Contacts of the strand formed by residues 278 - 285 (chain C) in PDB entry 4G8O
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 PHE 278 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235C MET* 4.8 5.6 - - + -
275C LEU* 5.4 4.0 - - + -
276C PRO* 3.3 24.2 - - + -
277C LYS* 1.3 73.9 - - - +
279C SER* 1.3 62.2 + - - +
280C LEU* 3.8 21.3 - - + -
326C ILE* 3.8 17.9 - - + +
327C GLU* 3.8 0.9 - - - -
328C VAL* 2.9 63.2 + - + -
358C PHE* 3.6 29.2 - + - -
360C PHE* 4.0 19.3 - + - -
376C VAL* 3.7 22.2 - - + -
379C PRO* 4.0 23.6 - - + -
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Residues in contact with SER 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278C PHE* 1.3 74.5 + - - +
280C LEU* 1.3 64.2 + - - +
326C ILE 3.3 6.3 - - - -
327C GLU* 3.4 33.6 + - - +
328C VAL 4.5 2.6 + - - -
329C ASN* 5.5 1.7 + - - +
379C PRO* 5.1 5.1 + - - +
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Residues in contact with LEU 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ASN* 4.0 33.0 - - + +
33C VAL* 3.8 28.2 - - + +
278C PHE* 3.8 29.1 - - + -
279C SER* 1.3 79.9 - - - +
281C GLU* 1.3 60.7 + - - +
282C THR* 5.2 1.1 - - - +
324C VAL 4.0 1.0 - - - +
325C LYS* 3.6 4.1 - - - +
326C ILE* 2.8 38.0 + - + +
375C GLN 5.2 0.9 - - - +
376C VAL* 3.9 24.2 - - + -
378C GLU 4.2 8.7 - - - +
379C PRO* 4.5 8.5 - - + +
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Residues in contact with GLU 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C LEU* 5.0 7.4 - - - +
280C LEU* 1.3 75.5 - - - +
282C THR* 1.3 70.5 + - - +
283C GLU 5.6 0.2 - - - +
323C LYS* 3.6 33.1 + - - -
324C VAL 3.8 4.3 - - - +
325C LYS* 3.4 35.4 + - + -
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Residues in contact with THR 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ASN* 4.0 12.3 + - - +
32C VAL* 4.1 10.5 - - + -
33C VAL* 3.3 50.5 + - - +
280C LEU* 5.2 1.2 - - - +
281C GLU* 1.3 80.6 + - - +
283C GLU* 1.3 64.4 + - - +
284C VAL* 4.0 17.1 + - + +
322C GLN 3.8 1.7 - - - +
323C LYS* 3.4 4.1 - - - -
324C VAL* 3.0 32.9 + - - +
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Residues in contact with GLU 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C LEU* 3.5 16.3 - - + -
152C LEU* 2.7 42.9 + - + +
153C GLY* 2.8 30.1 + - - -
281C GLU* 5.6 0.4 - - - +
282C THR* 1.3 75.3 - - - +
284C VAL* 1.3 66.3 + - - +
285C ASP 4.4 0.3 + - - -
321C LEU* 3.6 16.6 - - + +
322C GLN 3.4 9.2 - - - +
323C LYS* 3.5 22.0 - - + +
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Residues in contact with VAL 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C VAL* 3.8 30.3 - - + -
32C VAL* 5.1 4.0 - - + -
33C VAL 4.6 2.0 - - - +
34C PHE* 4.1 23.8 - - + -
282C THR* 4.0 19.3 - - + +
283C GLU* 1.3 78.3 - - - +
285C ASP* 1.3 72.4 + - - +
286C LEU* 3.6 15.7 + - + +
289C PRO* 4.8 0.2 - - + -
321C LEU* 3.4 12.6 - - - +
322C GLN* 2.8 38.9 + - + +
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Residues in contact with ASP 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C GLY* 5.8 1.6 - - - -
283C GLU 4.4 0.6 + - - -
284C VAL* 1.3 71.7 - - - +
286C LEU* 1.3 57.8 + - - +
287C ARG* 3.2 30.6 + - - +
288C LYS 4.5 0.5 + - - -
289C PRO* 3.5 15.4 - - - +
319C LEU* 4.5 13.3 - - - +
320C ALA 3.7 10.6 + - - +
321C LEU* 4.1 13.9 - - + +
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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