Contacts of the strand formed by residues 83 - 89 (chain M) in PDB entry 6MUO
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 TRP 83 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74M MET* 4.6 15.3 - - + -
78M GLN* 3.5 32.5 + - + +
81M LYS* 3.2 36.9 + - + +
82M VAL* 1.3 72.4 - - - +
84M ASP* 1.3 62.0 + - - +
132M TRP* 4.1 18.8 - + - -
151M TYR* 3.8 25.1 - - + -
153M VAL* 4.6 7.2 - - + -
162M PHE* 4.1 15.7 - - + -
163M THR 3.3 9.2 - - - -
164M SER* 3.5 33.2 - - - -
165M SER* 4.6 0.9 - - - -
193M LEU 4.5 0.2 - - - -
194M ARG* 3.3 30.5 - - - +
195M SER 2.9 13.7 + - - +
196M ARG 3.3 16.4 - - - -
197M TYR 4.6 6.7 - - - -
198M LEU* 5.6 11.1 - - + +
201M LEU* 4.0 24.5 - - + -
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Residues in contact with ASP 84 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83M TRP* 1.3 76.9 - - - +
85M VAL* 1.3 85.6 + - - +
86M PHE* 3.4 28.1 - - - -
162M PHE* 3.4 5.2 - - - +
163M THR* 2.5 52.0 + - + +
164M SER 5.2 2.5 - - - +
165M SER* 5.4 2.9 - - - +
190M LYS* 4.5 10.0 - - - +
191M MET 4.7 6.9 - - - +
193M LEU 3.0 15.7 + - - +
194M ARG* 4.8 10.3 - - + +
201M LEU* 5.4 0.2 - - - +
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Residues in contact with VAL 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84M ASP* 1.3 87.6 + - - +
86M PHE* 1.3 80.8 + - - +
160M TYR* 3.7 22.2 - - + -
161M ALA 3.4 2.7 - - - -
162M PHE* 3.8 23.3 - - + -
191M MET* 3.9 22.3 + - - +
193M LEU* 3.4 40.2 + - + +
201M LEU* 3.9 21.5 - - + -
205M VAL* 4.1 5.2 - - + -
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Residues in contact with PHE 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84M ASP* 3.4 25.1 - - - -
85M VAL* 1.3 87.6 - - - +
87M GLN* 1.3 64.1 + - - +
160M TYR* 3.3 4.0 - - - -
161M ALA* 2.8 39.8 + - + +
163M THR* 4.0 20.9 - - + -
172M THR* 4.5 27.1 - - + -
175M LEU* 4.6 17.9 - - + -
176M GLY* 5.0 3.1 - - - -
179M LEU* 6.2 2.0 - - + -
188M ILE* 3.8 27.6 - - + -
189M VAL* 3.2 24.7 - - - +
190M LYS* 4.1 17.9 - - + -
191M MET* 5.8 1.6 - - - -
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Residues in contact with GLN 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86M PHE* 1.3 79.7 - - - +
88M MET* 1.3 74.2 + - - +
159M PRO* 3.3 34.3 - - + +
160M TYR* 3.2 47.0 + - + +
161M ALA* 5.6 0.2 - - - -
187M GLN 4.7 0.2 - - - -
188M ILE* 3.6 4.9 - - - -
189M VAL* 3.6 30.4 + - + +
191M MET* 3.3 24.6 - - + +
209M TYR* 4.1 9.7 - - - -
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Residues in contact with MET 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87M GLN* 1.3 85.8 + - - +
89M SER* 1.3 65.3 + - - +
154M TYR* 3.3 41.5 - - + +
159M PRO* 3.1 27.5 + - + +
161M ALA* 6.4 0.7 - - + -
179M LEU* 3.7 21.5 - - + -
180M THR* 3.6 24.5 - - - +
183M SER* 3.1 31.9 - - - +
185M HIS* 3.4 22.7 - - + +
187M GLN 3.3 15.3 - - - +
188M ILE* 4.4 5.4 - - + -
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Residues in contact with SER 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88M MET* 1.3 76.6 - - - +
90M LYS* 1.3 76.6 + - - +
91M GLY 3.6 1.8 - - - -
185M HIS* 3.2 24.2 - - - +
186M HIS 3.4 2.8 + - - -
187M GLN* 2.8 38.6 + - - +
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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