Contacts of the helix formed by residues 209 - 217 (chain B) in PDB entry 3VF1
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 CYS 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207B TRP* 3.3 2.5 - - - +
208B ASP* 1.3 82.1 - - + +
210B LEU* 1.3 67.6 + - - +
211B GLU* 3.2 18.6 - - - -
212B ASP* 3.1 40.0 + - - +
213B PHE* 4.3 1.0 + - - -
590B HIS* 3.6 22.4 - - + +
594B MET* 3.5 14.8 - - - +
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Residues in contact with LEU 210 (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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209B CYS* 1.3 74.2 - - - +
211B GLU* 1.3 71.5 + - - +
212B ASP 3.3 0.9 + - - -
213B PHE* 3.4 19.0 + - - -
232B TRP* 3.8 32.1 - - + -
233B ARG* 3.7 20.2 - - - +
351B TRP* 4.2 15.9 - - + -
354B ILE* 5.5 0.4 - - + -
358B LEU* 5.4 0.2 - - + -
569B PHE* 3.5 12.6 - - - -
571B PRO* 4.4 5.4 - - + -
590B HIS* 3.1 24.9 + - + +
593B ILE* 4.1 10.5 - - + -
594B MET* 3.6 13.4 - - - -
597B LEU* 3.5 31.9 - - + -
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Residues in contact with GLU 211 (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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209B CYS* 3.2 14.2 - - - -
210B LEU* 1.3 82.3 - - + +
212B ASP* 1.3 63.0 + - - +
213B PHE 3.2 0.4 - - - -
214B ARG* 3.2 50.4 + - - +
229B ALA 4.9 2.4 - - - +
232B TRP* 4.3 8.1 + - - -
233B ARG* 3.3 30.6 + - - +
569B PHE* 4.4 3.9 - - - -
590B HIS* 6.0 2.0 - - + -
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Residues in contact with ASP 212 (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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207B TRP* 3.6 21.6 - - + -
208B ASP* 3.4 34.0 + - - +
209B CYS* 3.1 26.4 + - - +
211B GLU* 1.3 75.8 - - - +
213B PHE* 1.3 56.7 + - - +
214B ARG 3.0 4.9 - - - -
215B GLN* 3.0 54.5 + - - +
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Residues in contact with PHE 213 (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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207B TRP* 3.3 42.8 - + - -
209B CYS 4.5 1.6 - - - -
210B LEU* 3.4 19.9 + - - +
211B GLU 3.2 0.6 - - - -
212B ASP* 1.3 77.2 - - - +
214B ARG* 1.3 60.3 + - - +
215B GLN 3.0 1.7 + - - -
216B LEU* 3.2 33.1 + - + +
217B ILE* 4.5 1.4 + - - +
568B GLY 4.9 4.7 - - - +
569B PHE* 3.7 16.3 - - + -
570B HIS* 3.6 30.5 - + + +
571B PRO* 3.4 29.6 - - + -
594B MET* 3.9 21.3 - - + -
597B LEU* 3.9 19.7 - - + -
598B ALA 4.1 7.6 - - - -
603B ALA* 4.0 7.9 - - + -
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Residues in contact with ARG 214 (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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211B GLU* 3.2 39.9 + - - +
212B ASP 3.0 0.8 - - - -
213B PHE* 1.3 74.5 - - - +
215B GLN* 1.3 63.1 + - - +
216B LEU 3.1 1.0 + - - -
217B ILE* 3.3 22.9 + - - +
225B LEU* 3.5 43.7 - - + +
229B ALA* 3.2 32.9 + - - +
230B GLU* 4.5 6.3 + - - +
569B PHE* 3.7 19.1 - - + -
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Residues in contact with GLN 215 (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 LEU* 3.9 8.7 - - + +
199B HIS* 5.7 2.6 + - - -
200B LEU* 5.2 6.2 - - + +
207B TRP* 3.6 21.1 - - + -
212B ASP* 3.0 46.7 + - - +
214B ARG* 1.3 79.4 - - + +
216B LEU* 1.3 61.4 + - + +
217B ILE 3.3 2.0 + - - -
218B THR* 3.8 16.1 - - - +
600B LYS* 5.4 3.0 + - - +
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Residues in contact with LEU 216 (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 LEU* 5.7 0.5 - - - +
197B LEU* 3.9 23.5 - - + +
200B LEU* 4.3 4.0 - - + -
207B TRP* 3.7 24.5 - - + -
213B PHE* 3.5 22.7 - - + +
214B ARG 3.1 1.0 - - - -
215B GLN* 1.3 78.3 - - - +
217B ILE* 1.3 63.8 + - + +
218B THR* 3.3 6.7 + - - +
221B ILE* 3.9 10.6 - - - +
568B GLY 5.0 4.3 - - - +
570B HIS* 5.5 3.4 - - + -
603B ALA* 3.6 39.3 - - + +
604B VAL* 3.6 29.2 - - + -
607B VAL* 3.8 23.2 - - + +
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Residues in contact with ILE 217 (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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213B PHE 4.9 1.3 - - - +
214B ARG* 3.3 19.6 + - - +
215B GLN 3.1 3.5 - - - +
216B LEU* 1.3 81.6 - - + +
218B THR* 1.3 61.8 + - - +
221B ILE* 4.2 23.8 - - + -
224B GLY* 3.4 34.1 - - - +
225B LEU* 3.7 15.9 - - + +
226B PRO* 3.9 22.2 - - + -
564B MET* 4.8 3.4 - - - -
568B GLY* 3.9 27.4 - - - +
569B PHE* 6.0 1.6 - - + -
607B VAL* 5.3 3.1 - - + -
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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