Contacts of the helix formed by residues 209 - 217 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A TRP* 3.3 2.5 - - - +
208A ASP* 1.3 83.4 - - + +
210A LEU* 1.3 68.5 + - - +
211A GLU* 3.2 18.6 - - - -
212A ASP* 3.1 39.4 + - - +
213A PHE* 4.3 1.2 + - - -
590A HIS* 3.5 22.0 - - + +
594A MET* 3.5 16.0 - - - +
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Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A CYS* 1.3 75.7 - - - +
211A GLU* 1.3 70.2 + - - +
212A ASP 3.3 0.9 + - - -
213A PHE* 3.4 20.4 + - - -
232A TRP* 3.8 30.7 - - + -
233A ARG* 3.7 19.7 - - - +
351A TRP* 4.2 17.0 - - + -
354A ILE* 5.4 0.7 - - + -
358A LEU* 5.4 0.2 - - + -
569A PHE* 3.5 12.6 - - - -
571A PRO* 4.4 6.3 - - + -
590A HIS* 3.1 24.9 + - + +
593A ILE* 4.1 11.2 - - + -
594A MET* 3.6 12.7 - - - -
597A LEU* 3.5 31.6 - - + -
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Residues in contact with GLU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A CYS* 3.2 14.8 - - + -
210A LEU* 1.3 81.2 - - + +
212A ASP* 1.3 63.6 + - - +
213A PHE 3.2 0.4 - - - -
214A ARG* 3.2 50.1 + - - +
229A ALA 4.9 2.8 - - - +
232A TRP* 4.3 8.5 + - - -
233A ARG* 3.3 29.5 + - - +
569A PHE* 4.4 4.1 - - - -
590A HIS* 6.0 2.2 - - + -
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Residues in contact with ASP 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A TRP* 3.6 22.1 - - + -
208A ASP* 3.4 34.5 + - - +
209A CYS* 3.1 27.3 + - - +
211A GLU* 1.3 76.6 - - - +
213A PHE* 1.3 55.6 + - - +
214A ARG 3.0 6.3 - - - -
215A GLN* 3.0 54.2 + - - +
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Residues in contact with PHE 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A TRP* 3.3 40.8 - + + -
209A CYS 4.5 1.1 - - - -
210A LEU* 3.4 19.2 + - - +
211A GLU 3.2 1.0 - - - -
212A ASP* 1.3 78.3 - - - +
214A ARG* 1.3 59.4 + - - +
215A GLN 3.0 2.1 + - - -
216A LEU* 3.2 34.4 + - + +
217A ILE* 4.5 1.4 + - - +
568A GLY 4.9 4.7 - - - +
569A PHE* 3.7 17.1 - - + -
570A HIS* 3.6 29.6 - + + +
571A PRO* 3.4 29.6 - - + -
594A MET* 3.9 21.1 - - + -
597A LEU* 3.9 20.6 - - + -
598A ALA 4.1 8.1 - - - -
603A ALA* 4.0 8.3 - - + -
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Residues in contact with ARG 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLU* 3.2 39.7 + - - +
212A ASP 3.0 0.8 - - - -
213A PHE* 1.3 75.4 - - - +
215A GLN* 1.3 63.2 + - + +
216A LEU 3.1 1.0 + - - -
217A ILE* 3.3 22.6 + - - +
225A LEU* 3.5 44.5 - - + +
229A ALA* 3.2 32.5 + - - +
230A GLU* 4.5 7.1 - - - +
569A PHE* 3.7 18.4 - - + -
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Residues in contact with GLN 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A LEU* 3.9 9.2 - - + +
199A HIS* 5.7 2.6 + - - -
200A LEU* 5.2 6.5 - - + +
207A TRP* 3.6 20.5 - - + -
211A GLU 5.5 0.2 - - - +
212A ASP* 3.0 45.8 + - - +
214A ARG* 1.3 79.1 - - + +
216A LEU* 1.3 61.0 + - + +
217A ILE 3.1 3.0 + - - +
218A THR* 3.8 16.1 - - - +
600A LYS* 5.4 3.3 + - - +
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Residues in contact with LEU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LEU* 5.7 0.2 - - - +
197A LEU* 3.9 22.7 - - + +
200A LEU* 4.3 4.3 - - + -
207A TRP* 3.7 24.2 - - + -
213A PHE* 3.5 22.9 - - + +
214A ARG 3.1 0.6 - - - -
215A GLN* 1.3 78.8 - - - +
217A ILE* 1.3 63.6 + - + +
218A THR* 3.3 6.6 + - - +
221A ILE* 3.9 11.1 - - - +
568A GLY 5.0 4.3 - - - +
570A HIS* 5.5 3.1 - - + -
603A ALA* 3.6 38.8 - - + +
604A VAL* 3.6 28.9 - - + -
607A VAL* 3.8 23.4 - - + +
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Residues in contact with ILE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A PHE 4.9 0.9 - - - +
214A ARG* 3.3 18.3 + - - +
215A GLN 3.1 3.5 - - - +
216A LEU* 1.3 82.1 - - + +
218A THR* 1.3 62.8 + - - +
221A ILE* 4.2 22.4 - - + -
224A GLY* 3.4 33.9 - - - +
225A LEU* 3.7 15.5 - - + +
226A PRO* 3.9 22.4 - - + -
564A MET* 4.8 3.8 - - - -
568A GLY* 3.9 27.6 - - - +
569A PHE* 6.0 1.8 - - + -
607A 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