU* 2.8 37.4 + - - +
334A ILE 3.7 0.5 - - - +
335A TYR* 3.2 5.5 - - - -
336A ILE* 2.8 48.9 + - + +
338A THR* 6.5 0.4 - - + -
404A ASP* 4.4 13.9 + - - -
406A GLY* 5.6 0.4 - - - -
600A MPZ 3.9 31.4 + - + +
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Residues in contact with THR 296 (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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269A LEU* 5.4 2.5 - - + -
278A PHE 3.7 1.0 - - - +
279A GLY* 3.3 6.1 - - - -
280A GLU* 2.9 47.5 + - - +
282A TRP* 4.2 15.0 - - + +
294A ILE* 4.1 14.4 - - + +
295A LYS* 1.3 78.1 - - - +
297A LEU* 1.3 61.8 + - - +
307A PHE* 3.9 7.5 - - - -
333A PRO* 5.1 4.0 - - - -
334A ILE 3.4 4.3 - - - -
335A TYR* 3.5 31.4 - - + -
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Residues in contact with LEU 297 (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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278A PHE* 3.5 16.2 - - + +
296A THR* 1.3 74.0 - - - +
298A LYS* 1.3 66.5 + - - +
299A PRO* 3.3 13.5 - - + +
301A THR* 3.6 17.0 - - - +
302A MET* 3.7 37.0 - - + +
304A PRO* 3.9 11.7 - - + -
307A PHE* 3.8 37.0 - - + -
332A GLU* 5.9 1.8 - - + +
333A PRO* 3.7 16.3 - - - +
334A ILE* 3.0 35.8 + - + +
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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