Contacts of the helix formed by residues 195 - 207 (chain B) in PDB entry 3HS5
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 ASN 195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194B SER* 1.3 74.8 - - - +
196B MET* 1.3 68.9 + - - +
197B MET* 3.1 4.4 + - - +
198B PHE* 2.9 21.9 + - - +
199B ALA* 3.1 20.8 + - - +
426B PHE 3.4 8.3 - - - +
427B THR* 3.0 30.6 + - - +
429B GLN 3.2 15.7 - - - +
431B ALA* 3.9 1.7 - - - +
579B SER 2.8 22.4 + - - -
580B PHE 3.1 12.9 + - - +
581B ASN 3.3 12.9 + - - -
582B VAL 4.0 9.0 - - - +
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Residues in contact with MET 196 (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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195B ASN* 1.3 75.6 - - - +
197B MET* 1.3 60.5 + - - +
199B ALA* 3.9 12.6 - - + -
200B PHE* 3.0 45.7 + - + +
390B LEU 3.8 8.5 - - - +
391B LEU* 5.8 1.1 - - - -
392B PRO* 3.5 28.5 - - + -
395B PHE* 4.9 1.6 - - + -
426B PHE* 3.0 34.9 + - + +
429B GLN* 3.0 36.8 + - + +
430B ILE 3.8 4.0 - - - +
431B ALA* 3.2 45.8 - - + +
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Residues in contact with MET 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ASN* 3.1 8.7 + - - +
196B MET* 1.3 77.4 - - - +
198B PHE* 1.3 57.1 + - - +
200B PHE* 5.1 0.2 - - - -
201B PHE* 3.0 18.2 + - - +
300B MET* 3.9 16.8 - - + -
301B TYR* 2.6 39.0 + - + +
304B ILE* 5.3 0.4 - - + -
423B VAL* 4.1 21.1 - - + -
426B PHE* 3.4 17.2 + - - +
427B THR* 3.4 30.3 - - - +
564B ILE* 5.1 2.7 - - + -
568B ILE* 4.0 28.9 - - + -
578B THR* 3.6 16.6 - - + +
579B SER 3.8 9.2 - - - +
580B PHE* 3.9 4.9 - - + -
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Residues in contact with PHE 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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194B SER* 4.0 15.7 - - - -
195B ASN* 2.9 13.6 + - - +
197B MET* 1.3 74.3 - - - +
199B ALA* 1.3 64.9 + - - +
201B PHE* 3.2 1.4 + - - +
202B ALA* 2.9 29.2 + - + +
348B TYR* 3.4 34.5 - + - -
351B HIS* 3.8 19.1 - + - -
352B LEU* 3.1 43.7 - - + -
387B TRP* 3.8 13.0 - + - -
390B LEU* 4.0 26.5 - - + -
517B ILE* 5.0 1.3 - - + -
580B PHE* 3.3 37.2 - + + +
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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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195B ASN 3.1 15.4 + - - +
196B MET* 3.4 24.4 + - + +
198B PHE* 1.3 76.2 - - - +
200B PHE* 1.3 60.2 + - + +
202B ALA* 3.4 1.9 + - - +
203B GLN 3.1 20.3 + - - -
390B LEU* 3.9 34.8 - - + +
391B LEU* 5.5 2.5 - - + -
619B COH 3.4 21.8 - - + +
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Residues in contact with PHE 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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196B MET* 3.0 34.5 + - + +
199B ALA* 1.3 76.0 - - + +
201B PHE* 1.3 60.2 + - - +
203B GLN* 3.5 19.1 - - - +
204B HIS* 2.9 31.0 + - - +
295B VAL* 3.5 23.3 - - + -
297B GLY* 3.6 22.0 - - - +
298B LEU* 4.2 2.1 - - + +
300B MET* 4.8 1.3 - - + -
301B TYR* 3.5 17.0 - - + -
391B LEU* 5.3 4.0 - - + -
395B PHE* 3.8 18.4 - + - -
407B PHE* 3.7 21.5 - + - -
426B PHE* 3.6 41.3 - + - -
619B COH 3.9 7.4 - - + -
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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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197B MET 3.0 20.3 + - - +
198B PHE 3.7 4.3 - - - +
200B PHE* 1.3 74.0 - - - +
202B ALA* 1.3 61.1 + - - +
204B HIS* 4.5 2.7 - - - -
205B PHE* 2.8 50.5 + + + +
301B TYR* 3.3 30.0 - + - +
305B TRP* 4.5 24.5 - + - -
340B THR* 5.1 2.5 - - + -
343B ILE* 3.9 21.3 - - + -
344B VAL* 3.8 27.4 - - + -
348B TYR* 3.5 25.4 - + + -
564B ILE* 4.0 14.1 - - + -
567B LEU* 4.9 0.2 - - + -
580B PHE* 3.7 17.7 - + + -
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Residues in contact with ALA 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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198B PHE* 2.9 18.0 + - + +
199B ALA* 3.5 7.9 - - - +
201B PHE* 1.3 77.5 - - - +
203B GLN* 1.3 54.8 + - - +
205B PHE* 4.9 1.1 - - - -
206B THR* 2.8 39.3 + - - +
348B TYR* 3.1 31.6 - - + +
385B TYR* 4.6 0.2 - - + -
387B TRP* 4.4 8.3 - - + -
390B LEU* 4.7 0.4 - - + -
619B COH 3.8 19.1 - - + -
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Residues in contact with GLN 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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199B ALA 3.1 12.7 + - - +
200B PHE* 3.5 22.3 - - - +
201B PHE 3.2 0.2 - - - -
202B ALA* 1.3 79.6 - - - +
204B HIS* 1.3 61.8 + - - +
206B THR* 4.1 2.7 - - - -
207B HIS* 3.0 47.0 + - + +
295B VAL* 4.2 3.2 - - - +
298B LEU* 3.7 28.3 - - + +
619B COH 3.2 79.5 + - + +
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Residues in contact with HIS 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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200B PHE 2.9 18.2 + - - +
201B PHE* 3.9 4.5 - - + +
203B GLN* 1.3 79.2 - - - +
205B PHE* 1.3 63.4 + - - +
207B HIS 3.5 5.0 + - - -
232B HIS* 3.1 44.8 + + - -
233B ILE* 4.6 5.8 - - + +
292B PHE* 3.1 40.7 - + - -
298B LEU* 3.5 21.2 - - + +
301B TYR* 3.6 25.8 - - + +
302B ALA* 3.7 14.6 + - - -
305B TRP* 3.5 32.4 + + - -
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Residues in contact with PHE 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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1B ACD 3.4 42.2 - - + -
201B PHE* 2.8 37.3 + + + +
202B ALA 4.3 0.9 - - - +
204B HIS* 1.3 75.2 + - - +
206B THR* 1.3 70.4 + - + +
207B HIS 3.3 0.9 + - - -
208B GLN* 2.9 59.1 + - - +
209B PHE* 3.6 21.2 - + - -
228B VAL* 3.8 12.3 - - + -
232B HIS* 4.3 4.5 - - - -
340B THR* 3.7 27.4 - - + -
344B VAL* 3.7 22.2 - - + -
348B TYR* 5.1 5.4 - + - -
385B TYR* 5.0 2.0 - - - -
534B LEU* 4.0 3.1 - - + -
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Residues in contact with THR 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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202B ALA 2.8 23.1 + - - +
205B PHE* 1.3 77.1 - - + +
207B HIS* 1.3 72.2 + - - +
208B GLN 3.1 5.4 - - - -
209B PHE* 3.1 25.2 + - + -
210B PHE* 2.8 42.5 + - - +
348B TYR* 4.8 0.2 - - - +
385B TYR* 3.4 42.6 - - + +
619B COH 4.1 8.7 - - - +
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Residues in contact with HIS 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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203B GLN* 3.0 47.4 + - + +
204B HIS 3.5 1.5 + - - -
205B PHE 3.2 1.4 - - - -
206B THR* 1.3 87.3 - - - +
208B GLN* 1.3 58.2 + - - +
209B PHE 3.4 0.2 - - - -
210B PHE* 3.7 13.0 + - + -
211B LYS* 3.4 9.2 - - - +
289B GLN* 3.0 28.9 + - - +
291B VAL* 4.6 12.7 - - + +
292B PHE* 3.7 25.5 - + + -
298B LEU* 5.3 2.3 - - + +
619B COH 3.5 53.9 + + + -
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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