Contacts of the strand formed by residues 338 - 345 (chain F) in PDB entry 1EV2
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 338 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292F LYS* 4.2 5.6 - - - -
293F HIS 5.5 1.8 - - - -
336F ASP 3.5 1.0 + - - -
337F ALA* 1.3 75.6 - - - +
339F GLU* 1.3 60.6 + - - -
340F TYR* 3.4 11.4 - - - -
356F TRP* 3.5 4.1 - - - -
357F LEU 2.9 34.6 + - - -
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Residues in contact with GLU 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291F ILE 3.9 0.2 - - - +
292F LYS* 3.6 4.8 - - - +
293F HIS* 3.0 47.0 + - + +
338F GLY* 1.3 70.7 - - - -
340F TYR* 1.3 63.5 + - - +
341F THR* 4.4 5.3 + - - +
354F SER* 3.6 28.2 + - - +
355F ALA 3.5 12.1 - - - +
356F TRP* 4.5 4.0 - - + +
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Residues in contact with TYR 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263F PRO* 4.5 1.6 - - - +
276F PHE* 3.6 36.6 - + + -
290F TRP* 5.0 7.2 - + + -
291F ILE 3.4 4.9 - - - -
292F LYS* 3.3 31.7 - - + +
312F LEU* 3.5 25.8 - - + -
327F LEU* 4.0 15.0 - - + -
336F ASP* 2.5 44.2 + - - +
338F GLY 3.4 17.0 - - - -
339F GLU* 1.3 72.3 - - - +
341F THR* 1.3 63.7 + - - +
353F HIS 4.1 0.2 - - - +
354F SER* 3.2 3.3 - - - -
355F ALA* 2.8 35.7 + - - +
357F LEU* 3.7 11.4 - - + -
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Residues in contact with THR 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289F GLN 3.7 0.5 - - - +
290F TRP* 3.4 10.1 - - - -
291F ILE* 2.7 50.4 + - + +
293F HIS* 6.1 1.0 - - - +
339F GLU* 4.4 6.9 + - - +
340F TYR* 1.3 74.7 - - - +
342F CYS* 1.3 74.2 + - - +
343F LEU* 3.7 9.3 + - + +
352F PHE* 3.7 22.9 - - + -
353F HIS 3.5 4.3 - - - +
354F SER* 2.6 25.8 + - - +
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Residues in contact with CYS 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258F LEU* 3.9 5.6 - - + +
263F PRO* 4.4 3.4 - - + -
278F CYS* 2.5 49.4 - - + -
280F VAL* 4.7 3.6 - - - -
288F ILE* 3.9 23.3 - - - -
289F GLN 3.6 4.3 - - - -
290F TRP* 3.8 19.1 - - + -
341F THR* 1.3 73.2 - - - +
343F LEU* 1.3 62.1 + - - +
352F PHE* 3.2 4.9 - - - +
353F HIS 3.0 33.9 + - - +
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Residues in contact with LEU 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287F HIS 3.5 3.4 - - - +
288F ILE* 3.4 3.2 - - - -
289F GLN* 3.0 63.8 + - + +
291F ILE* 4.3 17.0 - - + -
341F THR* 3.7 7.4 + - + -
342F CYS* 1.3 75.6 - - - +
344F ALA* 1.3 65.6 + - - +
345F GLY* 4.7 2.5 - - - +
350F ILE* 3.8 35.0 - - + -
351F SER 3.5 3.8 - - - +
352F PHE* 3.9 18.4 - - + -
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Residues in contact with ALA 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256F PRO* 3.1 21.1 - - + +
258F LEU* 3.9 26.7 - - + -
280F VAL* 4.1 15.7 - - + -
286F PRO* 5.1 1.3 - - + -
287F HIS 3.4 5.6 - - - +
288F ILE* 4.3 7.0 - - + -
342F CYS* 4.2 0.6 - - - -
343F LEU* 1.3 76.0 - - - +
345F GLY* 1.3 58.6 + - - +
350F ILE* 3.5 3.0 - - - -
351F SER 2.8 38.0 + - - +
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Residues in contact with GLY 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ARG* 4.1 12.4 - - - +
61B GLY 4.8 0.3 + - - -
256F PRO* 3.8 4.0 - - - +
285F GLN 4.2 0.3 - - - +
286F PRO* 3.5 1.8 - - - +
287F HIS* 2.8 43.6 + - - +
343F LEU* 4.7 3.8 - - - +
344F ALA* 1.3 75.8 - - - +
346F ASN* 1.3 60.2 + - - -
349F GLY 3.4 9.9 - - - -
350F ILE* 4.2 11.0 - - - -
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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