Contacts of the strand formed by residues 182 - 186 (chain M) in PDB entry 5D4D
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 VAL 182 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174M LEU* 5.1 3.4 - - + -
175M GLU 3.8 9.6 - - - +
176M VAL* 4.9 3.6 - - + +
180M GLY 3.7 3.2 + - - -
181M VAL* 1.3 71.4 - - - +
183M SER* 1.3 65.3 + - - +
192M PRO* 3.3 6.4 - - - +
193M LEU* 2.8 56.0 + - + -
194M VAL* 4.2 6.7 - - + -
220M GLY 3.9 1.8 + - - -
221M LEU* 3.5 41.1 - - + -
307M LEU* 4.0 13.2 - - + -
310M LEU* 5.2 1.8 - - + -
311M PHE* 4.1 17.3 - - + -
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Residues in contact with SER 183 (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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174M LEU* 3.5 4.0 - - - +
175M GLU* 2.9 38.1 + - - +
177M GLU* 2.3 39.0 + - - -
181M VAL* 3.5 2.4 + - - -
182M VAL* 1.3 77.8 - - - +
184M MET* 1.3 60.5 + - - +
190M LYS* 3.3 22.8 - - - -
191M PHE 3.6 10.8 - - - -
192M PRO* 4.8 1.3 - - - -
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Residues in contact with MET 184 (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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172M ILE* 4.3 8.7 - - + -
173M ASP 3.1 12.1 - - - +
174M LEU* 3.8 4.3 - - + -
183M SER* 1.3 75.2 - - - +
185M LYS* 1.3 65.7 + - - +
186M VAL* 3.5 23.8 - - + -
189M ARG 3.6 2.1 - - - +
190M LYS* 3.4 4.8 - - - -
191M PHE* 2.9 64.7 + - + +
193M LEU* 3.5 35.4 - - + +
196M LEU* 3.7 21.5 - - + -
242M LEU* 6.5 0.2 - - + -
261M ILE* 5.0 2.9 - - + -
303M PHE* 4.0 19.3 - - + -
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Residues in contact with LYS 185 (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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171M TRP 3.8 1.2 - - - +
172M ILE* 3.5 3.6 - - - -
173M ASP* 2.9 60.6 + - + +
175M GLU* 5.5 4.7 + - - -
184M MET* 1.3 71.4 - - - +
186M VAL* 1.3 69.1 + - - +
188M LYS* 4.2 35.8 - - + +
189M ARG 3.7 8.5 - - - +
190M LYS* 4.3 21.5 - - + +
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Residues in contact with VAL 186 (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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170M PRO* 4.6 7.2 - - + -
171M TRP 4.1 4.0 - - - +
172M ILE* 3.6 27.8 - - + -
184M MET* 3.5 32.3 + - + -
185M LYS* 1.3 78.2 - - - +
187M ASN* 1.3 82.0 + - + +
188M LYS 3.2 0.9 - - - -
189M ARG* 2.9 33.8 + - - +
191M PHE* 4.8 5.4 - - + -
242M LEU* 4.9 11.5 - - + +
260M LEU* 4.1 20.9 - - + -
261M ILE* 5.2 1.6 - - + -
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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