Contacts of the strand formed by residues 184 - 187 (chain F) in PDB entry 6GL7
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 THR 184 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F HIS* 4.3 18.8 + - + +
55F ALA 4.9 2.6 - - - +
56F LEU* 3.3 13.0 - - - +
183F GLY* 1.3 70.2 - - - -
185F PHE* 1.3 61.9 + - - +
186F HIS 3.9 12.3 - - - +
187F GLN* 5.0 5.4 - - + +
222F GLU* 4.6 18.7 + - + +
223F VAL 3.7 12.3 - - - +
224F SER* 3.5 16.0 - - - -
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Residues in contact with PHE 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F SER* 3.4 19.4 + - - -
54F HIS* 3.1 27.3 - - - +
56F LEU* 4.0 23.8 - - + -
174F PHE* 3.6 37.5 - + + -
176F ILE* 6.3 0.2 - - + -
183F GLY 3.9 5.6 - - - -
184F THR* 1.3 75.6 - - - +
186F HIS* 1.3 63.0 + - + +
214F PHE* 3.4 40.2 - + - -
223F VAL* 3.5 22.1 + - + -
224F SER* 3.6 28.5 - - - -
225F THR* 3.9 9.2 - - + -
258F PHE* 3.6 12.8 - + - -
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Residues in contact with HIS 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F ARG* 3.7 30.4 + - - -
36F TYR* 5.3 2.8 - + - -
52F TYR 5.8 1.8 - - - -
54F HIS* 3.5 17.0 + - - -
168F PRO* 4.9 20.1 - - + +
172F PRO* 5.5 1.8 - - + +
174F PHE* 3.6 25.5 - + + -
184F THR* 3.9 2.8 - - - +
185F PHE* 1.3 83.1 + - + +
187F GLN* 1.3 95.5 + - - +
188F PHE* 3.8 24.9 + + - -
223F VAL* 3.0 38.2 + - + +
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Residues in contact with GLN 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F TYR* 3.3 54.8 + - + +
54F HIS* 3.5 17.5 + - + -
184F THR* 5.0 4.9 - - + +
186F HIS* 1.3 94.7 + - - +
188F PHE* 1.3 65.6 + - - +
189F ARG* 3.5 10.8 + - + +
221F LEU* 3.6 12.0 - - - +
222F GLU* 4.1 20.3 + - + +
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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