Contacts of the helix formed by residues 185 - 195 (chain Y) in PDB entry 5MG3
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 ASN 185 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394C ARG* 2.9 53.9 + - - +
395C GLU* 4.9 1.6 - - - +
397C LEU* 3.9 19.4 - - + +
398C GLY* 4.6 8.6 - - - +
175Y GLY 5.1 1.3 - - - +
176Y GLU* 4.9 2.6 - - - +
178Y ILE* 5.1 2.0 - - - +
184Y GLY* 1.4 76.4 - - - +
186Y GLY* 1.4 75.5 + - - +
187Y ILE 3.7 0.5 + - - -
188Y SER* 3.8 9.6 + - - -
189Y ILE* 3.7 19.1 + - - -
435Y LYS 4.7 14.6 + - - +
436Y ALA* 5.5 9.2 - - + +
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Residues in contact with GLY 186 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394C ARG* 4.4 17.7 + - - +
85Y TYR* 3.9 10.8 + - - -
185Y ASN* 1.4 90.0 + - - +
187Y ILE* 1.3 60.3 + - - +
189Y ILE* 3.3 14.4 - - - +
190Y ILE* 4.1 1.6 - - - +
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Residues in contact with ILE 187 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85Y TYR* 3.9 29.6 + - + -
86Y ILE* 4.3 18.2 - - + -
89Y SER* 4.7 7.6 - - - +
186Y GLY* 1.3 68.2 - - - -
188Y SER* 1.3 62.3 + - - +
190Y ILE* 2.8 24.6 + - - +
191Y ILE* 3.3 26.5 + - + -
278Y ILE* 6.1 3.6 - - + -
279Y PHE* 5.6 13.2 - - + -
438Y LEU* 4.2 24.2 - - + -
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Residues in contact with SER 188 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184Y GLY* 6.1 0.2 - - - -
185Y ASN 3.9 9.9 + - - -
187Y ILE* 1.3 79.6 - - - +
189Y ILE* 1.4 57.4 - - - +
191Y ILE* 3.5 4.9 + - - +
192Y PHE* 3.0 31.0 + - - +
412Y VAL* 3.9 22.2 - - - +
415Y ASP* 4.2 9.1 + - - -
416Y PHE* 4.2 14.0 - - - -
438Y LEU* 3.7 31.0 - - - +
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Residues in contact with ILE 189 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Y PHE 5.5 0.7 - - - +
26Y VAL* 4.4 15.9 - - + +
29Y ALA* 5.6 7.0 - - + -
30Y LEU* 5.2 0.4 - - + +
174Y LEU 4.6 3.6 - - - +
175Y GLY* 3.6 34.5 - - - +
178Y ILE* 4.3 15.9 - - + -
183Y ILE 3.9 20.4 - - - +
184Y GLY 4.6 5.4 - - - -
185Y ASN* 3.7 15.1 + - - +
186Y GLY 3.3 20.0 - - - +
188Y SER* 1.4 77.3 - - - +
190Y ILE* 1.3 70.7 + - + +
192Y PHE* 3.5 9.5 - - + +
193Y ALA* 3.2 22.1 + - + +
416Y PHE* 4.0 15.0 - - + -
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Residues in contact with ILE 190 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394C ARG* 6.2 2.2 - - - +
82Y ILE* 4.9 9.8 - - + +
85Y TYR* 3.5 54.5 - - + +
171Y LEU* 4.0 27.2 - - + +
172Y MET* 4.2 17.5 - - + +
174Y LEU* 6.0 0.2 - - + -
175Y GLY* 3.7 28.3 - - - -
186Y GLY 4.1 6.5 - - - +
187Y ILE 2.8 9.2 + - - +
189Y ILE* 1.3 79.3 - - + +
191Y ILE* 1.4 51.8 + - - +
193Y ALA* 3.2 9.3 + - + +
194Y GLY* 2.8 31.9 + - - -
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Residues in contact with ILE 191 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82Y ILE* 4.0 25.8 - - + -
85Y TYR* 4.8 6.7 - - + -
86Y ILE* 4.4 13.0 - - + -
187Y ILE* 3.3 32.7 + - + +
188Y SER* 3.8 9.0 - - - +
190Y ILE* 1.4 73.7 - - + +
192Y PHE* 1.3 64.3 + - - +
194Y GLY* 3.0 14.0 + - - +
195Y ILE* 3.3 30.2 + - + +
408Y ILE* 4.2 41.3 - - + +
409Y VAL* 4.0 8.5 - - - +
412Y VAL* 4.4 5.4 - - + -
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Residues in contact with PHE 192 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485E MET* 3.6 25.1 - - + -
26Y VAL* 3.8 19.1 - - + -
27Y ILE* 5.0 7.0 - - + -
30Y LEU* 3.4 59.0 - - + +
188Y SER 3.0 19.3 + - - +
189Y ILE* 3.5 8.5 - - + +
191Y ILE* 1.3 76.8 - - - +
193Y ALA* 1.3 58.6 + - - +
196Y VAL* 3.6 11.1 - - - +
409Y VAL* 4.3 5.2 - - + +
412Y VAL* 3.9 23.0 - - + +
413Y ILE* 4.4 10.1 - - + -
416Y PHE* 3.7 50.3 - + + -
420Y VAL* 6.4 0.4 - - + -
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Residues in contact with ALA 193 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Y ALA* 4.3 20.2 - - + +
30Y LEU* 3.6 20.0 - - + +
33Y PHE* 3.1 25.7 - - + +
171Y LEU* 4.5 15.5 - - + -
174Y LEU* 5.4 2.2 - - + -
189Y ILE* 3.2 10.7 + - + +
190Y ILE* 3.3 11.4 - - + +
192Y PHE* 1.3 78.6 - - - +
194Y GLY* 1.3 57.0 + - - +
196Y VAL* 3.1 11.8 - - - +
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Residues in contact with GLY 194 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Y PHE* 3.2 31.7 - - - -
69Y GLY* 4.9 4.7 + - - -
81Y GLY* 5.1 2.6 - - - -
82Y ILE* 4.0 20.5 - - - +
171Y LEU* 5.4 4.7 - - - -
190Y ILE* 2.8 18.6 + - - -
191Y ILE 3.0 6.5 + - - -
193Y ALA* 1.3 70.0 - - - +
195Y ILE* 1.4 56.4 + - - -
196Y VAL 3.3 4.7 - - - -
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Residues in contact with ILE 195 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66Y MET 4.7 3.4 - - - +
69Y GLY* 5.5 5.2 - - - +
82Y ILE* 3.6 33.2 - - + -
191Y ILE* 3.3 16.4 + - + +
194Y GLY* 1.4 73.4 - - - +
196Y VAL* 1.3 55.7 + - - +
197Y ALA* 2.9 14.3 + - - +
198Y GLY 4.0 5.9 + - - -
199Y LEU* 6.1 0.3 - - - +
399Y PHE* 4.6 7.8 - - - -
401Y PHE* 4.1 26.1 - - + -
405Y SER* 3.2 35.9 - - - +
406Y LEU* 4.7 3.1 - - + -
408Y ILE* 3.6 20.2 - - + -
409Y VAL* 3.9 25.3 - - + +
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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