Contacts of the strand formed by residues 211 - 216 (chain A) in PDB entry 4OA5
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 MET 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A LEU* 3.7 35.0 - - + -
44A GLU* 4.6 7.4 - - + -
47A MET* 3.8 32.1 - - + -
48A LEU* 4.5 6.7 - - + -
134A PHE* 3.9 14.8 - - + -
160A VAL* 3.9 16.6 - - + -
161A ALA 3.5 22.0 - - - +
162A ASP* 3.7 14.8 - - + +
203A THR 3.7 0.2 - - - +
204A ILE* 3.9 0.7 - - - -
205A ILE* 2.8 42.9 + - + +
207A THR* 3.6 7.3 + - - +
210A GLY* 1.3 70.8 - - - +
212A MET* 1.3 64.7 + - - +
213A VAL* 3.5 6.5 + - + +
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Residues in contact with MET 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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159A ILE 4.5 5.8 - - - +
160A VAL* 3.2 12.1 - - - +
161A ALA* 2.8 34.5 + - + +
164A THR* 3.5 24.0 + - + +
190A PHE* 4.2 4.5 - - + -
191A ASN* 3.5 24.0 - - - +
194A LEU* 3.7 34.3 - - + -
202A SER* 4.0 18.8 - - - -
203A THR 3.6 11.2 - - - +
204A ILE* 3.6 11.7 - - + +
211A MET* 1.3 71.8 - - - +
213A VAL* 1.3 68.5 + - - +
214A SER* 4.5 0.2 - - - -
17F PHE* 3.6 26.2 - - + -
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Residues in contact with VAL 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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51A LEU* 3.7 27.1 - - + -
158A LEU* 5.0 4.3 - - + -
159A ILE 3.6 2.5 - - - -
160A VAL* 4.4 10.8 - - + -
202A SER* 3.4 1.9 - - - -
203A THR 2.9 35.5 + - - +
205A ILE* 3.6 31.4 - - + -
211A MET* 3.8 4.7 - - + +
212A MET* 1.3 80.1 - - - +
214A SER* 1.3 62.5 + - - +
50F LEU* 3.6 25.8 - - + +
54F MET* 4.0 19.7 - - + -
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Residues in contact with SER 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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157A GLY 3.7 0.2 - - - +
158A LEU* 3.3 8.9 - - - +
159A ILE* 2.8 47.6 + - - +
194A LEU* 3.7 18.3 - - - +
200A TYR* 3.3 17.7 - - - +
201A LEU 3.4 4.3 - - - -
202A SER* 2.7 26.3 + - - -
212A MET* 4.5 4.9 - - - -
213A VAL* 1.3 76.7 - - - +
215A ILE* 1.3 63.1 + - - +
216A LYS 3.9 0.2 + - - -
50F LEU* 4.7 0.7 - - - -
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Residues in contact with ILE 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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156A GLY* 3.9 21.1 - - - +
157A GLY 3.5 2.7 - - - -
158A LEU* 3.9 7.0 - - + -
200A TYR* 3.2 7.1 - - - -
201A LEU* 2.9 37.8 + - + +
214A SER* 1.3 73.7 - - - +
216A LYS* 1.3 74.3 + - - +
217A LEU* 3.4 11.0 + - + +
50F LEU* 3.5 19.3 - - + -
53F ARG* 3.3 36.6 - - + +
54F MET* 3.5 30.7 - - + +
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Residues in contact with LYS 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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149A ALA 3.4 12.8 - - - +
150A LYS* 3.3 32.6 + - - +
151A MET 5.5 0.2 - - - -
153A ILE* 2.8 36.5 + - + +
154A ARG 3.7 11.6 - - - +
155A LYS 4.0 0.4 - - - +
156A GLY* 2.7 34.1 + - - -
157A GLY 2.9 15.4 + - - +
159A ILE* 4.4 20.6 - - + -
199A LYS 4.0 4.0 - - - +
200A TYR* 4.0 11.7 - - + -
214A SER 3.9 0.6 + - - -
215A ILE* 1.3 72.4 - - - +
217A LEU* 1.3 57.3 + - - +
218A THR* 2.8 34.7 + - - +
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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