Contacts of the strand formed by residues 174 - 177 (chain B) in PDB entry 5MR5
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 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B VAL* 4.0 29.4 - - + -
171B GLU* 3.7 22.0 - - - +
173B GLU* 1.3 76.2 - - - +
175B SER* 1.3 72.0 + - - +
176B PHE* 4.5 5.7 - - + -
185B THR* 3.4 0.3 - - - -
186B VAL* 2.9 40.2 + - + +
189B LEU* 4.2 21.3 - - + -
169D ASN* 4.1 4.3 - - - +
175D LYS* 3.8 26.9 - - + +
179D SER* 3.6 5.6 - - - -
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Residues in contact with SER 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B VAL* 1.3 76.9 - - - +
176B PHE* 1.3 71.7 + - - +
184B HIS 3.1 10.1 - - - -
185B THR* 2.7 22.3 + - - -
169D ASN* 3.3 21.2 + - - +
175D LYS 5.5 0.2 + - - -
178D ARG* 3.4 7.8 + - - -
179D SER* 2.7 31.4 + - - -
182D ILE* 3.7 28.2 - - - +
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Residues in contact with PHE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B VAL* 3.6 28.0 - - + -
119B TYR* 3.6 42.6 - + + -
121B SER* 3.8 16.8 - - - -
123B GLU* 3.5 31.0 - - + +
125B VAL* 4.7 5.8 - - + -
174B VAL* 4.5 6.1 - - + -
175B SER* 1.3 85.2 - - - +
177B LEU* 1.3 58.6 + - - +
183B TYR* 3.3 8.3 - - - -
184B HIS* 2.8 58.5 + + + -
186B VAL* 3.7 21.5 - - + -
189B LEU* 5.8 2.2 - - + -
169D ASN* 4.8 0.7 - - - +
178D ARG* 4.2 3.1 - - - +
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B SER* 2.8 20.0 + - - -
123B GLU* 2.9 7.4 + - - +
176B PHE* 1.3 72.7 - - - +
178B ASP* 1.3 68.5 + - - +
181B SER* 3.6 33.4 - - - +
182B ARG 3.6 7.6 - - - -
183B TYR* 3.8 35.8 - - + +
178D ARG* 4.9 0.2 - - - +
231D GLU* 5.9 0.4 - - + -
232D ARG* 3.2 69.4 + - + +
235D GLN* 4.2 12.1 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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