Contacts of the strand formed by residues 277 - 281 (chain A) in PDB entry 2IVF
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 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A GLU 2.9 11.4 + - - +
249A LEU* 3.5 19.9 - - + +
250A ILE* 2.9 27.5 + - - +
275A GLY 3.5 2.8 + - - +
276A ALA* 1.3 73.1 - - - +
278A VAL* 1.3 60.3 + - - +
279A VAL* 4.3 7.9 - - + -
293A ASP* 3.4 16.5 - - + +
294A LEU* 3.6 17.3 - - + +
430A GLU* 3.9 0.3 - - - +
434A LYS* 2.6 47.3 + - - +
438A LYS* 3.8 12.2 - - + -
279B ARG* 4.0 4.3 + - - -
317B ARG* 4.1 2.5 - - - +
321B ARG* 5.1 6.3 + - - +
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Residues in contact with VAL 278 (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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250A ILE* 3.6 13.2 - - + +
252A MET* 5.0 1.6 - - + -
268A LEU* 3.7 40.8 - - + +
272A ARG* 3.9 23.3 - - + -
276A ALA 4.0 3.1 - - - +
277A GLU* 1.3 75.5 - - - +
279A VAL* 1.3 67.4 + - - +
280A VAL* 4.8 2.9 - - + -
291A ALA 3.3 28.5 - - - +
292A ALA* 3.6 11.0 - - + -
293A ASP* 2.7 40.5 + - - +
294A LEU 3.2 7.1 + - - -
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Residues in contact with VAL 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU* 3.9 23.8 - - + -
250A ILE 2.8 16.2 + - - +
251A PHE* 3.4 21.8 - - + -
252A MET* 2.8 34.7 + - - +
277A GLU* 4.3 2.2 - - + -
278A VAL* 1.3 78.8 - - - +
280A VAL* 1.3 62.4 + - - +
281A ILE* 4.0 1.3 + - + -
294A LEU* 3.4 20.4 - - + +
296A VAL* 3.4 32.8 - - + -
431A LEU* 4.0 16.6 - - + -
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Residues in contact with VAL 280 (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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252A MET* 3.3 22.4 - - + +
255A SER 5.4 1.1 - - - +
278A VAL* 4.8 3.1 - - + -
279A VAL* 1.3 75.0 - - - +
281A ILE* 1.3 56.9 - - - +
282A ALA* 3.9 17.7 - - + -
286A ASN* 3.6 24.2 - - - +
288A THR* 4.2 23.8 - - + +
289A THR* 3.9 14.8 - - + -
292A ALA* 3.6 20.6 - - + -
294A LEU 2.9 9.6 + - - +
295A HIS* 3.3 5.8 - - + -
296A VAL 2.8 29.2 + - - -
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Residues in contact with ILE 281 (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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251A PHE* 3.7 22.9 - - + -
252A MET 2.8 9.7 + - - +
253A THR* 3.4 27.9 - - - +
254A CYS 3.6 2.9 + - - -
255A SER 5.2 0.9 + - - +
279A VAL* 4.2 1.3 - - + -
280A VAL* 1.3 71.6 - - - +
282A ALA* 1.3 61.1 + - - +
296A VAL* 3.5 19.3 - - + +
298A VAL* 3.6 24.7 - - + -
303A ASP* 3.6 9.9 - - - +
306A PHE* 3.7 15.7 - - + -
307A TRP* 3.4 36.3 - - + +
1986A MGD 2.8 29.0 + - - +
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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