Contacts of the helix formed by residues 195 - 209 (chain A) in PDB entry 1C3Q
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 195 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A VAL* 3.3 27.1 - - - -
31A PHE* 3.9 5.9 - - - -
32A THR* 5.2 0.2 + - - -
193A VAL 3.5 0.4 + - - -
194A THR* 1.3 77.3 + - - +
196A ALA* 1.3 57.6 - - - +
197A GLY 3.1 2.7 - - - -
198A CYS* 3.5 7.6 - - - +
199A LEU* 2.7 36.0 + - - +
302A TZE 3.3 13.7 + - - -
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Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PHE* 4.2 6.7 - - + -
190A LEU* 3.2 44.4 - - + +
193A VAL* 3.2 12.7 + - + +
194A THR 3.2 4.2 + - - -
195A GLY* 1.3 78.9 - - - +
197A GLY* 1.3 61.0 + - - +
200A LEU* 3.3 13.5 + - - +
225A TYR* 2.8 30.4 + - + +
248A LEU* 5.8 0.4 - - + -
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Residues in contact with GLY 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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121A ARG* 3.2 25.1 + - - -
195A GLY* 3.1 0.6 - - - -
196A ALA* 1.3 78.9 - - - +
198A CYS* 1.3 63.4 + - - +
200A LEU* 3.3 8.8 + - - +
201A THR* 3.0 26.0 + - - -
302A TZE 5.4 1.8 + - - -
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Residues in contact with CYS 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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24A THR* 4.8 0.9 - - - +
25A ASN* 3.5 11.2 - - - -
28A VAL* 3.6 24.2 - - + -
32A THR* 4.4 1.8 - - - +
63A VAL* 5.4 0.5 - - - +
65A ASN* 3.3 27.6 + - - +
94A ASP* 3.7 8.5 - - - -
96A VAL* 4.4 6.1 - - - -
121A ARG* 5.8 0.4 - - - -
195A GLY* 3.1 5.8 + - - +
197A GLY* 1.3 76.3 - - - +
199A LEU* 1.3 61.4 + - - +
201A THR* 3.3 5.4 + - - -
202A SER* 3.0 23.4 + - - -
302A TZE 3.5 33.0 - - - -
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Residues in contact with LEU 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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31A PHE* 3.6 34.3 - - + +
32A THR* 3.6 32.4 + - - +
35A GLY* 3.7 28.7 - - - -
36A LEU* 4.0 5.2 - - + +
195A GLY 2.7 20.5 + - - +
198A CYS* 1.3 70.0 - - - +
200A LEU* 1.3 62.5 + - - +
202A SER* 2.8 10.3 + - - -
203A VAL* 2.8 38.8 + - + +
225A TYR* 3.6 27.6 - - + +
248A LEU* 5.0 0.2 - - + -
252A LEU* 4.1 8.7 - - + -
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Residues in contact with LEU 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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121A ARG* 4.4 12.1 - - - +
168A THR* 3.9 31.6 - - + +
196A ALA 3.3 12.8 + - - +
197A GLY* 3.3 11.2 + - - +
199A LEU* 1.3 78.7 - - - +
201A THR* 1.3 57.4 + - - +
203A VAL* 3.1 7.1 + - + +
204A VAL* 2.9 28.9 + - + +
221A ALA 4.5 1.6 - - - +
222A ILE* 3.9 33.4 - - + +
225A TYR* 3.8 41.9 + - + -
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Residues in contact with THR 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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63A VAL* 3.9 16.3 - - + +
65A ASN* 5.6 0.2 - - - -
92A ILE* 3.7 25.0 - - + +
94A ASP* 2.6 43.8 + - + +
121A ARG* 3.0 25.8 + - + +
197A GLY 3.0 3.9 + - - -
198A CYS* 3.5 9.4 - - - -
199A LEU 3.1 0.2 - - - -
200A LEU* 1.3 76.6 - - - +
202A SER* 1.3 63.3 + - - +
204A VAL* 3.2 11.4 + - - +
205A GLY* 3.1 15.9 + - - -
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Residues in contact with SER 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.1 4.5 - - - +
22A SER* 5.0 2.5 + - - -
24A THR* 6.1 0.5 - - - -
32A THR* 3.3 29.5 - - - +
36A LEU* 3.8 23.9 - - - +
63A VAL* 4.0 22.9 - - - +
198A CYS 3.0 12.7 + - - -
199A LEU* 2.8 9.7 + - - -
201A THR* 1.3 75.4 - - - +
203A VAL* 1.3 60.2 + - - +
205A GLY* 3.1 3.5 + - - -
206A ALA 3.0 21.5 + - - -
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLY 5.6 1.3 - - - +
36A LEU* 4.4 3.6 - - + -
39A LEU* 3.9 21.1 - - + -
199A LEU* 2.8 38.1 + - + +
200A LEU* 3.5 10.3 - - + +
202A SER* 1.3 72.3 - - - +
204A VAL* 1.3 67.8 + - - +
206A ALA* 3.1 7.4 + - - +
207A PHE* 3.0 46.1 + - + -
221A ALA* 4.0 16.6 - - + +
224A SER* 6.1 0.7 - - - -
225A TYR* 4.2 17.7 - - + +
252A LEU* 5.4 4.0 - - + -
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Residues in contact with VAL 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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92A ILE* 4.2 18.2 - - + -
119A ALA* 4.8 6.3 - - + -
121A ARG* 4.5 12.6 - - + -
166A ALA* 5.9 0.9 - - + -
200A LEU* 2.9 21.2 + - + +
201A THR* 3.3 12.3 - - - +
203A VAL* 1.3 77.0 - - - +
205A GLY* 1.3 58.3 + - - +
207A PHE* 3.3 2.3 + - - +
208A CYS* 2.9 41.7 + - - -
217A ALA* 4.9 0.2 - - - +
218A ALA* 4.3 19.7 - - + -
221A ALA* 3.6 19.5 - - + -
222A ILE* 4.3 18.8 - - + -
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Residues in contact with GLY 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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20A VAL* 4.5 1.1 - - - -
61A ALA* 3.2 23.4 - - - +
63A VAL* 4.2 6.7 - - - -
92A ILE* 3.8 21.1 - - - +
201A THR 3.1 8.2 + - - -
202A SER 3.1 8.1 + - - -
203A VAL 3.1 0.8 - - - -
204A VAL* 1.3 77.1 - - - +
206A ALA* 1.3 61.9 + - - +
208A CYS* 3.1 3.5 + - - +
209A ALA 3.1 17.7 + - - -
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Residues in contact with ALA 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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13A VAL* 4.0 8.1 - - + +
18A PRO* 3.7 12.1 - - + +
20A VAL* 3.7 23.6 - - + +
36A LEU* 4.1 6.3 - - + -
39A LEU* 4.2 12.3 - - + -
41A ALA* 4.1 18.8 - - + -
202A SER 3.0 10.8 + - - +
203A VAL 3.1 7.6 + - - +
205A GLY* 1.3 74.9 - - - +
207A PHE* 1.3 63.5 + - - +
209A ALA* 3.2 17.1 + - - +
210A VAL* 3.7 2.9 + - - +
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Residues in contact with PHE 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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6A ALA 4.4 0.2 - - - -
9A CYS* 3.7 15.0 - - + -
10A LEU* 3.6 43.1 - - + -
13A VAL* 3.7 18.6 - - + -
39A LEU* 4.1 12.3 - - + -
203A VAL* 3.0 36.1 + - + +
204A VAL 3.7 5.6 - - - +
206A ALA* 1.3 73.1 - - + +
208A CYS* 1.3 59.4 + - - +
209A ALA 3.0 4.9 - - - -
210A VAL* 3.0 5.9 + - - +
211A GLU* 3.0 28.1 + - - +
217A ALA* 3.5 18.8 - - + +
220A ALA* 3.7 21.8 - - + -
221A ALA* 3.6 20.6 - - + -
224A SER* 3.8 15.7 - - - -
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Residues in contact with CYS 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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-10A ARG* 2.9 31.2 + - - +
90A PRO* 3.8 20.7 - - + +
92A ILE* 3.7 23.6 - - + -
118A ALA* 4.9 1.8 - - - -
119A ALA* 5.3 1.1 - - - -
204A VAL* 2.9 25.2 + - - +
205A GLY* 3.1 8.7 + - - +
207A PHE* 1.3 76.3 - - - +
209A ALA* 1.3 58.5 + - - +
210A VAL 3.2 0.2 - - - -
211A GLU 3.3 4.8 - - - +
214A PRO* 4.3 21.1 - - - -
217A ALA* 3.7 20.2 - - - -
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Residues in contact with ALA 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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-11A MET* 3.5 9.5 - - - +
-10A ARG* 3.2 25.7 + - - +
18A PRO* 3.5 23.8 - - + -
20A VAL* 5.5 0.2 - - + -
60A GLY* 3.3 34.6 - - - +
61A ALA* 4.2 1.3 - - + -
90A PRO* 4.6 0.4 - - - -
205A GLY 3.1 8.7 + - - +
206A ALA* 3.3 14.1 - - - +
207A PHE 3.0 0.8 - - - -
208A CYS* 1.3 79.8 - - - +
210A VAL* 1.3 57.9 + - - +
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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