Contacts of the strand formed by residues 197 - 205 (chain B) in PDB entry 3O9Z
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 ALA 197 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B ARG* 1.3 74.6 + - - +
198B LEU* 1.3 64.0 + - - +
199B HIS 4.4 1.1 - - - +
200B VAL* 4.0 20.3 - - + +
214B LEU* 4.7 1.6 - - + -
215B GLU 3.6 1.8 - - - +
216B LEU* 3.4 25.2 - - + +
284B GLU* 2.9 17.7 + - - +
287B ARG* 2.9 26.4 + - - +
288B VAL* 3.9 15.3 - - + -
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ARG* 4.0 15.3 - - + +
197B ALA* 1.3 76.2 - - - +
199B HIS* 1.3 61.0 + - + +
215B GLU* 2.8 36.4 + - - +
216B LEU 4.3 13.2 - - - +
217B GLU* 4.1 24.7 - - + +
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Residues in contact with HIS 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ALA* 3.4 1.5 - - - +
198B LEU* 1.3 79.0 + - - +
200B VAL* 1.3 78.8 + - - +
201B GLU* 2.8 37.1 + - + +
213B TYR* 4.4 15.0 - + - -
214B LEU* 3.5 4.3 - - - +
215B GLU* 2.9 46.8 + - + +
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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
----------------------------------------------------------
197B ALA* 4.0 16.6 - - + +
199B HIS* 1.3 87.7 + - - +
201B GLU* 1.3 71.6 + - - +
213B TYR 3.6 4.0 - - - -
214B LEU* 3.9 22.9 - - + -
223B TRP* 5.7 0.4 - - + -
288B VAL* 4.5 8.3 - - + +
291B LEU* 4.4 25.1 - - + -
292B LEU* 3.8 33.2 - - + -
295B LEU* 3.5 21.9 - - + +
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Residues in contact with GLU 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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199B HIS* 2.8 35.7 + - + +
200B VAL* 1.3 75.8 - - - +
202B VAL* 1.3 61.0 + - - +
203B HIS* 2.8 38.3 + - - +
212B GLY* 3.3 2.4 - - - -
213B TYR* 2.9 44.8 + - + +
223B TRP* 4.0 6.9 - - - -
295B LEU* 3.9 5.4 - - - -
298B SER* 3.9 14.2 + - - +
299B GLN 5.3 0.8 - - - +
300B PRO* 4.7 4.3 - - - +
301B SER 5.3 0.5 + - - -
304B ASN* 3.9 18.8 + - - +
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Residues in contact with VAL 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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201B GLU* 1.3 73.0 - - - +
203B HIS* 1.3 64.9 + - - +
204B ALA 3.6 15.7 - - - +
205B ARG* 3.6 20.0 - - + +
210B ASN* 5.3 4.9 - - + +
211B ALA 3.5 13.0 - - - +
223B TRP* 4.7 5.4 - - + -
292B LEU* 3.9 15.9 - - + -
295B LEU* 3.5 35.3 - - + +
296B PRO 3.6 12.5 + - - +
297B LEU* 3.4 9.6 - - + -
298B SER* 3.0 27.7 + - - +
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Residues in contact with HIS 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 GLU* 2.8 31.8 + - + +
202B VAL* 1.3 79.7 - - - +
204B ALA* 1.3 57.9 + - - +
211B ALA 2.7 12.2 + - - +
212B GLY* 3.5 13.9 + - - -
213B TYR* 3.7 12.1 - - + -
297B LEU* 3.5 11.1 - - - +
298B SER* 3.6 27.9 - - - +
300B PRO* 3.3 34.1 - - + +
304B ASN 3.2 26.9 + - - -
305B ARG* 4.5 1.6 - - - -
306B HIS 5.0 0.4 + - - -
309B LEU* 4.0 23.1 - - + +
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Residues in contact with ALA 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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202B VAL* 3.6 6.8 - - - +
203B HIS* 1.3 80.0 - - - +
205B ARG* 1.3 64.8 + - - +
206B THR* 5.8 3.4 - - + -
209B VAL* 4.3 11.2 - - + -
210B ASN* 3.3 4.9 - - - -
211B ALA* 3.1 36.8 + - + +
297B LEU* 3.6 4.9 - - - +
309B LEU* 4.2 16.2 - - + -
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Residues in contact with ARG 205 (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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202B VAL* 3.6 19.9 - - + +
204B ALA* 1.3 76.9 - - - +
206B THR* 1.3 70.2 + - - +
209B VAL 3.5 4.0 - - - -
210B ASN* 3.8 19.3 - - - +
292B LEU 2.8 28.1 + - - -
293B ARG* 4.4 7.9 + - - +
294B THR 5.4 0.2 - - - -
295B LEU 2.7 31.9 + - - +
296B PRO* 4.6 1.0 - - - +
297B LEU* 3.9 39.9 - - + +
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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