Contacts of the helix formed by residues 195 - 206 (chain A) in PDB entry 3R7G
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 SER 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A GLU* 3.0 16.4 - - - -
126A ILE* 3.5 14.9 - - - +
193A ILE* 3.9 0.6 - - - +
194A ARG* 1.3 79.9 - - - +
196A TYR* 1.3 66.5 + - - +
197A ARG* 2.9 35.2 + - - -
198A ASP* 3.1 28.1 + - - +
199A VAL* 3.4 8.8 + - - +
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Residues in contact with TYR 196 (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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66A CYS* 3.9 26.3 - - + +
69A LEU* 3.8 48.9 - - + +
70A ARG* 3.9 24.9 - - + -
73A ALA* 4.4 11.0 - - + -
79A ARG* 3.8 20.3 - - - +
122A GLU* 2.9 41.2 + - + +
125A VAL* 3.7 23.9 - - + +
126A ILE* 3.9 23.6 - - + -
195A SER* 1.3 70.6 - - - +
197A ARG* 1.3 62.9 + - - +
199A VAL* 3.3 6.1 + - - +
200A MET* 3.2 25.8 + - - +
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Residues in contact with ARG 197 (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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70A ARG* 3.7 35.7 - - - +
195A SER* 2.9 28.9 + - - +
196A TYR* 1.3 79.8 - - - +
198A ASP* 1.3 67.2 + - - +
200A MET* 3.3 8.7 + - + +
201A LYS* 3.0 57.5 + - + +
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Residues in contact with ASP 198 (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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192A ALA 4.0 3.7 - - - +
193A ILE* 3.9 18.5 - - + -
194A ARG* 2.9 31.2 + - - +
195A SER* 3.1 20.1 + - - +
197A ARG* 1.3 87.7 + - - +
199A VAL* 1.3 66.4 + - - +
201A LYS* 3.5 14.2 + - - +
202A LEU* 3.2 29.0 + - + +
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Residues in contact with VAL 199 (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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62A CYS* 3.4 34.1 - - - +
66A CYS* 3.8 17.0 - - - -
126A ILE* 3.8 22.0 - - + -
156A LEU* 4.3 3.8 - - + -
160A MET* 4.1 13.0 - - + -
193A ILE* 3.7 27.1 - - + -
195A SER 3.8 7.4 - - - +
196A TYR 3.3 7.5 + - - +
198A ASP* 1.3 77.2 - - - +
200A MET* 1.3 62.5 + - - +
202A LEU* 3.1 9.2 + - - +
203A CYS* 3.0 24.7 + - - -
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Residues in contact with MET 200 (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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63A TYR* 3.7 51.5 - - + +
66A CYS* 3.7 15.9 - - + -
67A GLY* 3.7 32.8 - - - -
70A ARG* 4.0 33.4 - - - +
196A TYR 3.2 12.5 + - - +
197A ARG* 3.3 8.5 + - + +
199A VAL* 1.3 74.4 - - - +
201A LYS* 1.3 52.5 + - - +
203A CYS* 3.1 4.0 + - - +
204A ALA* 2.8 36.4 + - - +
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Residues in contact with LYS 201 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A ARG* 3.0 44.6 + - + +
198A ASP* 3.7 17.5 + - - +
199A VAL 3.3 0.2 - - - -
200A MET* 1.3 74.6 - - - +
202A LEU* 1.3 67.4 + - + +
204A ALA* 3.4 8.0 + - - +
205A ALA* 3.1 23.0 + - - +
210A GLU* 6.0 1.0 - - - -
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Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A TRP* 3.8 11.2 - - + -
155A GLN 5.9 0.2 - - - +
156A LEU* 4.1 22.0 - - + -
159A HIS* 5.4 4.5 - - + -
193A ILE* 3.8 33.0 - - + -
198A ASP* 3.2 12.7 + - + +
199A VAL 3.1 7.7 + - - +
201A LYS* 1.3 83.7 - - + +
203A CYS* 1.3 63.5 + - - +
205A ALA* 3.3 15.8 + - + +
206A HIS 3.5 7.6 + - - -
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Residues in contact with CYS 203 (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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59A TRP* 3.7 36.1 - - + +
62A CYS* 4.0 16.8 - - - -
63A TYR* 3.8 31.4 - - + -
156A LEU* 4.2 6.7 - - - -
199A VAL* 3.0 18.9 + - - -
200A MET 3.6 6.5 - - - +
202A LEU* 1.3 75.2 - - - +
204A ALA* 1.3 65.3 + - - +
206A HIS* 3.2 10.4 + - - +
217A TYR* 2.7 29.9 + - + +
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Residues in contact with ALA 204 (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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63A TYR* 4.4 3.3 - - + -
200A MET 2.8 20.5 + - - +
201A LYS* 3.7 8.3 - - - +
203A CYS* 1.3 72.6 - - - +
205A ALA* 1.3 56.2 + - - +
207A LEU* 3.2 24.6 + - - +
210A GLU* 3.8 35.7 - - + +
213A ALA* 3.9 27.1 - - + -
217A TYR* 4.3 1.2 - - - -
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Residues in contact with ALA 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 LYS 3.1 16.6 + - - +
202A LEU* 3.7 11.7 - - + +
203A CYS 3.2 0.8 - - - -
204A ALA* 1.3 70.9 - - - +
206A HIS* 1.3 64.4 + - - +
207A LEU 3.2 9.5 + - - +
210A GLU* 5.3 7.0 - - - +
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Residues in contact with HIS 206 (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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56A GLU* 2.7 34.2 + - - -
59A TRP* 3.4 55.0 - + + -
152A PRO* 5.5 4.7 - - + +
202A LEU 3.5 3.2 + - - -
203A CYS 3.2 11.8 + - - +
205A ALA* 1.3 79.5 - - - +
207A LEU* 1.3 61.9 + - + +
208A PRO* 3.9 4.0 - - - +
217A TYR* 3.3 18.8 - - - +
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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