Contacts of the helix formed by residues 196 - 211 (chain A) in PDB entry 2IVF
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 GLY 196 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.9 12.1 - - - -
193A VAL* 2.7 16.2 + - - +
194A HIS 3.0 1.4 + - - -
195A ALA* 1.3 80.4 - - - +
197A SER* 1.3 55.8 + - - -
198A ILE 3.1 2.7 - - - -
199A ALA* 3.1 3.2 + - - +
200A TRP* 2.8 33.8 + - - +
660A GLU* 3.1 16.8 - - - -
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Residues in contact with SER 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 5.3 0.4 - - - +
193A VAL* 3.6 13.5 - - - +
196A GLY* 1.3 70.6 - - - -
198A ILE* 1.3 56.4 + - - +
200A TRP 3.4 0.2 + - - -
201A GLY* 2.8 25.1 + - - -
487A ASN* 3.8 5.1 + - - -
488A MET* 3.4 34.3 - - - +
660A GLU* 2.9 19.8 + - - -
661A MET* 3.7 6.6 + - - +
663A THR* 3.7 18.7 - - - +
743A MET* 3.4 21.3 - - - +
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Residues in contact with ILE 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A SER* 1.3 72.6 - - - +
199A ALA* 1.3 53.7 + - - +
201A GLY 3.4 0.7 + - - -
202A ALA* 2.7 33.2 + - - +
491A LEU* 4.4 2.2 - - + -
659A HIS 3.5 21.3 - - - +
660A GLU* 2.8 20.3 + - - +
688A TRP* 3.8 10.0 - - + -
736A ASN* 3.4 45.8 - - - +
739A CYS* 3.5 29.8 - - + -
740A LEU* 3.9 14.1 - - + +
743A MET* 3.8 23.8 - - + -
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Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ALA* 3.4 36.6 - - + +
196A GLY 3.1 9.9 + - - +
198A ILE* 1.3 80.5 - - - +
200A TRP* 1.3 60.7 + - - +
202A ALA* 3.3 4.7 + - - +
203A GLY 3.0 18.5 + - - -
606A LEU* 3.6 13.4 - - + +
660A GLU* 3.8 1.2 + - - -
687A GLU* 3.5 30.0 + - + +
688A TRP 5.0 0.4 - - - +
691A ILE* 4.5 0.2 - - - +
736A ASN* 5.5 1.0 + - - +
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Residues in contact with TRP 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A PRO* 3.1 34.3 + - + +
192A HIS 3.3 31.6 + - - +
193A VAL* 3.9 14.4 - - + +
196A GLY 2.8 18.7 + - - +
197A SER 3.7 4.3 - - - +
199A ALA* 1.3 70.3 - - - +
201A GLY* 1.3 71.5 + - - +
203A GLY* 3.2 2.1 + - - -
204A PHE* 2.9 65.9 + + + -
217A ILE* 4.7 7.5 - - + +
488A MET* 3.9 37.2 - - + -
489A VAL* 4.8 7.6 - - + -
543A LEU* 5.2 6.1 - - + -
606A LEU* 5.1 3.8 - - - -
956A PHE* 3.9 33.4 - + - -
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Residues in contact with GLY 201 (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 SER 2.8 18.8 + - - -
198A ILE 3.6 3.1 - - - -
200A TRP* 1.3 83.3 - - - +
202A ALA* 1.3 55.9 + - - +
204A PHE* 3.8 0.7 - - - +
205A ARG* 2.8 34.1 + - - +
488A MET 4.3 13.7 - - - -
491A LEU* 4.5 9.2 - - - -
492A GLY* 4.2 4.0 - - - -
688A TRP* 4.2 5.2 - - - -
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Residues in contact with ALA 202 (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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198A ILE 2.7 19.7 + - - +
199A ALA* 3.5 7.9 - - - +
201A GLY* 1.3 72.9 - - - +
203A GLY* 1.3 57.3 + - - +
205A ARG 3.3 0.2 + - - -
206A MET* 2.8 28.8 + - - +
688A TRP* 3.5 34.2 - - + -
691A ILE* 3.5 20.4 - - + -
727A PHE* 3.3 17.3 - - + -
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Residues in contact with GLY 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 3.1 22.0 - - - +
191A PRO* 5.8 0.4 - - - -
199A ALA 3.0 14.6 + - - -
200A TRP 3.8 1.8 - - - -
202A ALA* 1.3 75.3 - - - +
204A PHE* 1.3 57.1 + - - +
206A MET* 3.2 13.1 - - - +
207A THR* 2.8 33.6 + - - -
606A LEU* 4.0 6.1 - - - -
691A ILE* 3.7 6.4 - - - +
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Residues in contact with PHE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 4.1 2.8 - - - +
191A PRO* 5.6 1.2 - - + +
200A TRP* 2.9 54.1 + + + +
201A GLY 3.9 1.1 - - - +
203A GLY* 1.3 75.2 - - - +
205A ARG* 1.3 57.0 + - - +
207A THR* 3.3 3.6 + - - -
208A TYR* 2.8 37.3 + - + +
214A SER* 5.0 7.4 - - - -
488A MET 4.9 0.4 - - - -
489A VAL* 4.4 11.0 - - + -
492A GLY* 3.8 18.6 - - - -
493A VAL* 3.6 27.4 - - + -
541A VAL* 3.6 47.8 - - + -
543A LEU* 4.1 20.0 - - + -
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Residues in contact with ARG 205 (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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201A GLY 2.8 22.2 + - - +
202A ALA 3.6 3.6 - - - +
204A PHE* 1.3 72.9 - - - +
206A MET* 1.3 59.8 + - - +
208A TYR* 3.7 1.5 - - - +
209A LEU* 2.8 45.0 + - + +
491A LEU 2.7 28.6 + - - -
492A GLY* 3.4 26.8 + - - +
493A VAL 4.0 0.8 - - - -
494A MET 2.9 29.9 + - - +
495A SER* 4.6 2.6 - - - +
688A TRP* 3.4 26.8 - - - -
726A LYS 2.9 22.8 + - - -
727A PHE* 2.8 30.4 + - + +
729A MET* 3.5 23.2 - - - +
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Residues in contact with MET 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ILE* 5.8 0.4 - - - -
186A PHE* 4.0 11.2 - - + -
188A LEU* 3.8 0.4 - - + -
202A ALA 2.8 13.6 + - - +
203A GLY* 3.2 22.4 - - - +
205A ARG* 1.3 76.8 - - - +
207A THR* 1.3 67.7 + - - +
209A LEU* 3.3 2.7 + - - +
210A MET* 3.0 42.6 + - + +
604A MET* 3.2 46.2 - - + +
633A PHE* 5.4 2.9 - - - -
691A ILE* 3.7 25.8 - - + -
694A ILE* 5.4 8.5 - - - -
695A LEU* 3.9 18.8 - - + -
727A PHE* 3.8 7.7 - - + -
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Residues in contact with THR 207 (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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186A PHE* 3.7 14.7 - - + -
188A LEU* 3.1 20.8 - - - +
203A GLY 2.8 17.6 + - - -
204A PHE* 3.8 4.5 - - - -
206A MET* 1.3 74.9 - - - +
208A TYR* 1.3 52.1 + - - +
210A MET* 3.0 3.3 + - - -
211A ASP* 2.7 31.2 + - - -
212A GLY* 2.8 44.0 + - - +
213A VAL 3.6 6.1 - - - +
214A SER* 2.9 27.4 - - - +
541A VAL 5.3 1.6 - - - +
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Residues in contact with TYR 208 (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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204A PHE* 2.8 28.1 + - + +
205A ARG 3.7 2.9 - - - +
207A THR* 1.3 78.0 - - - +
209A LEU* 1.3 74.1 + - + +
211A ASP* 3.2 7.0 + - - +
492A GLY 3.7 17.5 - - - -
493A VAL* 3.8 34.8 + - + +
540A ALA* 4.2 10.1 - - + -
541A VAL* 3.9 42.8 + - + +
718A ARG* 3.0 21.3 + - - -
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Residues in contact with LEU 209 (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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205A ARG* 2.8 32.8 + - + +
206A MET* 3.3 4.5 + - - +
208A TYR* 1.3 85.4 - - + +
210A MET* 1.3 59.8 + - + +
695A LEU* 4.7 2.9 - - + -
718A ARG* 2.9 24.7 + - - +
723A LEU* 3.7 25.8 - - + +
726A LYS* 3.5 39.9 - - + +
727A PHE* 3.3 48.7 - - + +
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Residues in contact with MET 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ILE* 4.0 17.7 - - + -
178A PHE* 3.9 22.9 - - + -
183A SER* 3.1 19.8 - - - -
186A PHE* 3.6 48.2 - - + -
206A MET* 3.0 32.8 + - + +
207A THR* 3.8 2.9 - - - +
209A LEU* 1.3 76.9 - - - +
211A ASP* 1.3 65.6 + - - +
212A GLY* 4.2 2.7 - - - +
695A LEU* 4.0 18.4 - - + -
698A VAL* 5.4 0.7 - - - -
710A PHE* 3.4 17.1 - - - -
718A ARG* 4.1 0.2 - - - -
723A LEU* 4.1 21.3 - - + -
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Residues in contact with ASP 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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183A SER* 2.6 26.9 + - - +
207A THR 2.7 7.3 + - - -
208A TYR* 3.2 10.4 + - - +
209A LEU 3.3 0.6 - - - -
210A MET* 1.3 81.2 - - - +
212A GLY* 1.3 62.0 + - - +
540A ALA 4.9 7.3 - - - +
541A VAL 5.4 1.5 - - - -
542A GLY* 5.0 2.8 + - - -
593A ARG* 2.9 15.6 + - - -
712A ASP* 3.1 8.9 - - + +
713A HIS* 2.6 58.0 + - - -
718A ARG* 3.6 25.7 + - - -
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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
------------------------------------------------------------
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