Contacts of the strand formed by residues 200 - 208 (chain B) in PDB entry 5INQ
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 LYS 200 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198B ARG 4.1 0.8 + - - -
199B VAL* 1.3 71.9 - - - +
201B PHE* 1.3 69.5 + - - +
202B LYS* 3.6 19.4 + - + +
223B VAL* 3.1 10.3 - - - +
224B SER* 2.9 49.7 + - - +
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Residues in contact with PHE 201 (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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179B THR* 4.6 17.9 - - + +
181B ILE* 3.6 31.2 - - + -
194B LEU* 3.6 27.6 - - + -
199B VAL* 3.8 3.4 + - - +
200B LYS* 1.3 78.4 + - - +
202B LYS* 1.3 61.6 + - - +
203B SER* 3.3 39.3 - - - -
204B GLN* 3.7 13.2 - - + -
221B VAL* 4.1 7.0 - - + -
222B ASN 4.2 3.8 - - - -
223B VAL* 4.2 3.1 - - - -
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Residues in contact with LYS 202 (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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200B LYS* 4.0 28.6 - - + +
201B PHE* 1.3 79.6 - - - +
203B SER* 1.3 66.3 + - - +
222B ASN* 2.9 22.3 + - + +
223B VAL* 4.2 9.6 - - - +
224B SER* 3.5 13.3 + - - +
229B GLU* 3.4 37.8 + - - +
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Residues in contact with SER 203 (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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201B PHE* 3.3 20.7 - - - -
202B LYS* 1.3 82.7 - - - +
204B GLN* 1.3 63.2 + - - +
205B GLU* 5.9 0.2 - - - +
221B VAL* 3.3 0.7 - - - -
222B ASN* 2.8 58.2 + - - +
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Residues in contact with GLN 204 (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* 3.5 41.7 - - + +
182B THR 4.3 6.8 + - - -
201B PHE* 3.7 11.0 - - + -
203B SER* 1.3 80.3 - - - +
205B GLU* 1.3 62.4 + - - +
206B ILE* 4.1 25.7 - - - +
219B LEU* 4.9 1.3 - - + -
220B CYS 3.4 10.3 - - - +
222B ASN* 5.6 0.2 - - - -
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Residues in contact with GLU 205 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B GLN* 1.3 75.6 - - - +
206B ILE* 1.3 77.2 + - - +
207B ILE* 4.2 11.8 - - + +
218B LEU 3.8 0.7 - - - +
219B LEU* 3.7 0.6 - - - +
220B CYS* 2.8 46.7 + - + +
222B ASN* 5.3 11.3 + - - +
257B LYS* 2.8 35.7 + - - -
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Residues in contact with ILE 206 (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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182B THR 3.9 20.4 - - - +
183B GLY* 4.0 14.8 - - - +
204B GLN* 4.1 14.8 - - - +
205B GLU* 1.3 82.0 - - - +
207B ILE* 1.3 70.5 + - - +
208B PRO* 4.1 6.7 - - + +
217B ASN* 3.7 25.6 - - + +
218B LEU 3.3 5.8 - - - +
219B LEU* 3.6 17.3 - - + -
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Residues in contact with ILE 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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205B GLU* 4.3 13.9 - - + +
206B ILE* 1.3 79.7 - - - +
208B PRO* 1.3 77.7 - - + +
209B PHE* 4.5 0.5 - - - -
217B ASN* 3.4 2.3 - - - +
218B LEU* 2.8 53.0 + - + +
220B CYS* 4.5 2.9 - - - -
253B THR* 4.2 20.6 - - + -
257B LYS* 3.4 50.0 - - + +
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Residues in contact with PRO 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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206B ILE* 4.1 6.9 - - + +
207B ILE* 1.3 100.0 - - + +
209B PHE* 1.3 69.0 + - - +
210B PRO* 3.2 22.7 - - + +
217B ASN* 4.3 7.0 - - + -
253B THR* 4.8 1.4 - - - +
403B GOL 4.6 0.9 + - - -
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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