Contacts of the strand formed by residues 277 - 281 (chain C) in PDB entry 4BZ5
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 TYR 277 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C LEU* 4.2 13.0 - - + -
126C ILE* 3.7 9.2 + - + +
128C ARG* 3.0 35.5 + - - -
164C LEU* 3.8 64.4 - - + -
167C SER* 3.6 14.2 + - - -
168C THR 6.0 0.7 - - - -
178C THR* 4.4 4.7 - - + -
179C ARG 3.5 1.4 + - - -
180C VAL* 3.5 14.5 - - + -
181C LEU 3.0 22.7 + - - -
275C PRO* 3.3 6.8 - - - +
276C SER* 1.3 97.1 - - - +
278C VAL* 1.3 63.9 + - - +
331C VAL* 3.8 2.0 - - - -
332C PRO* 3.3 27.4 - - + +
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Residues in contact with VAL 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C LEU* 5.4 0.3 - - - +
181C LEU* 3.3 13.5 - - + +
183C VAL* 4.5 11.7 - - + -
275C PRO* 4.1 12.1 - - + -
277C TYR* 1.3 78.9 - - - +
279C VAL* 1.3 68.1 + - - +
280C VAL* 3.8 23.1 - - + -
326C ILE* 3.9 11.9 - - + -
329C TRP* 4.1 25.4 - - + -
331C VAL* 4.0 17.3 - - + -
332C PRO 3.0 5.9 + - - +
333C THR* 3.2 15.6 - - + +
334C LEU 2.9 24.4 + - - -
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Residues in contact with VAL 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C ILE* 4.3 7.6 - - + -
160C ALA* 5.9 0.4 - - + -
161C ILE* 4.1 15.9 - - + -
164C LEU* 3.6 32.8 - - + -
180C VAL* 4.1 6.5 - - + -
181C LEU 2.9 8.8 + - - +
182C TYR* 3.4 23.5 - - + -
183C VAL* 2.9 25.3 + - - +
278C VAL* 1.3 77.7 - - - +
280C VAL* 1.3 63.1 + - - +
334C LEU* 3.4 19.1 - - + +
336C LEU* 4.0 25.8 - - + -
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Residues in contact with VAL 280 (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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183C VAL* 3.3 10.8 - - + +
185C LEU* 3.9 28.3 - - + -
278C VAL* 3.8 14.6 - - + -
279C VAL* 1.3 79.3 - - - +
281C GLN* 1.3 62.0 + - - +
282C CYS* 4.6 1.6 - - + +
323C ILE* 4.0 18.8 - - + -
326C ILE* 3.8 26.5 - - + -
333C THR* 4.1 10.8 - - + -
334C LEU 2.7 17.1 + - - +
335C ILE* 3.5 5.5 - - + +
336C LEU* 2.7 34.8 + - - +
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Residues in contact with GLN 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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139C GLY* 3.1 28.0 + - - +
141C HIS* 3.5 14.1 + - - +
157C ILE* 3.8 9.0 - - + -
182C TYR* 3.4 29.3 - - + +
183C VAL 2.8 10.1 + - - +
184C ASP* 3.5 6.9 - - - +
185C LEU* 2.8 33.8 + - - +
186C ASP* 3.2 34.9 + - - +
279C VAL 4.1 0.6 + - - -
280C VAL* 1.3 71.7 - - - +
282C CYS* 1.3 56.7 + - - +
283C GLY 2.8 20.8 + - - -
336C LEU* 3.9 4.9 - - + -
337C GLY 3.3 14.8 - - - +
338C GLY* 3.5 8.3 - - - -
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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