Contacts of the strand formed by residues 337 - 344 (chain A) in PDB entry 2YWE
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 GLY 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A TYR* 3.2 6.6 - - - -
332A SER* 3.1 4.4 - - - -
333A SER 2.8 38.5 + - - -
334A PRO 4.6 1.1 - - - -
335A ALA 3.4 2.6 + - - -
336A LEU* 1.3 80.1 - - - +
338A MET* 1.3 61.6 + - - -
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Residues in contact with MET 338 (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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302A TYR* 3.6 2.8 - - - -
303A PRO* 3.2 24.4 - - - +
309A TYR* 3.3 43.3 - - + +
331A GLU 3.5 5.4 - - - +
332A SER* 4.0 15.9 - - - -
336A LEU 3.9 0.7 + - - +
337A GLY* 1.3 75.3 - - - -
339A GLY* 1.3 59.2 + - - +
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Residues in contact with GLY 339 (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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301A ILE 3.3 11.9 - - - -
302A TYR* 3.4 14.5 - - - -
303A PRO* 4.4 0.7 - - - -
309A TYR* 3.5 10.2 - - - -
330A PRO* 3.4 4.9 - - - +
331A GLU* 2.8 29.1 + - - +
338A MET* 1.3 75.3 - - - +
340A PHE* 1.3 74.0 + - - -
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Residues in contact with PHE 340 (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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300A GLY* 3.3 2.9 - - - -
301A ILE* 2.7 41.4 + - + +
302A TYR* 4.9 0.2 - - - -
309A TYR* 3.7 34.5 - + - -
312A LEU* 3.9 15.7 - - + -
313A ARG* 3.4 49.4 - - + -
316A LEU* 3.4 17.7 - - + -
328A TYR* 3.7 29.8 - + + -
329A GLU 3.2 16.8 - - - +
330A PRO* 4.0 10.3 - - + -
331A GLU* 3.9 7.7 - - - +
339A GLY* 1.3 76.2 - - - -
341A ARG* 1.3 60.6 + - - +
342A VAL* 3.6 19.2 + - + +
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Residues in contact with ARG 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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298A TYR* 4.0 21.5 - - + -
299A ALA* 3.4 9.5 - - - +
300A GLY* 3.4 24.8 - - - +
328A TYR* 3.1 2.9 - - - -
329A GLU* 2.7 50.6 + - + +
331A GLU* 2.7 48.1 + - + +
340A PHE* 1.3 69.9 - - - +
342A VAL* 1.3 59.5 + - - +
368A THR* 4.1 11.7 + - - +
369A ALA 5.0 0.6 + - - -
371A ASN* 3.0 24.9 + - - -
388A ARG* 3.6 19.5 - - + +
389A ASN* 3.3 29.1 + - + +
390A PRO* 4.0 7.3 - - - +
391A MET* 5.6 0.6 - - - -
499A ALA* 5.2 8.1 + - - +
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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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298A TYR* 3.2 7.4 - - - -
299A ALA 2.9 30.7 + - - +
301A ILE* 3.5 27.6 - - + -
316A LEU* 4.6 8.1 - - + -
326A ILE* 3.5 25.1 - - + -
327A VAL 3.2 15.3 - - - +
328A TYR* 3.8 12.6 - - + -
340A PHE* 3.9 13.5 - - + -
341A ARG* 1.3 77.7 - - - +
343A GLY* 1.3 58.9 + - - +
344A PHE* 3.4 32.8 - - + -
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Residues in contact with GLY 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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295A PRO* 4.2 3.5 - - - +
297A VAL 3.7 2.2 - - - -
298A TYR* 3.4 28.5 - - - -
325A ALA 4.4 1.6 - - - +
326A ILE* 3.7 11.8 - - - +
327A VAL* 2.8 41.1 + - - +
342A VAL* 1.3 73.9 - - - +
344A PHE* 1.3 62.1 + - - -
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Residues in contact with PHE 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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295A PRO* 4.2 3.8 - - - -
296A MET 2.8 24.2 + - - -
297A VAL* 2.7 30.6 + - + +
299A ALA* 4.3 10.8 - - + -
301A ILE* 3.7 16.2 - - + -
325A ALA 5.9 0.7 - - - -
326A ILE* 4.3 1.3 - - + -
342A VAL* 3.4 42.8 - - + -
343A GLY* 1.3 76.2 - - - -
345A LEU* 1.3 58.5 + - - +
346A GLY 3.1 17.9 - - - +
349A HIS* 3.5 12.1 - + - +
350A MET* 3.6 46.4 - - + +
353A VAL* 3.7 36.3 - - + -
354A GLN* 5.7 0.9 - - + -
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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