Contacts of the strand formed by residues 210 - 217 (chain A) in PDB entry 3OF6
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 HIS 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A TRP 4.6 2.0 + - - -
164A VAL* 3.3 8.5 - - - +
165A ASN* 2.8 46.0 + - - +
166A GLY 5.3 2.6 + - - -
208A ARG 3.4 0.6 + - - +
209A ASN* 1.3 73.9 - - - +
211A PHE* 1.3 63.4 + - - +
212A ARG* 3.8 19.3 - - + +
241A GLU* 2.9 51.3 + - + +
242A ALA 4.4 3.6 - - - -
243A TRP* 3.5 47.8 - + + -
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Residues in contact with PHE 211 (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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130A VAL* 5.6 2.3 - - - +
146A LEU* 3.5 26.2 - - + -
162A TRP* 5.2 4.3 - - + -
163A TRP 4.0 1.6 - - - -
164A VAL* 3.8 24.5 - - + +
197A LEU* 4.5 6.1 - - + -
199A VAL* 4.6 10.5 - - + -
203A PHE* 3.5 44.2 - + - -
204A TRP* 3.4 37.5 - + + -
209A ASN* 3.7 25.4 - - + -
210A HIS* 1.3 75.6 - - - +
212A ARG* 1.3 60.6 + - - +
240A ALA 4.2 0.2 - - - +
241A GLU* 3.2 4.5 - - - +
242A ALA* 3.0 42.1 + - + +
244A GLY* 4.1 5.6 - - - -
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Residues in contact with ARG 212 (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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162A TRP* 3.5 10.7 - - - -
163A TRP* 2.7 90.9 + - - +
166A GLY* 5.7 1.8 - - - -
210A HIS* 3.8 13.0 - - + -
211A PHE* 1.3 76.3 - - - +
213A CYS* 1.3 62.0 + - - +
214A GLN* 3.6 21.4 + - - +
237A ILE* 4.8 2.4 - - - +
239A SER* 3.1 35.4 + - - -
240A ALA 3.5 11.0 - - - +
241A GLU* 4.1 16.6 - - + -
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Residues in contact with CYS 213 (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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128A VAL* 3.8 2.6 - - - +
130A VAL* 3.5 13.5 - - + -
148A CYS* 2.0 56.8 - - + -
160A LEU* 3.7 27.4 - - - -
161A SER 3.9 2.5 - - - -
162A TRP* 3.7 12.7 - - + -
212A ARG* 1.3 72.9 - - - +
214A GLN* 1.3 60.6 + - - +
215A VAL* 4.4 0.4 - - - -
239A SER* 3.1 25.5 - - - -
240A ALA 2.9 11.3 + - - -
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Residues in contact with GLN 214 (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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159A GLU 4.4 1.6 + - - -
160A LEU* 3.1 5.7 - - - +
161A SER* 2.7 54.8 + - - +
163A TRP* 2.8 40.5 - - + +
212A ARG* 3.6 20.4 + - - +
213A CYS* 1.3 70.5 - - - +
215A VAL* 1.3 73.0 + - - +
216A GLN* 4.1 8.5 + - - +
237A ILE* 4.1 23.5 - - + +
239A SER* 3.4 15.0 - - - +
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Residues in contact with VAL 215 (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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126A PRO* 3.8 26.0 - - + -
128A VAL* 3.4 26.9 - - + -
148A CYS* 4.4 1.3 - - - -
150A ALA* 4.1 11.0 - - + -
158A VAL* 4.0 21.5 - - + -
159A GLU 3.6 5.4 - - - +
160A LEU* 3.7 25.1 - - + +
193A LEU* 5.5 0.7 - - + -
214A GLN* 1.3 83.1 - - - +
216A GLN* 1.3 61.2 + - - +
217A PHE* 3.1 5.5 + - - +
237A ILE* 4.5 0.9 - - - -
238A VAL* 3.0 33.3 + - - +
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Residues in contact with GLN 216 (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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157A HIS 3.7 0.2 - - - +
158A VAL* 3.0 6.4 - - - -
159A GLU* 2.7 51.5 + - + +
214A GLN* 4.1 10.9 + - - +
215A VAL* 1.3 68.9 - - - +
217A PHE* 1.3 72.9 + - - +
218A TYR* 3.4 35.0 - - + +
235A THR* 3.7 16.1 - - - +
236A GLN 4.0 3.0 - - - +
237A ILE* 3.1 30.8 - - - +
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Residues in contact with PHE 217 (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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123A VAL* 3.8 11.9 - - + -
124A PHE 3.2 26.7 - - - -
125A PRO* 4.0 13.2 - - + -
126A PRO* 3.4 30.5 - - + -
153A PHE* 4.4 0.7 - - + -
154A TYR 3.5 20.0 - - - -
155A PRO 3.9 14.1 - - - -
157A HIS 3.5 12.6 - - - -
158A VAL* 3.8 11.7 - - + -
215A VAL 3.1 2.3 + - - +
216A GLN* 1.3 75.0 - - - +
218A TYR* 1.3 72.8 + - - +
219A GLY* 3.6 16.4 - - - -
233A PRO 4.5 3.6 - - - -
234A VAL 3.8 16.2 - - - -
235A THR* 3.5 6.2 - - - +
236A GLN* 2.8 47.5 + - + +
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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