Contacts of the strand formed by residues 339 - 345 (chain A) in PDB entry 1YHV
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 GLU 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A GLN* 4.7 13.4 - - + +
301A MET 3.4 11.9 - - - +
302A ASN* 4.6 8.4 + - - +
334A TYR 3.9 0.3 - - - +
335A LEU* 3.4 4.0 - - - -
336A VAL* 2.7 50.1 + - + +
337A GLY 3.1 0.4 - - - -
338A ASP* 1.3 77.8 - - - +
340A LEU* 1.3 60.8 + - - +
341A TRP* 3.0 38.9 + - + +
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Residues in contact with LEU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 4.0 26.7 - - + -
261A VAL* 4.1 20.2 - - + -
299A ARG 3.5 1.6 - - - +
300A GLN* 3.4 2.9 - - - -
301A MET* 2.8 48.2 + - + +
303A LEU* 4.1 9.9 - - + -
312A ILE* 3.0 40.8 - - + -
316A ILE* 5.9 1.1 - - + -
333A SER* 4.7 2.5 - - - -
334A TYR 3.3 17.0 - - - +
335A LEU* 3.9 14.8 - - + -
338A ASP 3.7 0.8 + - - -
339A GLU* 1.3 73.9 - - - +
341A TRP* 1.3 67.3 + - - +
342A VAL* 4.2 8.1 - - + -
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Residues in contact with TRP 341 (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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265A ASP* 5.0 2.9 - - - -
266A PRO* 3.0 43.7 - - + -
267A LYS* 3.3 42.0 - - + -
273A PHE* 3.5 25.6 - + - -
298A ILE* 3.8 19.7 - - + -
299A ARG 3.3 5.2 - - - +
300A GLN* 3.2 28.8 - - + +
333A SER* 3.1 8.3 - - - -
334A TYR* 2.9 44.6 + + + +
336A VAL* 4.8 7.3 - - + +
339A GLU* 3.0 42.0 + - + +
340A LEU* 1.3 83.4 - - - +
342A VAL* 1.3 62.0 + - - +
343A VAL* 5.0 1.8 - - + -
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Residues in contact with VAL 342 (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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297A ALA 3.7 2.1 - - - +
298A ILE* 3.4 2.7 - - - -
299A ARG* 3.0 47.8 + - + +
301A MET* 3.5 28.7 - - + -
312A ILE* 4.9 1.8 - - + -
316A ILE* 3.6 35.0 - - + -
319A MET* 4.6 3.1 - - + -
330A TYR* 4.1 12.8 - - + -
332A ASP 3.8 2.2 - - - -
333A SER* 4.7 2.7 - - - -
340A LEU* 4.2 11.4 - - + -
341A TRP* 1.3 77.6 - - - +
343A VAL* 1.3 62.9 + - - +
344A MET* 4.0 16.8 + - + +
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Residues in contact with VAL 343 (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 TYR* 3.8 33.9 - - + +
296A VAL* 3.9 35.0 - - + -
297A ALA 3.7 2.7 - - - -
298A ILE* 4.0 17.5 - - + -
330A TYR* 3.8 1.0 - - - -
331A LEU* 2.8 37.7 + - + -
332A ASP 2.8 28.7 + - - +
334A TYR* 4.4 11.9 - - + -
341A TRP* 4.9 1.6 - - + +
342A VAL* 1.3 76.8 - - - +
344A MET* 1.3 60.0 + - - +
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Residues in contact with MET 344 (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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296A VAL* 3.4 7.6 - - - +
297A ALA* 2.9 35.6 + - + +
299A ARG* 6.0 4.7 - - + +
319A MET* 3.6 38.6 - - - -
328A VAL* 3.7 32.8 - - + +
329A ASN 3.4 9.6 - - - +
330A TYR* 3.7 17.7 - - - -
331A LEU* 3.8 5.2 - - - +
342A VAL* 4.1 12.6 - - + +
343A VAL* 1.3 77.4 - - - +
345A GLU* 1.3 72.8 + - - +
406A THR* 4.6 8.5 - - - +
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Residues in contact with GLU 345 (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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294A GLN* 3.6 24.1 + - - +
295A GLU 4.6 1.1 - - - -
297A ALA* 4.2 4.0 - - - +
327A ILE 4.1 0.3 - - - +
328A VAL* 3.6 14.4 - - + +
329A ASN* 2.9 54.0 + - + +
331A LEU* 3.7 9.7 - - + +
344A MET* 1.3 83.6 - - - +
346A TYR* 1.3 63.0 + - - +
347A LEU* 4.2 11.5 + - + +
396A LEU* 6.1 0.2 - - - +
404A LYS* 2.8 40.2 + - - +
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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