Contacts of the strand formed by residues 198 - 208 (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 GLU 198 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193G ALA* 4.2 0.7 - - - +
194G VAL* 3.7 21.7 + - + +
195G SER* 3.3 29.1 + - - +
196G ASP 3.6 1.5 - - - +
197G HIS* 1.3 91.0 - - + +
199G ALA* 1.3 63.2 + - - +
248G VAL* 3.7 26.8 - - + +
249G VAL 3.4 6.3 - - - -
250G PRO* 4.4 10.8 - - + +
251G SER* 4.4 3.4 + - - +
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Residues in contact with ALA 199 (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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191G HIS* 3.4 37.5 - - + +
192G HIS 3.5 8.5 - - - +
193G ALA* 4.4 3.8 - - + -
194G VAL* 4.3 5.8 - - - +
198G GLU* 1.3 78.2 - - - +
200G THR* 1.3 63.9 + - - +
201G LEU 3.8 0.3 + - - -
247G VAL 3.7 0.2 - - - +
248G VAL* 3.6 4.2 - - - -
249G VAL* 2.8 38.3 + - + +
251G SER* 6.0 0.9 - - - +
254G GLU* 4.1 5.4 - - - +
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Residues in contact with THR 200 (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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190G THR 3.3 6.6 - - - +
191G HIS* 3.4 2.9 - - - -
192G HIS* 2.7 40.9 + - - -
194G VAL* 3.1 25.3 - - - +
199G ALA* 1.3 72.1 - - - +
201G LEU* 1.3 67.7 + - - +
202G ARG* 4.0 29.3 + - - +
246G ALA* 4.2 15.7 - - + -
247G VAL 3.7 7.0 - - - +
248G VAL* 4.9 7.4 - - + +
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Residues in contact with LEU 201 (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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189G MET* 4.4 4.0 - - - -
190G THR 3.5 9.6 - - - +
191G HIS* 3.4 32.5 - - + +
199G ALA 3.8 0.2 + - - -
200G THR* 1.3 72.9 - - - +
202G ARG* 1.3 60.4 + - - +
217G TRP* 3.7 24.3 - - + -
246G ALA* 3.1 2.9 - - - -
247G VAL* 2.9 48.1 + - + +
249G VAL* 3.5 25.4 - - + -
254G GLU* 4.3 15.7 - - + +
257G TYR* 4.2 12.1 - - + -
274G TRP* 4.1 27.6 - - + +
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Residues in contact with ARG 202 (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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189G MET* 3.3 9.2 - - - +
190G THR* 3.1 48.5 + - - +
192G HIS* 4.8 5.3 + - - -
200G THR* 4.0 22.3 - - + +
201G LEU* 1.3 74.2 - - - +
203G CYS* 1.3 61.2 + - - +
204G TRP* 3.3 28.7 - - + +
217G TRP* 4.3 2.0 - - - -
229G GLU* 4.6 4.2 + - - -
244G TRP* 3.3 55.7 - - + -
245G ALA 3.6 2.0 - - - -
246G ALA* 4.1 5.9 - - + +
98H ASP* 2.9 32.7 + - - +
99H MET* 3.7 26.6 - - - +
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Residues in contact with CYS 203 (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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188G HIS 4.0 2.7 - - - -
189G MET* 4.9 3.1 - - + -
202G ARG* 1.3 72.4 - - - +
204G TRP* 1.3 62.0 + - - +
215G LEU* 4.0 7.0 - - - +
217G TRP* 3.7 12.3 - - + +
244G TRP* 2.9 31.1 - - - +
245G ALA* 2.6 23.7 + - + +
259G CYS* 2.0 47.6 - - - -
261G VAL* 4.4 11.7 - - - -
272G LEU* 4.4 11.2 - - - -
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Residues in contact with TRP 204 (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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186G LYS 4.3 0.2 - - - -
187G THR* 3.1 29.8 - - - +
188G HIS* 2.9 50.9 + + + +
190G THR* 3.7 17.5 + - + +
202G ARG* 3.3 37.0 - - + +
203G CYS* 1.3 76.1 - - - +
205G ALA* 1.3 59.6 + - - +
206G LEU* 3.7 31.2 - - + -
215G LEU* 5.0 1.1 - - - +
234G ARG* 3.5 19.5 - - - -
242G GLN* 5.6 0.9 - - + -
243G LYS 4.0 2.7 - - - -
244G TRP* 3.7 13.9 - + + -
97H ARG 4.4 5.4 - - - -
98H ASP* 3.4 28.7 + - - -
99H MET* 3.5 27.6 - - - -
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Residues in contact with ALA 205 (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* 4.0 8.7 - - + -
186G LYS 3.7 3.1 - - - -
187G THR* 4.4 2.7 - - + -
204G TRP* 1.3 75.1 - - - +
206G LEU* 1.3 65.3 + - - +
208G PHE* 3.3 23.2 - - + -
213G ILE* 3.8 17.7 - - + -
215G LEU* 4.1 14.4 - - + -
242G GLN* 3.4 0.5 - - - -
243G LYS* 2.9 35.5 + - + +
261G VAL* 5.0 0.2 - - + -
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Residues in contact with LEU 206 (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* 3.3 1.7 - - - +
186G LYS* 2.8 47.7 + - + +
188G HIS* 4.3 20.0 - - + +
204G TRP* 3.7 27.8 - - + -
205G ALA* 1.3 83.8 - - - +
207G SER* 1.3 74.1 + - - +
208G PHE* 3.2 4.6 + - - -
241G PHE 4.1 1.8 - - - -
242G GLN* 3.7 31.4 - - + +
12H ARG 6.0 0.7 - - - +
14H PRO* 4.1 29.8 - - + -
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Residues in contact with SER 207 (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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183G ASP* 3.5 18.9 - - - +
184G ALA 3.9 5.0 - - - +
186G LYS* 4.2 21.8 + - - +
206G LEU* 1.3 79.8 - - - +
208G PHE* 1.3 58.5 + - - +
236G ALA* 5.9 0.4 - - - +
238G ASP* 5.3 2.8 + - - -
240G THR* 3.5 28.9 + - - +
241G PHE 3.4 6.9 + - - -
242G GLN* 4.9 2.4 - - - +
13H HIS* 5.8 2.4 + - - -
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Residues in contact with PHE 208 (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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183G ASP 3.0 11.9 - - - +
185G PRO* 3.6 17.9 - - + -
205G ALA* 3.3 38.8 - - + -
207G SER* 1.3 80.0 - - - +
209G TYR* 1.3 63.6 + - - +
210G PRO 3.3 12.3 - - - -
211G ALA 3.4 22.0 - - - -
213G ILE* 3.8 23.3 - - + -
233G THR* 3.9 7.2 - - + -
240G THR* 3.6 1.5 - - - -
241G PHE* 2.9 67.8 + - + -
242G GLN* 3.6 12.3 - - - -
243G LYS* 4.1 0.7 - - + -
263G HIS* 3.7 12.6 - + + -
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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
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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