Contacts of the strand formed by residues 184 - 190 (chain A) in PDB entry 2FY5
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 GLU 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A LEU* 5.6 0.3 - - - +
128A LYS* 4.0 20.8 + - - +
132A ASP* 5.3 0.9 - - - +
180A MET* 2.8 41.0 - - + +
181A PRO* 3.7 13.7 - - + +
182A GLU* 3.3 16.2 + - - +
183A PRO* 1.3 73.2 - - - +
185A HIS* 1.3 60.3 + - - +
198A ASP* 3.6 2.6 - - - +
199A VAL* 2.9 26.4 + - + -
200A VAL* 3.3 41.0 + - + +
203A PHE* 5.1 4.3 - - - -
267A ILE* 4.4 10.0 - - + +
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Residues in contact with HIS 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PRO* 5.4 1.5 - - + +
183A PRO* 3.4 13.5 + - - +
184A GLU* 1.3 74.3 - - - +
186A VAL* 1.3 65.5 + - - +
187A ILE* 4.1 8.5 - - + -
196A VAL* 3.4 23.1 - - + -
197A LEU 3.3 16.2 - - - +
198A ASP* 3.4 17.7 + - - +
199A VAL* 4.1 3.5 - - - +
262A MET* 3.2 44.3 + - + +
265A ARG* 3.8 33.2 + - - -
266A CYS* 3.3 12.2 - - + +
267A ILE* 2.9 28.8 + - - +
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Residues in contact with VAL 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 4.4 17.7 - - + -
124A VAL* 5.7 2.5 - - + -
125A LEU* 5.4 1.3 - - + -
185A HIS* 1.3 77.0 - - - +
187A ILE* 1.3 62.0 + - - +
188A VAL* 4.1 8.7 - - + -
196A VAL* 3.8 0.9 - - - -
197A LEU* 2.8 61.9 + - + +
199A VAL* 3.9 16.8 - - + -
266A CYS* 4.3 0.2 - - - -
267A ILE* 4.0 23.6 - - + +
268A CYS* 3.7 23.1 - - - +
270A VAL* 4.6 6.1 - - + -
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Residues in contact with ILE 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A HIS* 4.1 11.4 - - + -
186A VAL* 1.3 73.2 - - - +
188A VAL* 1.3 61.7 + - - +
194A PHE* 4.0 31.6 - - + -
195A PHE 3.1 19.5 - - - +
196A VAL* 4.0 20.2 - - + -
262A MET 4.3 9.6 - - - +
263A ILE* 4.2 9.9 - - + -
266A CYS* 3.6 16.8 - - + -
268A CYS 3.2 6.3 + - - -
269A LEU* 2.9 33.1 - - + +
270A VAL 2.9 22.9 + - - -
365A LEU* 4.0 14.6 - - + -
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 4.9 0.2 - - + -
186A VAL* 4.1 6.3 - - + -
187A ILE* 1.3 76.0 - - - +
189A ALA* 1.3 62.7 + - - +
193A GLN 3.5 2.3 - - - +
195A PHE* 3.0 34.7 + - - +
197A LEU* 3.8 33.9 - - + -
215A LEU* 4.0 9.2 - - + -
218A ILE* 3.8 31.0 - - + -
270A VAL* 3.4 21.8 - - + +
272A LEU* 3.9 26.9 - - + -
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Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ILE* 3.9 1.8 + - + -
188A VAL* 1.3 71.9 - - - +
190A CYS* 1.3 60.0 + - - +
193A GLN 3.1 5.6 - - - +
194A PHE* 3.6 32.3 - - + -
269A LEU* 5.4 3.4 - - + -
270A VAL 3.1 7.5 + - - +
271A CYS* 3.5 10.0 - - - -
272A LEU* 2.9 26.9 + - - +
301A ASN* 3.1 27.9 + - - +
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Residues in contact with CYS 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A VAL* 3.9 1.0 + - + -
189A ALA* 1.3 73.9 - - - +
191A CYS* 1.3 88.9 + - - +
192A ASN 3.1 0.4 - - - -
193A GLN* 3.0 24.2 + - - +
218A ILE* 4.6 10.3 - - + -
219A VAL* 4.4 18.4 - - - -
222A ALA* 3.5 18.3 - - + +
272A LEU* 4.2 34.3 - - + -
301A ASN* 3.3 4.4 + - - +
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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