Contacts of the strand formed by residues 197 - 204 (chain B) in PDB entry 5N9G
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 PHE 197 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B TYR* 4.4 1.0 - - - -
193B ASN 2.8 25.1 + - - +
194B PRO* 3.6 7.9 - - - +
196B ARG* 1.3 75.8 - - + +
198B ALA* 1.3 59.6 + - + +
199B ALA* 3.2 44.6 + - + +
201B ILE* 5.0 9.9 - - + -
212B LEU* 4.4 9.6 - - + -
214B PHE* 4.0 17.9 - + - -
11D T 3.2 36.1 - + + -
12D A 3.3 70.9 - + - +
18E A 3.7 12.8 - + - -
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Residues in contact with ALA 198 (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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180B LEU* 3.3 19.4 - - - +
192B TYR* 4.1 5.6 + - - -
194B PRO* 4.3 12.4 + - - +
197B PHE* 1.3 76.4 - - + +
199B ALA* 1.3 55.6 + - - +
214B PHE* 4.9 12.0 - - + -
215B SER* 5.0 3.5 + - - -
11D T 5.5 0.2 + - - -
18E A 5.6 3.8 - - + +
19E G 3.5 41.3 - - + +
20E G 5.8 3.4 - - - -
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Residues in contact with ALA 199 (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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180B LEU* 4.0 1.3 - - - -
191B GLU 4.1 2.6 - - - +
192B TYR* 3.7 16.4 - - - -
197B PHE* 3.2 35.5 + - + +
198B ALA* 1.3 78.1 - - - +
200B VAL* 1.3 65.7 + - - +
201B ILE* 3.8 5.5 + - - +
212B LEU* 4.6 2.2 - - + -
213B ILE 3.3 15.7 - - - +
214B PHE* 3.7 26.7 - - + -
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Residues in contact with VAL 200 (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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180B LEU* 3.7 45.0 - - + +
183B ILE* 4.0 15.5 - - + -
184B ALA 4.6 1.1 - - - +
190B ALA* 3.8 28.5 - - + -
191B GLU 3.5 5.4 - - - +
192B TYR* 3.9 15.3 - - + -
199B ALA* 1.3 71.0 - - - +
201B ILE* 1.3 64.6 + - - +
202B MET* 3.8 7.4 + - + +
211B ALA 3.5 1.6 - - - +
212B LEU* 3.4 6.1 - - - -
213B ILE* 2.8 45.5 + - + +
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Residues in contact with ILE 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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189B ASN 3.5 1.7 - - - +
190B ALA* 3.3 3.1 - - - -
191B GLU* 2.8 65.8 + - + +
197B PHE* 5.0 6.5 - - + -
199B ALA 4.4 6.3 - - - +
200B VAL* 1.3 71.5 - - - +
202B MET* 1.4 57.1 + - - +
203B ARG* 3.9 22.9 + - - +
210B THR* 3.6 26.0 - - + -
211B ALA 3.5 3.6 - - - +
212B LEU* 3.7 18.2 - - + -
334C ARG* 4.3 1.3 - - - +
12D A 3.7 30.3 - - - +
13D T 3.9 11.0 - - - +
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Residues in contact with MET 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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183B ILE* 3.7 29.6 - - + -
187B ALA* 3.9 8.1 - - + -
189B ASN* 3.2 38.4 - - - +
190B ALA* 4.3 4.3 - - + -
200B VAL* 3.8 2.2 + - + -
201B ILE* 1.4 71.5 - - - +
203B ARG* 1.3 65.8 + - - +
210B THR* 3.4 4.3 - - - +
211B ALA 2.7 39.3 + - - +
213B ILE* 3.8 24.2 - - + -
237B TYR* 3.5 27.7 - - + +
240B VAL* 3.8 27.1 - - + -
241B VAL* 5.2 1.3 - - + -
244B LEU* 4.8 0.4 - - + -
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Residues in contact with ARG 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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392A TYR* 3.9 2.6 - - - -
189B ASN* 2.8 41.7 + - - +
191B GLU* 6.2 0.4 - - - +
201B ILE* 3.9 18.4 + - - +
202B MET* 1.3 79.9 - - - +
204B ILE* 1.3 62.9 + - - +
205B ARG* 5.5 0.5 + - - -
209B THR 3.6 8.5 - - - +
210B THR* 3.2 17.4 + - + +
237B TYR* 3.6 0.7 - - - -
320C THR* 3.8 33.8 + - + +
322C PHE* 3.2 27.6 - - - -
338C LYS* 2.5 35.3 - - - +
341C PHE* 3.9 22.2 - - + -
342C LYS* 4.0 7.5 - - - +
345C GLU* 4.2 1.6 + - - -
14D T 2.7 21.1 + - - -
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Residues in contact with ILE 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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392A TYR* 3.6 25.6 - - + +
189B ASN* 3.7 11.2 - - - +
203B ARG* 1.3 80.2 - - - +
205B ARG* 1.3 63.7 + - - +
206B GLU 3.8 10.3 - - - +
207B PRO 3.5 8.5 - - - +
208B ARG* 3.7 4.2 - - - +
209B THR* 3.5 24.8 + - - +
233B ALA* 3.9 19.7 - - - +
236B LYS* 3.7 41.7 - - + -
237B TYR* 3.2 31.0 + - + +
240B VAL* 5.0 4.5 - - + -
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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