Contacts of the strand formed by residues 319 - 324 (chain A) in PDB entry 3CFV
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 ILE 319 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A ASN* 3.1 24.1 + - - +
277A CYS* 4.3 0.2 - - - -
291A GLY* 4.1 15.8 - - - -
292A SER 3.0 20.7 + - - +
295A LYS 3.6 25.6 - - - +
296A THR* 3.6 18.6 - - - +
297A VAL* 3.7 9.0 - - + -
312A PHE 5.5 0.4 - - - +
315A HIS* 3.4 36.3 - - + +
317A ASP 4.0 2.0 - - - +
318A GLU* 1.3 75.4 - - - +
320A PHE* 1.3 63.5 + - - +
321A GLN 3.8 15.9 - - - +
322A VAL* 4.5 0.7 - - + -
334A SER* 4.1 9.9 - - - -
335A SER 3.4 12.6 - - - +
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Residues in contact with PHE 320 (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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128A ARG* 5.0 5.9 + - - -
230A GLU* 5.1 8.5 - - - -
276A ASN* 3.6 35.6 - - + +
277A CYS* 3.4 19.2 - - - +
318A GLU* 3.6 30.1 - - + -
319A ILE* 1.3 74.8 - - - +
321A GLN* 1.3 65.5 + - - +
335A SER 2.9 7.5 + - - +
336A GLY* 3.9 5.3 - - - -
337A THR* 3.5 18.6 - - - -
375A LYS* 3.4 39.3 - - - -
376A ILE 5.0 4.9 - - - +
377A SER* 5.0 7.0 - - - +
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Residues in contact with GLN 321 (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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128A ARG* 3.5 26.4 + - - +
130A ARG* 4.7 2.3 + - - +
231A ASP* 4.8 6.1 + - - -
277A CYS* 3.5 10.0 - - - +
278A LEU 5.5 0.8 + - - -
319A ILE* 3.8 1.0 - - - +
320A PHE* 1.3 85.3 + - + +
322A VAL* 1.3 89.4 + - - +
323A HIS* 3.3 36.7 + - + +
334A SER* 3.2 6.8 - - - -
335A SER* 3.2 40.1 + - - +
376A ILE 5.7 0.2 - - - +
377A SER 4.5 8.9 - - - +
378A ASP* 2.9 24.7 - - - +
379A PHE* 3.7 8.1 - - + -
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A CYS* 3.7 21.4 - - + -
278A LEU 4.6 2.2 - - - +
279A SER* 3.3 33.7 - - - +
289A ALA* 3.8 16.6 - - + -
291A GLY* 4.0 17.7 - - - +
297A VAL* 4.4 8.7 - - + -
319A ILE* 4.5 0.9 - - + -
321A GLN* 1.3 90.5 + - - +
323A HIS* 1.3 78.1 + - - +
332A LEU* 3.8 18.6 - - + -
333A ALA 3.5 4.9 - - - +
334A SER* 4.1 14.4 - - - -
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Residues in contact with HIS 323 (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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130A ARG* 4.7 14.0 + - - -
279A SER* 3.9 8.4 + - - -
321A GLN* 3.3 40.0 + - + -
322A VAL* 1.3 83.1 + - - +
324A TRP* 1.3 59.8 + - - +
332A LEU* 3.2 4.7 - - - +
333A ALA 3.0 31.8 + - - +
378A ASP* 3.8 2.0 + - - -
379A PHE* 3.2 46.9 + + + -
380A SER* 5.0 2.2 - - - -
381A TRP* 3.1 18.5 + + + -
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Residues in contact with TRP 324 (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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279A SER* 2.7 40.4 + - - -
280A PHE 3.2 21.1 - - - +
281A ASN* 3.2 31.6 - - + +
282A PRO* 3.6 19.5 - - + +
287A ILE* 3.8 24.2 - - + -
288A LEU 4.1 2.7 - - - -
289A ALA* 3.7 23.0 - - + +
299A LEU* 3.7 21.3 - - + -
323A HIS* 1.3 75.0 - - - +
325A SER* 1.3 63.8 + - - +
326A PRO* 3.6 3.1 - - - +
328A ASN 5.6 0.2 - - - -
329A GLU 4.3 4.3 - - - -
330A THR 4.8 0.2 - - - -
331A ILE 3.6 19.5 - - - -
332A LEU* 3.7 22.2 - - + -
346A LEU* 3.8 20.6 - - + -
381A TRP* 3.1 16.8 - - - -
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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