Contacts of the strand formed by residues 254 - 258 (chain E) in PDB entry 5MNI
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 ALA 254 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E CYS* 3.6 12.8 - - + +
165E VAL* 5.4 0.9 - - + -
188E LYS* 3.7 4.9 - - - +
189E ILE* 2.7 45.8 + - + +
245E ILE* 5.1 2.0 - - + +
248E ILE* 3.9 9.8 - - + +
249E THR* 3.6 36.7 - - - +
252E GLY 3.5 2.0 - - - -
253E LEU* 1.3 77.4 - - - +
255E TYR* 1.3 56.3 + - - +
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Residues in contact with TYR 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E LYS* 4.1 38.5 + - + -
160E GLY 5.2 0.7 - - - -
161E ALA* 3.3 35.9 - - + -
163E CYS 2.9 8.1 + - - +
164E THR* 3.3 7.0 - - - +
165E VAL 3.0 22.7 + - - -
186E ASN* 3.4 33.2 + - + +
187E ASP 3.3 3.8 - - - +
188E LYS* 3.6 34.7 - - + +
189E ILE* 3.8 7.0 - - - +
252E GLY 4.4 8.3 - - - -
253E LEU* 4.4 4.0 - - - -
254E ALA* 1.3 80.3 - - - +
256E ALA* 1.3 60.0 + - - +
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Residues in contact with ALA 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159E LYS* 3.4 25.3 - - - +
164E THR* 4.3 1.6 - - - -
165E VAL 3.4 5.4 - - - +
167E CYS* 3.7 19.3 - - - -
181E MET* 3.8 10.3 - - - -
183E VAL* 3.7 24.5 - - + -
187E ASP* 2.6 25.7 + - + +
189E ILE* 3.9 2.0 - - + +
255E TYR* 1.3 75.5 - - - +
257E HIS* 1.3 61.7 + - - +
258E PRO* 4.0 1.9 - - - +
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Residues in contact with HIS 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E GLN* 4.8 0.4 - - - -
151E ARG* 4.2 3.4 - - + -
152E MET* 3.7 40.2 - - + +
155E ASP* 3.0 30.8 + - + +
164E THR* 3.5 19.3 - - + -
165E VAL 2.9 13.0 + - - +
166E ALA* 3.4 10.9 - - + -
167E CYS* 2.9 27.8 + - - -
256E ALA* 1.3 75.4 - - - +
258E PRO* 1.3 83.6 + - - +
259E PHE* 3.2 1.8 + - - -
261E LEU* 3.8 21.3 - - + +
262E SER* 3.1 28.5 + - - -
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Residues in contact with PRO 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E ASP* 4.6 1.3 - - - +
167E CYS* 3.7 13.0 - - - +
187E ASP* 3.9 26.2 - - - +
256E ALA 4.0 2.2 - - - +
257E HIS* 1.3 87.9 - - - +
259E PHE* 1.3 67.7 + - - +
260E PRO* 3.3 9.9 - - + -
261E LEU* 3.0 45.1 + - + +
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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