Contacts of the strand formed by residues 211 - 218 (chain A) in PDB entry 3IAY
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 LEU 211 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A SER* 3.3 7.6 - - - -
199A LYS 2.8 35.0 + - - +
200A GLN* 6.2 2.2 - - - -
209A THR* 4.5 11.2 - - + +
210A LYS* 1.3 79.5 - - - +
212A PRO* 1.3 81.1 - - + +
213A PHE* 3.4 14.7 + - + -
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Residues in contact with PRO 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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163A PRO* 3.9 2.1 - - - +
164A ALA* 3.0 34.5 + - + +
196A VAL* 4.6 13.5 - - + -
197A VAL 3.4 7.2 - - - +
198A SER* 4.7 2.7 - - - +
210A LYS 4.7 0.4 - - - +
211A LEU* 1.3 96.3 - - + +
213A PHE* 1.3 65.8 + - - +
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Residues in contact with PHE 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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161A TYR* 4.3 17.0 - - + -
162A VAL* 3.5 20.9 - - - +
163A PRO* 3.6 13.9 - - + -
164A ALA 3.9 0.4 - - - +
196A VAL* 3.6 4.5 - - - +
197A VAL* 2.7 51.1 + - + +
199A LYS* 3.6 33.2 - - + -
200A GLN* 4.7 1.6 - - - -
201A SER* 4.7 8.1 - - - -
211A LEU* 3.4 28.5 - - + -
212A PRO* 1.3 77.5 - - - +
214A TRP* 1.3 65.0 + - - +
249A TYR* 3.8 35.2 - + - -
574A VAL* 3.9 17.0 - - + -
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Residues in contact with TRP 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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160A LEU 3.4 2.6 - - - +
161A TYR* 3.3 5.8 - - - -
162A VAL* 2.8 43.8 + - + +
164A ALA* 3.4 18.7 - - + +
165A PRO* 3.4 34.5 - - + -
170A ALA* 3.5 23.8 + - + -
176A ILE* 3.9 15.0 - - + +
179A PHE* 3.8 16.2 - + - -
194A ILE* 3.8 27.6 - - + -
195A GLU 3.7 2.0 - - - -
196A VAL* 3.9 25.6 - - + +
213A PHE* 1.3 79.0 - - - +
215A LYS* 1.3 62.2 + - - +
216A ILE* 3.6 6.4 + - + +
241A TRP* 3.3 38.6 - + - -
242A PHE* 3.9 13.5 - + - -
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Residues in contact with LYS 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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159A TYR* 3.5 53.4 + - + -
160A LEU 3.6 3.6 - - - -
161A TYR* 3.6 33.0 + - + +
193A SER 3.8 1.0 - - - +
194A ILE* 3.3 2.9 - - - -
195A GLU* 2.8 52.9 + - + +
197A VAL* 4.5 9.0 - - + -
213A PHE 3.9 1.4 + - - -
214A TRP* 1.3 70.9 - - - +
216A ILE* 1.3 61.4 + - - +
217A TYR* 3.0 35.1 + - + +
261A ASP* 5.3 0.8 + - - -
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Residues in contact with ILE 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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159A TYR* 3.1 22.2 - - - -
160A LEU* 2.9 25.7 + - + +
162A VAL* 4.2 12.8 - - + -
179A PHE* 4.8 1.8 - - + -
183A LEU* 4.5 7.2 - - + -
191A ILE* 4.0 22.9 - - + -
193A SER 3.6 5.6 - - - +
194A ILE* 3.8 25.4 - - + -
214A TRP* 3.8 13.0 - - + +
215A LYS* 1.3 75.1 - - - +
217A TYR* 1.3 62.4 + - - +
218A VAL* 4.0 3.8 + - - +
227A LEU* 4.0 19.0 - - + +
231A PHE* 3.8 35.4 - - + -
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Residues in contact with TYR 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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157A LYS* 4.0 33.7 - - + -
158A ASN 3.4 2.9 - - - +
159A TYR* 4.0 13.5 - + + -
191A ILE* 3.6 7.1 - - - +
192A ASP* 2.8 41.9 + - + +
193A SER* 3.0 31.0 + - - +
195A GLU* 2.5 41.2 + - + -
215A LYS* 3.0 41.7 + - + -
216A ILE* 1.3 75.0 - - - +
218A VAL* 1.3 56.0 + - - +
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Residues in contact with VAL 218 (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 LYS* 3.3 26.2 - - - +
158A ASN* 3.0 15.7 + - + +
190A ALA 3.1 13.2 - - - +
191A ILE* 4.6 4.0 - - + -
192A ASP 4.7 0.2 - - - -
216A ILE 4.5 1.3 - - - +
217A TYR* 1.3 78.0 - - - +
219A THR* 1.3 62.9 + - - +
220A TYR 3.2 26.9 - - - +
221A PRO* 4.2 0.4 - - - +
223A MET* 4.5 6.5 - - + -
224A VAL* 3.5 36.1 - - + +
227A LEU* 3.9 27.6 - - + -
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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