Contacts of the strand formed by residues 210 - 220 (chain A) in PDB entry 1YA8
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 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ARG* 4.0 9.7 - - - +
133A LEU 3.5 8.3 - - - -
135A VAL* 3.7 13.7 - - - -
164A VAL* 4.0 7.1 - - - +
205A ILE* 2.8 17.2 + - - -
206A ALA* 3.4 18.4 - - - +
208A PHE 3.4 1.8 - - - -
209A GLY* 1.3 82.1 - - - +
211A ASN* 1.3 60.8 + - - -
212A PRO* 3.5 4.2 - - - +
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Residues in contact with ASN 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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132A ARG* 3.8 30.0 + - + +
133A LEU 2.9 17.9 + - - +
135A VAL* 3.6 7.5 - - - +
210A GLY* 1.3 72.0 - - - -
212A PRO* 1.3 62.6 - - - +
213A GLY* 2.6 36.3 + - - -
214A SER* 2.9 38.1 + - - +
215A VAL* 4.2 0.2 - - - +
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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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132A ARG* 5.4 3.1 - - + +
202A GLN* 3.9 34.4 - - + +
205A ILE* 3.9 19.0 - - + -
206A ALA* 4.3 13.7 - - + -
210A GLY 3.5 10.7 - - - +
211A ASN* 1.3 85.1 - - - +
213A GLY* 1.3 55.5 + - - +
214A SER 3.2 1.9 + - - -
215A VAL* 4.0 12.1 - - + +
239A LEU 5.6 0.5 - - - +
241A HIS* 3.2 16.6 + - - -
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Residues in contact with GLY 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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211A ASN* 2.6 23.3 + - - -
212A PRO* 1.3 73.9 - - - +
214A SER* 1.3 57.1 + - - +
241A HIS* 3.1 27.7 + - - +
242A ARG* 5.6 0.9 + - - -
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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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134A PRO* 3.9 9.9 - - - +
135A VAL 3.1 24.3 + - - +
211A ASN* 2.9 26.5 + - - +
213A GLY* 1.3 80.4 - - - +
215A VAL* 1.3 58.4 + - - +
216A THR* 3.9 1.2 + - - -
241A HIS* 3.5 6.7 - - - -
242A ARG* 3.8 15.8 + - - +
504A ALA 3.3 20.4 + - - +
505A ARG* 4.2 4.0 + - - -
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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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135A VAL* 3.3 20.6 - - + +
137A VAL* 3.9 26.0 - - + -
198A LEU* 4.5 7.0 - - + -
201A VAL* 3.9 19.5 - - + -
202A GLN* 5.9 1.3 - - - +
211A ASN 4.2 4.3 - - - +
212A PRO* 4.0 16.8 - - + +
214A SER* 1.3 74.1 - - - +
216A THR* 1.3 65.8 + - - +
239A LEU 4.0 22.2 - - - +
240A PHE* 3.5 7.1 - - + +
241A HIS* 2.7 41.9 + - + -
242A ARG 3.6 1.4 + - - -
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Residues in contact with THR 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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135A VAL 2.6 14.3 + - - -
136A MET* 3.1 12.4 - - + +
137A VAL* 2.7 32.1 + - - +
214A SER 4.6 0.2 + - - -
215A VAL* 1.3 72.7 - - - +
217A ILE* 1.3 64.5 + - - +
218A PHE* 5.1 0.4 - - + -
242A ARG* 3.3 33.0 - - + +
243A ALA 4.5 1.3 - - - +
244A ILE* 4.6 19.3 - - + -
503A PHE* 4.7 0.9 - - + -
504A ALA* 3.2 41.5 + - + +
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Residues in contact with ILE 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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137A VAL* 3.5 11.4 - - + +
139A ILE* 5.2 6.1 - - + -
198A LEU* 3.6 33.2 - - + -
215A VAL* 4.5 1.1 - - + -
216A THR* 1.3 76.0 - - - +
218A PHE* 1.3 62.5 + - - +
227A VAL* 3.8 27.5 - - + +
230A LEU* 3.9 30.3 - - + -
240A PHE* 3.8 31.9 - - + -
242A ARG 3.2 15.2 + - - +
243A ALA* 3.2 6.9 - - + +
244A ILE 3.0 21.1 + - - +
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Residues in contact with PHE 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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136A MET* 3.6 45.5 - - + -
137A VAL 2.9 29.3 + - - +
138A TRP* 3.3 43.8 - + + -
139A ILE* 2.9 23.6 + - - +
157A LEU* 4.4 9.9 - - + -
165A VAL* 5.2 2.5 - - + -
216A THR* 4.3 1.1 - - + -
217A ILE* 1.3 77.8 - - - +
219A GLY* 1.3 59.3 + - - +
227A VAL* 3.8 6.7 - - - +
244A ILE* 3.4 28.7 - - + -
246A GLU* 3.7 10.3 - - - +
475A VAL* 4.1 19.3 - - + -
476A PHE* 4.1 8.1 - + - -
500A TRP* 3.9 10.8 - + - -
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Residues in contact with GLY 219 (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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138A TRP* 3.5 11.3 - - - -
139A ILE 3.2 16.6 - - - -
218A PHE* 1.3 77.4 - - - +
220A GLU* 1.3 58.5 + - - -
223A GLY 3.9 8.1 - - - -
224A GLY* 3.3 12.7 - - - -
227A VAL* 3.7 2.6 - - - +
244A ILE 3.4 4.2 + - - -
245A SER* 3.8 0.7 - - - -
246A GLU* 2.9 26.0 + - - +
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Residues in contact with GLU 220 (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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101A PHE* 3.7 19.8 - - - -
138A TRP* 3.4 23.5 - - + -
139A ILE 3.7 3.0 + - - -
141A GLY* 3.3 14.1 + - - +
152A TYR* 5.3 0.7 + - - -
219A GLY* 1.3 73.7 - - - -
221A SER* 1.3 76.6 + - - +
222A ALA 3.2 0.2 + - - -
223A GLY 2.9 14.0 + - - -
224A GLY 3.4 2.4 - - - +
246A GLU* 3.2 16.5 - - + +
247A SER* 4.2 2.1 - - - -
468A HIS* 3.1 34.2 + - - -
469A GLY* 3.7 9.4 + - - -
471A GLU* 3.2 24.7 - - - +
472A LEU* 3.9 14.6 - - + +
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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