Contacts of the strand formed by residues 272 - 277 (chain C) in PDB entry 3VI4
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 272 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C THR* 4.2 5.2 - - - +
264C ILE 4.0 0.2 - - - -
265C LEU* 3.7 17.7 - - - +
271C ARG* 1.3 76.9 - - - +
273C LEU* 1.3 68.2 + - - +
274C TYR 5.1 1.3 - - - -
1N NAG 3.5 52.4 + - - +
2N NAG 5.8 0.2 + - - -
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Residues in contact with LEU 273 (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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240C PHE 4.8 3.6 - - - +
241C SER* 4.0 26.2 - - - +
247C ASP* 4.0 11.7 - - - +
264C ILE* 2.8 17.4 + - + +
265C LEU 4.5 0.7 - - - -
266C ASN* 3.6 43.3 - - + +
271C ARG* 5.0 1.8 - - + -
272C SER* 1.3 82.9 - - - +
274C TYR* 1.3 79.7 + - + +
2009C NAG 4.0 24.2 - - + +
1N NAG 3.2 15.2 - - - +
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Residues in contact with TYR 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C PHE* 3.8 20.4 + - + -
262C VAL 4.3 0.4 - - - -
263C THR* 3.3 4.0 - - - +
264C ILE* 3.1 35.2 + - + +
272C SER* 5.0 0.2 + - - -
273C LEU* 1.3 98.8 + - + +
275C ASN* 1.3 70.5 + - - +
276C PHE* 3.3 30.3 - + + -
329C GLN* 5.5 0.3 + - - -
333C GLY* 3.3 13.5 - - - -
334C ILE* 3.3 58.0 + - + +
1N NAG 4.2 5.3 + - - -
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Residues in contact with ASN 275 (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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261C TYR* 3.4 14.4 - - + -
262C VAL 3.2 2.9 - - - -
263C THR* 2.8 25.6 - - - +
274C TYR* 1.3 71.8 - - - +
276C PHE* 1.3 76.3 + - - +
277C SER 4.4 0.2 - - - -
336C PRO* 5.1 2.9 - - - +
1N NAG 1.4 67.4 + - - +
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Residues in contact with PHE 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C TYR* 3.1 2.1 - - - +
262C VAL* 2.7 48.5 + - + +
264C ILE* 3.6 8.7 - - + -
274C TYR* 3.3 42.8 - + + -
275C ASN* 1.3 79.6 - - - +
277C SER* 1.3 60.6 + - - +
285C PHE* 3.0 12.7 - - + -
302C LEU* 3.4 28.9 - - + -
304C VAL* 5.5 0.2 - - + -
327C TYR* 3.6 37.5 - + + +
334C ILE* 3.8 18.8 - - + -
335C GLU 3.2 26.2 - - - -
336C PRO* 3.9 11.7 - - + -
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Residues in contact with SER 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ASN* 3.2 34.7 + - - -
260C GLY 3.7 4.5 - - - -
261C TYR* 3.9 2.7 - - - -
275C ASN 4.4 0.2 - - - -
276C PHE* 1.3 73.2 - - - +
278C GLY* 1.3 69.2 + - - +
285C PHE* 3.6 12.1 - - - -
325C TYR* 6.1 0.2 - - - -
327C TYR* 4.1 6.7 + - - -
336C PRO 5.5 1.4 + - - -
2008C NAG 4.5 6.6 + - - -
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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
------------------------------------------------------------
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