Contacts of the strand formed by residues 257 - 262 (chain G) in PDB entry 3MGO
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 257 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201G LEU* 4.2 5.1 - - + +
217G TRP* 3.6 19.8 - + + -
218G GLN 3.2 13.0 - - - -
219G ARG* 3.7 38.5 + - + -
224G GLN* 4.6 8.2 + - + -
247G VAL* 3.6 34.5 - - + +
248G VAL 3.8 11.4 + - - -
249G VAL* 3.5 33.9 - - + -
250G PRO* 3.9 9.4 - - - +
253G GLN* 3.4 24.2 + - + -
254G GLU 3.2 11.5 + - - +
255G GLN 4.1 1.4 - - - +
256G ARG* 1.3 85.7 - - + +
258G THR* 1.3 67.4 + - - +
273G ARG* 3.5 17.8 - - - +
274G TRP 4.6 0.5 + - - -
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Residues in contact with THR 258 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217G TRP* 3.4 6.0 - - - -
218G GLN* 2.8 49.3 + - - +
221G GLY* 5.3 2.4 + - - -
255G GLN 5.2 0.4 - - - +
256G ARG 4.7 5.5 + - - +
257G TYR* 1.3 80.8 - - - +
259G CYS* 1.3 59.7 + - - +
260G HIS* 2.9 31.0 + - + -
271G THR* 4.2 9.6 - - + -
272G LEU 3.3 7.4 - - - +
273G ARG* 3.3 39.9 - - + +
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Residues in contact with CYS 259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G MET* 4.4 4.7 - - + -
203G CYS* 2.0 52.7 - - + -
215G LEU* 4.4 4.5 - - - -
216G THR 3.4 10.8 - - - -
217G TRP* 3.6 19.8 - - + -
258G THR* 1.3 73.4 - - - +
260G HIS* 1.3 65.8 + - - +
261G VAL* 4.0 11.4 - - - -
270G LEU 3.7 0.9 - - - +
271G THR* 3.5 4.0 - - - -
272G LEU* 2.7 44.4 + - + +
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Residues in contact with HIS 260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214G THR* 3.3 6.8 - - - +
215G LEU* 3.6 2.3 - - - +
216G THR* 2.8 45.5 + - - +
218G GLN* 3.0 40.9 + - + -
258G THR* 2.9 36.8 + - - -
259G CYS* 1.3 73.0 + - - +
261G VAL* 1.3 61.6 - - - +
262G GLN* 5.1 9.2 - - + +
269G PRO* 6.3 1.6 - - + -
270G LEU 3.3 5.3 + - - +
271G THR* 3.5 31.4 + - + -
131J ARG* 3.6 24.0 + - - +
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Residues in contact with VAL 261 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185G PRO* 4.2 15.5 - - + -
187G THR* 4.2 20.2 - - + -
203G CYS* 4.4 1.1 - - - -
205G ALA* 5.0 0.2 - - + -
213G ILE* 4.4 9.9 - - + -
214G THR 3.5 1.8 - - - -
215G LEU* 3.5 26.7 - - + -
259G CYS* 4.0 11.9 - - - -
260G HIS* 1.3 78.1 - - - +
262G GLN* 1.3 63.3 + - - +
266G LEU* 3.8 18.3 - - + +
269G PRO* 3.3 6.2 - - - +
270G LEU* 2.9 42.3 + - + +
272G LEU* 4.3 13.0 - - + -
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Residues in contact with GLN 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213G ILE* 3.3 5.6 - - - +
214G THR* 3.0 61.3 + - - +
216G THR* 5.0 7.7 + - - +
260G HIS* 5.1 5.8 + - + +
261G VAL* 1.3 80.1 - - - +
263G HIS* 1.3 62.5 + - - +
266G LEU* 4.5 0.2 - - - -
269G PRO* 4.3 21.5 - - + +
131J ARG* 6.1 0.2 - - - +
157J ARG* 4.5 13.9 - - - +
161J GLU* 4.0 21.1 + - - +
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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