Contacts of the strand formed by residues 206 - 213 (chain B) in PDB entry 4GAW
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 VAL 206 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B LEU* 3.9 6.3 - - - -
123B ARG* 3.9 13.9 - - + +
124B LEU 4.0 12.8 - - - +
125B PRO* 3.2 34.8 - - + -
126B SER 5.6 0.2 - - - +
129B ALA* 5.6 0.4 - - + -
202B VAL* 3.4 2.5 - - - +
203B CYS 3.0 29.1 + - - +
204B LYS 3.1 6.8 - - - +
205B ASP* 1.3 85.6 - - - +
207B ALA* 1.3 66.6 + - - +
208B GLN* 3.4 14.9 + - + +
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Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 3.5 32.3 - - + -
122B LEU* 3.6 13.2 - - + +
123B ARG 4.0 9.3 + - - +
124B LEU* 5.6 2.7 - - + -
125B PRO* 3.0 30.1 - - + +
200B PRO* 4.5 11.2 - - + -
201B LEU 3.7 6.3 - - - -
202B VAL* 4.7 0.7 - - - +
206B VAL* 1.3 70.2 - - - +
208B GLN* 1.3 60.6 + - - +
209B GLY 3.6 1.3 - - - +
210B ILE* 5.0 0.7 - - + -
227B VAL* 3.8 16.3 - - + +
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Residues in contact with GLN 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PRO* 3.2 33.2 - - - +
129B ALA* 3.3 27.4 + - - +
130B GLN* 5.1 0.8 + - - +
131B VAL* 4.4 23.3 - - + +
181B ILE* 4.0 8.9 - - + +
201B LEU* 2.8 16.7 + - + +
203B CYS* 4.0 26.7 - - + +
206B VAL* 3.4 15.0 + - + +
207B ALA* 1.3 73.3 - - - +
209B GLY* 1.3 58.7 + - - +
225B ILE 3.7 1.0 - - - +
226B LYS* 3.8 6.4 - - - +
227B VAL* 3.0 23.2 + - - -
228B SER* 4.6 11.7 - - - +
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Residues in contact with GLY 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B ILE* 5.3 0.7 - - - -
200B PRO* 3.2 3.8 - - - +
201B LEU* 2.8 40.9 + - - +
208B GLN* 1.3 83.9 + - - +
210B ILE* 1.3 74.9 + - - +
224B TYR* 4.0 6.7 - - - -
225B ILE 2.9 11.9 - - - -
227B VAL* 3.5 2.3 - - - +
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Residues in contact with ILE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 4.7 12.3 - - + -
55B LEU* 3.7 33.9 - - + +
56B THR* 3.6 25.4 - - - +
57B ALA* 4.1 4.9 - - + +
103B ASP 4.2 7.6 - - - +
104B ILE* 4.9 2.5 - - + -
198B GLY* 3.4 28.9 - - - +
199B GLY 3.4 2.2 - - - +
200B PRO* 4.8 3.6 - - + -
207B ALA* 5.0 0.7 - - + -
209B GLY* 1.3 92.0 - - - +
211B LEU* 1.3 69.7 + - - +
212B SER* 3.2 0.9 + - - -
224B TYR* 3.1 5.6 - - - +
225B ILE* 2.9 40.3 + - + +
227B VAL* 3.7 11.9 - - + -
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ALA* 4.1 2.4 - - - +
139B VAL* 4.8 5.2 - - + -
192B GLY* 3.9 29.4 - - - +
193B PHE 4.5 1.3 - - - +
196B ASP* 4.0 24.5 - - + +
197B SER* 3.1 22.5 - - - +
198B GLY* 3.1 19.8 - - - -
199B GLY 2.9 16.9 + - - +
210B ILE* 1.3 74.2 - - - +
212B SER* 1.3 68.7 + - - +
213B TYR 3.6 22.9 - - - +
214B GLY* 5.6 0.2 - - - -
222B GLY* 4.7 2.7 - - - -
223B VAL 3.8 0.7 - - - +
224B TYR* 3.4 45.1 - - + +
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Residues in contact with SER 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ALA* 5.3 0.2 - - - -
59B HIS* 3.2 22.5 + - - -
100B PHE* 3.8 6.8 + - - +
103B ASP* 2.7 37.3 + - - +
197B SER* 3.7 7.8 + - - -
210B ILE 3.2 4.2 + - - -
211B LEU* 1.3 76.9 - - - +
213B TYR* 1.3 80.7 + - - +
223B VAL* 2.9 21.8 + - - -
225B ILE* 4.7 9.9 - - - -
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Residues in contact with TYR 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ASN 5.1 4.5 - - - -
100B PHE* 3.9 32.8 - + + -
171B PHE* 3.0 43.8 - + + +
174B ASN* 3.1 32.1 + - + +
175B TYR* 4.3 0.9 - - - -
180B GLU* 4.1 2.9 + - - -
197B SER* 5.5 0.4 - - - -
211B LEU* 3.6 8.9 - - - +
212B SER* 1.3 95.6 - - - +
214B GLY* 1.3 62.4 + - - +
222B GLY* 3.5 2.1 - - - -
223B VAL* 2.9 56.1 + - + +
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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