Contacts of the strand formed by residues 185 - 191 (chain F) in PDB entry 4BQ7
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 GLY 185 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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991B ASP* 4.9 1.1 - - - -
993B THR* 3.3 13.9 - - - -
183F VAL 3.7 0.9 - - - +
184F GLU* 1.3 77.9 - - - +
186F ALA* 1.4 63.2 + - - -
187F TRP* 3.6 4.7 - - - -
199F VAL 3.4 1.4 - - - +
200F THR* 3.3 13.9 - - - -
201F ASN* 2.9 34.1 + - - -
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Residues in contact with ALA 186 (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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991B ASP 3.7 7.9 + - - +
993B THR* 3.0 9.5 + - - -
1007B ASN* 2.7 38.6 + - + +
1008B TRP* 3.6 44.4 - - - +
1009B GLN* 4.1 10.5 - - + +
185F GLY* 1.4 69.5 - - - -
187F TRP* 1.4 57.7 + - - +
198F GLN* 4.1 2.5 - - - +
199F VAL 3.2 8.1 - - - +
200F THR* 4.1 2.2 - - - +
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Residues in contact with TRP 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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993B THR* 4.7 1.8 - - - +
995B VAL* 3.9 30.3 - - + -
1005B ILE* 6.1 0.4 - - + -
1007B ASN* 4.1 6.5 - - - +
183F VAL* 3.2 35.1 - - + -
184F GLU 2.9 24.3 + - - -
185F GLY 3.6 2.9 - - - -
186F ALA* 1.4 87.9 + - - +
188F PRO* 1.3 65.4 - - + +
189F LEU 3.6 1.2 + - - -
198F GLN* 3.7 5.8 - - - +
199F VAL* 2.8 44.0 + - + +
201F ASN* 4.7 0.9 - - - +
309F LEU* 3.8 38.1 - - + -
311F LEU* 3.9 30.3 - - + -
317F PRO* 4.0 16.8 - - + -
320F GLU* 3.8 36.8 - - + -
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Residues in contact with PRO 188 (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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1007B ASN* 4.0 10.1 - - - +
1047B THR* 4.0 22.2 - - + -
187F TRP* 1.3 86.1 - - + +
189F LEU* 1.3 61.0 + - - +
190F ILE 4.4 2.5 - - - +
191F ASP* 4.4 12.6 - - + -
197F VAL 3.6 1.6 - - - +
198F GLN* 3.2 19.3 - - - +
309F LEU* 3.4 49.1 - - + +
310F GLN* 3.7 1.4 - - - -
311F LEU* 3.1 25.8 + - - +
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Residues in contact with LEU 189 (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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163E CYS* 5.0 1.3 - - - -
164E GLY 5.7 0.4 - - - -
165E LEU* 3.9 29.8 - - + +
171F LEU* 4.9 1.6 - - + -
187F TRP 3.6 0.4 + - - +
188F PRO* 1.3 74.2 - - - +
190F ILE* 1.3 61.0 + - - +
197F VAL* 2.8 18.7 + - + +
199F VAL* 3.5 30.1 - - + -
291F LEU* 3.7 30.3 - - + -
293F ILE* 4.8 0.9 - - + -
310F GLN* 3.4 6.5 - - - +
311F LEU* 3.4 33.3 + - + +
312F CYS* 3.1 47.7 + - - +
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Residues in contact with ILE 190 (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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174F PHE* 3.9 17.7 - - + -
188F PRO* 4.4 2.5 - - - +
189F LEU* 1.3 84.7 + - - +
191F ASP* 1.3 63.4 + - - +
192F ASN* 3.2 31.6 - - - +
195F LEU* 3.5 24.7 - - + +
196F SER* 3.4 3.6 - - - -
197F VAL* 2.8 43.8 + - + +
198F GLN* 5.2 0.3 - - - +
293F ILE* 3.8 44.0 - - + -
295F MET* 4.8 1.3 - - - -
310F GLN* 3.8 6.3 - - - +
312F CYS* 3.9 12.1 - - + -
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Residues in contact with ASP 191 (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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1045B ARG* 3.1 47.0 + - - +
1047B THR* 4.0 11.7 - - + +
188F PRO* 4.4 7.6 - - + -
190F ILE* 1.3 75.8 - - - +
192F ASN* 1.3 58.8 + - - +
195F LEU 3.8 2.9 - - - -
196F SER* 4.4 7.2 + - - +
221F LYS* 4.7 0.5 + - - -
307F GLN* 3.1 41.7 + - - +
309F LEU 4.2 8.6 - - - +
310F GLN* 3.1 24.9 + - + -
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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