Contacts of the strand formed by residues 278 - 285 (chain A) in PDB entry 4OIB
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 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A PRO* 5.2 3.1 - - - +
193A PHE* 3.5 34.0 - - + -
195A LEU* 3.2 35.5 - - + +
273A VAL 3.8 0.2 - - - +
274A THR* 3.5 3.3 - - - -
275A LEU 3.1 31.8 + - - +
276A GLY 3.4 0.4 - - - -
277A GLY* 1.3 83.7 - - - +
279A ASN* 1.3 66.5 + - - +
280A ARG* 4.2 11.2 + - - +
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Residues in contact with ASN 279 (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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195A LEU* 5.3 0.9 - - - -
272A ASN* 5.0 2.0 - - + +
273A VAL 3.2 17.9 - - - +
274A THR* 3.9 15.3 - - + +
277A GLY 4.2 4.3 - - - +
278A GLU* 1.3 81.5 - - - +
280A ARG* 1.3 83.5 + - - +
281A GLU* 4.2 3.1 + - - +
1F NAG 3.7 33.0 + - - +
2F NAG 6.2 0.4 - - - +
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Residues in contact with ARG 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 3.5 44.1 - - + +
196A SER 4.1 14.9 + - - +
197A PRO* 5.4 4.2 - - - +
199A ALA* 5.0 9.6 - - + +
200A PRO* 3.8 23.8 - - + +
220A LEU* 6.4 0.2 - - + -
271A CYS 3.7 2.3 - - - +
272A ASN* 3.4 18.8 - - - -
273A VAL* 3.5 11.8 + - + +
278A GLU* 4.2 11.1 + - - +
279A ASN* 1.3 109.9 + - - +
281A GLU* 1.3 62.0 + - - +
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Residues in contact with GLU 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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199A ALA* 4.7 6.6 - - - +
200A PRO* 4.4 2.7 - - - +
232A TYR* 6.0 0.2 - - - -
270A VAL* 4.0 19.2 - - - +
271A CYS 3.5 6.3 - - - +
272A ASN* 3.6 15.5 - - + +
279A ASN* 4.2 3.7 + - - +
280A ARG* 1.3 74.3 - - - +
282A THR* 1.3 68.4 + - - +
283A ARG* 4.2 27.1 + - + +
1F NAG 3.6 44.9 + - - +
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Residues in contact with THR 282 (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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199A ALA* 4.4 7.6 - - - +
200A PRO* 3.2 45.2 + - + +
202A LEU* 4.0 23.6 - - + +
269A LEU 3.6 0.9 - - - +
270A VAL* 3.8 0.2 - - - -
271A CYS* 3.0 36.0 + - + +
281A GLU* 1.3 75.6 - - - +
283A ARG* 1.3 71.1 + - - +
284A GLU* 4.5 6.2 + - - +
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Residues in contact with ARG 283 (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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268A GLN* 3.5 32.5 + - + +
269A LEU 3.3 5.2 - - - +
270A VAL* 3.7 25.8 - - + +
281A GLU* 4.2 22.9 + - + +
282A THR* 1.3 79.8 + - - +
284A GLU* 1.3 79.7 + - - +
285A ASN* 5.3 2.7 - - - +
1F NAG 5.5 2.6 + - - -
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Residues in contact with GLU 284 (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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202A LEU* 3.6 39.1 + - + +
204A ALA* 5.7 5.6 - - + +
268A GLN* 3.4 5.3 - - - -
269A LEU* 2.8 52.9 + - + +
282A THR* 4.5 8.0 + - + +
283A ARG* 1.3 84.2 - - - +
285A ASN* 1.3 73.1 + - - +
286A VAL* 3.8 0.6 + - + +
2320A NAG 6.2 0.2 - - - +
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Residues in contact with ASN 285 (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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206A ARG* 4.8 6.6 - - - +
265A GLY 5.2 0.4 - - - +
266A ALA* 6.0 2.5 - - - -
267A ARG 4.2 7.6 - - - +
268A GLN* 3.7 17.2 + - - +
283A ARG* 5.3 2.6 - - - +
284A GLU* 1.3 84.8 + - - +
286A VAL* 1.3 61.7 + - - +
2320A NAG 1.4 81.4 + - + +
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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