Contacts of the strand formed by residues 274 - 278 (chain A) in PDB entry 3MYV
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 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A TYR* 3.3 16.3 - - - -
255A TYR* 3.9 0.4 + - - -
270A PHE* 4.3 5.1 - - - +
271A GLY 2.9 19.7 + - - +
272A SER 3.4 0.4 - - - -
273A GLU* 1.3 76.1 - - - +
275A PHE* 1.3 60.1 + - - +
276A PHE 3.8 6.9 + - - -
277A GLU* 2.7 42.7 + - - +
356A VAL* 5.0 2.7 - - - +
358A LEU 3.9 4.0 - - - -
359A ARG* 4.2 3.1 - - - -
509A EDO 3.8 13.0 - - - -
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Residues in contact with PHE 275 (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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212A ARG 3.8 12.0 - - - +
214A ASN* 4.2 6.1 - - - +
216A TYR* 3.7 28.7 - + + -
217A ALA* 3.6 27.1 - - - +
220A ALA* 3.6 15.7 - - + -
242A LEU* 4.3 10.8 - - + -
246A ALA* 5.4 1.3 - - + -
252A TYR* 3.7 40.3 + + + +
273A GLU 3.2 1.0 + - - -
274A SER* 1.3 74.7 - - - +
276A PHE* 1.3 61.7 + - - +
358A LEU* 2.8 21.9 + - + +
359A ARG 3.6 8.7 - - - -
360A LEU* 3.5 40.8 - - + -
363A VAL* 3.6 21.5 - - + -
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Residues in contact with PHE 276 (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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50A TYR* 3.6 24.0 - + - -
53A MSE 3.9 6.3 - - - -
145A LEU* 4.1 15.9 - - + -
211A GLY 3.5 21.3 - - - +
212A ARG 3.7 16.4 - - - -
213A MSE 3.6 24.0 - - + -
217A ALA* 4.1 0.7 - - + -
274A SER* 3.5 2.7 + - - -
275A PHE* 1.3 80.1 - - - +
277A GLU* 1.3 74.0 + - - +
278A ILE* 3.8 20.2 - - + -
356A VAL* 4.1 0.5 - - - +
357A VAL* 2.9 55.5 + - + -
358A LEU* 3.1 30.3 + - + +
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Residues in contact with GLU 277 (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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211A GLY* 3.4 25.6 - - - +
269A LYS* 3.8 3.8 - - - +
270A PHE* 3.0 46.6 + - + -
271A GLY 4.2 1.0 + - - -
274A SER* 2.7 30.2 + - - +
276A PHE* 1.3 80.1 - - - +
278A ILE* 1.3 62.3 + - - +
354A ASN* 2.9 32.3 + - + +
355A ASN 3.3 15.0 - - - +
356A VAL* 3.8 14.8 - - - +
357A VAL* 4.2 1.1 - - - +
509A EDO 4.5 6.6 + - - -
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Residues in contact with ILE 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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50A TYR* 5.3 4.3 - - + +
53A MSE 4.4 12.8 - - + -
54A SER* 3.4 36.8 - - - +
59A TYR* 3.8 39.5 - - + +
60A GLY* 5.4 0.9 - - - -
211A GLY 5.1 1.6 - - - +
276A PHE* 3.8 26.2 - - + -
277A GLU* 1.3 70.1 - - - +
279A ALA* 1.3 65.8 + - - +
280A ASN* 4.5 3.5 - - + +
354A ASN* 3.0 30.3 - - - +
355A ASN* 2.8 25.3 + - + +
357A VAL* 4.0 7.2 - - + -
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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