Contacts of the strand formed by residues 277 - 283 (chain A) in PDB entry 4UU5
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 SER 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A ASN* 2.9 18.9 + - - -
274A GLU* 2.9 45.3 + - - +
275A MET 3.2 0.4 - - - -
276A ASP* 1.3 82.2 - - - +
278A VAL* 1.3 59.5 + - - +
279A ILE* 3.8 8.4 - - - +
300A GLU* 3.2 30.3 - - - -
310A ARG* 3.2 18.5 - - - +
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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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271A VAL* 3.8 32.5 - - + -
272A ARG 3.5 3.4 - - - -
273A ASN* 3.7 4.9 - - - +
276A ASP 4.1 0.9 - - - +
277A SER* 1.3 77.4 - - - +
279A ILE* 1.3 61.7 + - - +
300A GLU* 3.4 5.5 + - - +
301A VAL* 2.8 40.4 + - + +
309A ILE* 3.7 40.4 - - + +
310A ARG* 5.1 0.2 - - - +
312A LYS 3.5 24.5 - - - +
314A VAL* 4.5 4.0 - - + -
317A VAL* 4.1 11.9 - - + -
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Residues in contact with ILE 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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271A VAL* 3.2 5.4 - - - -
272A ARG* 2.8 58.6 + - + +
274A GLU* 3.6 33.2 - - + +
277A SER* 3.8 16.2 - - - +
278A VAL* 1.3 76.2 - - - +
280A ILE* 1.3 76.2 + - - +
281A SER* 3.3 1.9 + - - -
298A GLY* 3.6 26.2 - - - +
299A ASP 3.4 1.6 - - - -
300A GLU* 3.6 31.6 - - + +
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Residues in contact with ILE 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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269A ALA* 4.5 7.0 - - + -
270A THR 3.5 8.1 - - - +
271A VAL* 3.9 13.5 - - + -
272A ARG* 3.6 1.7 + - - -
278A VAL 4.3 0.4 - - - -
279A ILE* 1.3 75.5 - - - +
281A SER* 1.3 62.8 + - - +
282A ARG 4.7 0.2 - - - +
283A ILE* 4.1 21.3 - - + -
295A LEU* 4.4 27.1 - - + -
296A HIS 3.4 30.5 - - - +
297A GLU* 3.5 1.9 - - - +
298A GLY 2.9 25.1 + - - -
299A ASP* 2.8 29.1 + - + +
301A VAL* 3.9 23.1 - - + -
330A PHE* 5.1 1.1 - - + -
1406B ILE* 4.9 5.2 - - + -
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Residues in contact with SER 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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270A THR* 2.8 23.5 + - - -
271A VAL* 4.6 1.3 - - - -
272A ARG* 2.9 49.9 + - - +
279A ILE 3.3 3.1 + - - -
280A ILE* 1.3 74.9 - - - +
282A ARG* 1.3 68.0 + - - +
283A ILE* 5.6 0.2 - - - +
297A GLU* 3.3 26.3 + - - +
1403B GLU* 4.2 9.0 - - - -
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Residues in contact with ARG 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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269A ALA* 3.4 4.0 - - - +
270A THR* 2.8 43.1 + - + +
281A SER* 1.3 82.9 + - - +
283A ILE* 1.3 70.1 + - - +
1403B GLU* 2.8 36.5 + - - +
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Residues in contact with ILE 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 GLY 3.7 3.1 - - - +
269A ALA* 4.0 17.0 - - + -
280A ILE* 4.1 13.5 - - + -
282A ARG* 1.3 86.7 - - - +
284A VAL* 1.3 66.9 + - - +
285A LYS* 3.7 5.9 + - - +
289A ALA* 4.5 5.6 - - + -
290A GLU* 3.6 43.3 - - + +
295A LEU* 3.6 26.9 - - + +
296A HIS* 5.1 4.0 - - - -
297A GLU 5.2 2.7 - - - +
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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