Contacts of the strand formed by residues 203 - 211 (chain A) in PDB entry 3MY0
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 ALA 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A GLN 3.3 4.6 + - - +
202A VAL* 1.3 74.5 - - - +
204A LEU* 1.3 62.9 + - - +
205A VAL* 3.8 4.8 + - + +
219A GLY* 3.1 3.6 - - - -
220A LEU* 2.7 48.3 + - + +
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Residues in contact with LEU 204 (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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202A VAL* 4.5 5.8 - - + +
203A ALA* 1.3 75.0 - - - +
205A VAL* 1.3 59.8 + - - +
217A TRP* 3.7 41.6 - - + -
218A ARG 4.0 1.6 - - - -
219A GLY* 4.9 1.3 - - - -
228A VAL* 3.9 38.6 - - + -
230A ILE* 4.5 9.4 - - + -
274A TRP* 4.2 26.5 - - + -
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Residues in contact with VAL 205 (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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203A ALA* 4.0 13.7 - - + +
204A LEU* 1.3 77.9 - - - +
206A GLU* 1.3 66.6 + - + +
217A TRP* 4.3 6.7 - - - -
218A ARG* 2.9 34.7 + - - +
219A GLY 4.8 0.7 - - - -
220A LEU* 4.3 26.2 - - + +
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Residues in contact with GLU 206 (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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205A VAL* 1.3 84.8 - - + +
207A CYS* 1.3 68.9 + - - +
208A VAL* 3.5 16.4 + - + +
217A TRP* 3.2 8.0 - - - -
218A ARG* 2.6 78.9 + - + +
279A TYR* 5.2 0.2 + - - -
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Residues in contact with CYS 207 (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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206A GLU* 1.3 76.4 - - - +
208A VAL* 1.3 59.8 + - - +
209A GLY 3.4 26.9 - - - -
210A LYS* 4.8 4.9 - - - -
215A GLU* 4.7 9.4 - - - -
216A VAL 3.8 6.1 - - - -
217A TRP* 3.6 38.0 - - + -
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Residues in contact with VAL 208 (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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206A GLU* 3.9 31.9 - - - +
207A CYS* 1.3 76.1 - - - +
209A GLY* 1.3 57.1 + - - +
216A VAL* 3.0 31.1 + - + +
218A ARG* 4.3 7.4 - - + +
279A TYR* 3.7 33.7 - - + +
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Residues in contact with GLY 209 (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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207A CYS* 3.4 13.4 + - - -
208A VAL* 1.3 81.2 - - - +
210A LYS* 1.3 62.1 + - - +
213A TYR* 3.7 13.2 - - - -
215A GLU* 3.4 3.6 - - - -
216A VAL* 3.0 28.3 + - - -
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Residues in contact with LYS 210 (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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207A CYS* 4.8 6.5 - - - -
209A GLY* 1.3 75.0 - - - +
211A GLY* 1.3 58.3 + - - +
213A TYR* 3.5 11.3 + - - -
214A GLY 3.6 9.0 - - - +
215A GLU* 4.3 12.1 - - + +
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Residues in contact with GLY 211 (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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210A LYS* 1.3 75.5 - - - +
212A ARG* 1.3 63.5 + - - -
213A TYR* 3.2 14.7 - - - -
214A GLY* 3.0 20.9 + - - +
232A SER* 5.3 1.0 - - - -
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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