Contacts of the helix formed by residues 198 - 207 (chain B) in PDB entry 3V4K
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 ASP 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196B SER 3.8 2.2 + - - -
197B MET* 1.3 76.5 - - - +
199B PRO* 1.3 73.4 - - - +
200B PRO* 3.1 31.7 - - - +
201B THR* 3.0 39.0 + - - +
202B PHE* 3.1 10.4 + - - +
352B ASP* 5.0 2.2 - - - -
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Residues in contact with PRO 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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197B MET 3.7 3.1 - - - +
198B ASP* 1.3 87.1 - - - +
200B PRO* 1.3 72.7 - - + +
202B PHE* 3.1 4.7 + - + +
203B THR* 3.0 27.3 + - - +
347B TRP* 3.8 23.1 - - + -
351B VAL* 3.8 16.4 - - + -
352B ASP* 3.4 28.9 - - + +
353B HIS* 4.6 2.2 - - - -
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Residues in contact with PRO 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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198B ASP* 3.1 22.4 - - - +
199B PRO* 1.3 97.5 - - + +
201B THR* 1.3 60.3 + - - +
203B THR* 4.0 6.3 - - - +
204B PHE* 3.0 26.5 + - - +
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Residues in contact with THR 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* 4.3 9.2 - - + -
198B ASP* 3.0 31.6 + - - +
200B PRO* 1.3 73.9 - - - +
202B PHE* 1.3 66.0 + - - +
204B PHE* 4.7 1.6 - - - -
205B ASN* 2.9 38.7 + - - +
217B GLU* 5.5 0.2 - - - +
219B TYR* 3.5 39.9 - - + +
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Residues in contact with PHE 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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197B MET* 3.8 18.3 - - + -
198B ASP 3.1 8.9 + - - +
199B PRO* 3.4 8.1 - - + +
201B THR* 1.3 76.7 - - - +
203B THR* 1.3 64.5 + - - +
205B ASN 3.2 0.2 + - - -
206B PHE* 2.8 69.6 + + + +
221B CYS* 5.9 0.9 - - - -
343B PHE* 3.8 26.7 - + - -
346B CYS* 3.9 20.9 - - + -
347B TRP* 3.6 31.2 - + + -
350B PHE* 6.2 0.2 - - + -
351B VAL* 3.5 26.7 - - + -
358B PHE* 4.1 17.0 - + - -
361B TRP* 4.7 7.2 - + - -
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Residues in contact with THR 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 PRO 3.0 17.4 + - - -
200B PRO* 4.0 6.7 - - - +
202B PHE* 1.3 85.0 - - - +
204B PHE* 1.3 62.7 + - - +
207B ASN* 3.3 25.8 + - + +
347B TRP* 4.2 9.0 - - - -
361B TRP* 5.0 17.6 - - + -
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Residues in contact with PHE 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 PRO 3.0 18.2 + - - +
201B THR* 4.0 4.5 - - - +
203B THR* 1.3 80.7 - - - +
205B ASN* 1.3 75.5 + - - +
207B ASN* 3.8 6.7 + - - +
213B ARG 4.7 5.2 - - - -
214B GLY* 3.6 31.4 - - - -
215B ARG* 3.6 33.9 - - + -
216B HIS* 6.1 0.2 - + - -
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Residues in contact with ASN 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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197B MET* 6.0 0.2 - - - -
201B THR* 2.9 35.7 + - - +
202B PHE 4.2 0.4 - - - +
204B PHE* 1.3 98.0 - - - +
206B PHE* 1.3 63.3 + - + +
207B ASN 3.5 0.2 - - - -
215B ARG* 4.8 6.1 - - - +
217B GLU* 4.1 22.4 + - - +
219B TYR* 3.5 41.9 - - + -
284B SER* 3.2 9.3 + - - -
313B ARG* 2.7 33.8 + - - +
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Residues in contact with PHE 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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197B MET* 4.3 11.0 - - + -
202B PHE* 2.8 57.2 + + + +
205B ASN* 1.3 80.8 - - + +
207B ASN* 1.3 66.5 + - - +
208B ASN 3.2 2.6 + - - -
219B TYR* 3.8 32.8 - - + -
221B CYS* 4.3 11.2 - - - -
282B PHE* 3.9 19.7 - - + -
283B THR 3.8 20.6 - - - -
284B SER* 3.8 3.6 - - - -
312B ALA* 3.6 13.2 - - + +
313B ARG* 3.9 1.3 - - - +
338B MET* 4.0 29.6 - - + -
343B PHE* 3.3 23.4 - - + -
346B CYS* 5.3 0.7 - - - -
361B TRP* 4.1 4.3 - - + -
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Residues in contact with ASN 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 THR* 3.3 21.3 + - + +
204B PHE* 3.8 11.0 + - - +
205B ASN 3.5 0.2 - - - -
206B PHE* 1.3 73.3 - - - +
208B ASN* 1.3 56.6 + - - +
209B GLU* 2.9 36.1 + - - +
212B VAL* 3.9 19.6 - - - +
215B ARG* 3.0 11.7 + - - +
313B ARG* 2.8 23.9 + - - -
361B TRP* 3.9 26.4 + - + -
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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