Contacts of the helix formed by residues 189 - 202 (chain D) in PDB entry 1GPM
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 GLN 189 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389C LEU* 3.8 21.2 - - + +
395C TYR* 4.0 7.8 - - + +
125D ILE* 3.8 14.8 - - + +
126D GLU 2.9 38.6 + - - +
127D ASP* 3.0 19.4 + - - +
187D THR* 3.5 1.6 - - - +
188D ARG* 1.3 85.2 - - + +
190D GLY* 1.3 63.8 + - - +
191D MET 3.3 2.5 - - - +
192D ARG* 2.7 48.8 + - + +
193D MET* 3.0 29.4 + - + +
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Residues in contact with GLY 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D PRO* 3.3 29.1 - - - +
187D THR* 3.1 28.5 + - - +
188D ARG 3.3 0.8 - - - -
189D GLN* 1.3 75.9 - - - +
191D MET* 1.3 61.9 + - - +
193D MET* 2.9 17.7 + - - +
194D LEU* 3.0 15.1 + - - +
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Residues in contact with MET 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D ARG* 3.4 45.8 - - - +
29D GLU* 3.3 30.3 - - + +
30D LEU* 3.4 31.5 - - + +
182D PRO 3.8 3.5 + - - +
187D THR 4.9 0.2 + - - -
188D ARG 5.0 1.2 + - - +
189D GLN* 3.3 1.3 - - - -
190D GLY* 1.3 74.6 - - - +
192D ARG* 1.3 57.4 + - - +
194D LEU* 3.2 9.8 + - - +
195D GLU* 2.9 28.9 + - - +
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Residues in contact with ARG 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C LEU* 3.1 44.0 + - - +
390C GLU* 3.7 24.8 + - - +
393C LEU 5.1 0.8 + - - -
124D GLY* 3.2 20.8 + - - -
125D ILE* 3.6 20.1 - - + +
126D GLU 4.7 0.4 - - - +
189D GLN* 2.7 52.6 + - + +
191D MET* 1.3 79.7 - - - +
193D MET* 1.3 56.9 + - - +
195D GLU* 3.8 15.2 - - + +
196D ARG* 2.9 44.6 + - - +
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Residues in contact with MET 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D PHE* 5.2 5.6 - - + -
121D LEU* 4.0 32.6 - - + +
122D VAL* 4.5 10.8 - - + -
125D ILE* 4.2 14.4 - - + -
127D ASP* 5.9 0.9 - - - +
137D LEU* 4.2 29.8 - - + -
139D VAL* 5.1 0.2 - - + -
178D VAL* 5.4 1.3 - - - -
180D PHE* 3.6 39.5 - - + -
182D PRO* 4.7 10.3 - - + -
187D THR* 4.5 8.5 - - + -
189D GLN* 3.0 23.6 + - + +
190D GLY 2.9 11.0 + - - +
192D ARG* 1.3 75.4 - - - +
194D LEU* 1.3 63.4 + - - +
196D ARG* 3.3 5.7 + - - +
197D PHE* 3.1 21.0 + - - +
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Residues in contact with LEU 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D VAL* 4.9 10.5 - - + +
26D ARG* 3.8 28.7 - - + -
27D VAL* 5.1 5.4 - - + +
30D LEU* 3.7 13.2 - - + -
55D ILE* 4.7 14.1 - - + -
83D PHE* 3.9 26.0 - - + -
85D VAL* 6.2 0.9 - - + -
182D PRO* 4.1 29.2 - - + +
183D GLU* 4.1 12.3 - - + +
190D GLY 3.0 11.4 + - - +
191D MET* 3.6 12.8 - - - +
193D MET* 1.3 73.9 - - - +
195D GLU* 1.3 61.5 + - - +
197D PHE* 3.2 3.7 + - + +
198D VAL* 2.9 37.9 + - + +
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Residues in contact with GLU 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 3.6 19.9 - - + +
191D MET 2.9 16.6 + - - +
192D ARG* 3.8 15.8 - - + +
194D LEU* 1.3 74.3 - - - +
196D ARG* 1.3 61.3 + - - +
198D VAL* 4.8 0.2 - - - -
199D ARG* 2.6 83.4 + - + +
200D ASP* 3.6 2.3 + - - +
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Residues in contact with ARG 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ALA 2.9 33.2 + - - +
121D LEU* 3.7 16.6 + - - +
122D VAL 4.0 0.4 - - - -
123D ARG* 2.6 41.3 + - - +
124D GLY* 4.6 0.4 - - - -
125D ILE* 3.6 20.3 - - + +
192D ARG* 2.9 35.3 + - - +
193D MET 3.4 7.4 - - - +
194D LEU 3.2 0.2 - - - -
195D GLU* 1.3 78.0 - - - +
197D PHE* 1.3 56.7 + - - +
200D ASP* 3.0 39.5 + - - +
201D ILE* 2.9 29.7 + - + +
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Residues in contact with PHE 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ILE* 4.6 5.2 - - + -
54D ILE 3.8 10.5 - - - -
55D ILE* 4.0 16.4 - - + -
81D PRO* 3.7 26.5 - - + -
82D VAL 3.9 6.1 - - - -
83D PHE* 3.5 52.3 - + + -
121D LEU* 4.3 7.6 - - + -
176D TYR* 4.1 19.5 - + - -
193D MET 3.1 10.0 + - - +
194D LEU* 3.6 7.4 - - - +
196D ARG* 1.3 80.7 - - - +
198D VAL* 1.3 71.6 + - + +
201D ILE* 3.4 11.7 + - + +
202D CYS* 2.8 52.8 + - - -
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Residues in contact with VAL 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ILE* 3.9 17.5 - - + -
27D VAL* 4.3 25.1 - - + -
30D LEU* 4.7 11.0 - - + -
32D VAL* 3.5 37.9 - - + -
55D ILE* 4.9 3.6 - - + -
194D LEU* 2.9 24.0 + - + +
195D GLU* 4.5 1.1 - - - +
197D PHE* 1.3 94.2 - - + +
199D ARG* 1.3 58.2 + - + +
202D CYS* 3.2 17.7 - - - +
204D CYS* 3.2 22.7 + - + +
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Residues in contact with ARG 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 2.5 47.4 + - - +
32D VAL* 4.5 6.9 - - - +
195D GLU* 2.6 58.5 + - + +
198D VAL* 1.3 74.7 - - - +
200D ASP* 1.3 66.6 + - - +
203D GLN* 3.1 23.0 - - - -
204D CYS 3.1 25.2 + - - +
205D GLU* 4.5 0.7 - - - +
206D ALA* 4.0 22.4 - - - +
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Residues in contact with ASP 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D GLU* 4.5 3.1 - - - +
196D ARG* 3.0 44.9 + - - +
199D ARG* 1.3 84.6 - - - +
201D ILE* 1.3 68.7 + - + +
203D GLN* 3.3 18.9 + - - +
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Residues in contact with ILE 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D PRO* 3.6 33.5 - - + +
120D ALA* 4.1 34.1 - - + +
121D LEU* 4.1 10.1 - - + +
174D ARG* 4.1 18.3 + - - -
176D TYR* 3.9 36.8 - - + +
196D ARG* 2.9 21.8 + - + +
197D PHE* 3.5 17.9 - - + +
200D ASP* 1.3 75.6 - - + +
202D CYS* 1.3 60.4 + - - +
203D GLN* 4.4 5.5 - - - +
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Residues in contact with CYS 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D HIS* 5.7 0.5 - - - -
10D ILE* 4.1 3.8 - - + -
52D SER* 4.0 16.6 - - - +
53D GLY* 3.8 18.6 - - - -
81D PRO* 3.8 14.4 - - - -
197D PHE* 2.8 52.2 + - - -
198D VAL* 3.2 16.4 - - - +
200D ASP 3.4 0.2 - - - -
201D ILE* 1.3 71.5 - - - +
203D GLN* 1.3 71.9 + - - +
204D CYS* 3.4 14.6 + - - -
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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