Contacts of the helix formed by residues 189 - 203 (chain A) in PDB entry 1SG4
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A VAL* 3.8 9.9 - - + +
186A PRO* 2.7 43.1 + - - +
188A GLU* 1.3 94.1 + - + +
190A VAL* 1.3 62.0 + - - +
191A GLN 3.3 2.9 - - - -
192A SER* 3.1 14.0 + - - +
193A THR* 2.9 31.7 + - - +
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Residues in contact with VAL 190 (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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103A ALA* 4.2 6.3 - - - -
104A ILE 4.2 12.1 - - - +
105A ASN* 4.4 14.6 - - + -
123A ILE* 3.8 31.7 - - + +
124A LEU 4.5 0.2 - - - -
125A ALA* 4.1 20.0 - - + +
185A VAL* 3.8 10.1 - - + -
186A PRO 3.5 1.6 + - - -
187A GLU* 3.3 18.1 + - + +
188A GLU 3.6 0.4 - - - -
189A GLN* 1.3 78.1 - - - +
191A GLN* 1.3 79.5 + - + +
193A THR* 3.4 2.3 + - - -
194A ALA* 3.0 27.4 + - - +
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Residues in contact with GLN 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 4.9 5.3 - - - +
19A LYS* 6.3 0.6 - - - +
53A ILE* 4.2 11.6 - - - +
55A THR* 3.0 34.9 + - - +
56A SER 5.1 0.2 - - - +
103A ALA* 3.6 19.5 - - - +
105A ASN* 4.0 7.4 + - - -
188A GLU 5.1 1.6 + - - +
189A GLN 3.3 0.2 - - - -
190A VAL* 1.3 87.0 - - + +
192A SER* 1.3 65.2 + - - +
194A ALA* 3.2 3.4 + - - +
195A LEU* 3.0 27.3 + - - +
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Residues in contact with SER 192 (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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188A GLU 4.6 2.2 + - - -
189A GLN* 3.1 29.5 + - - +
191A GLN* 1.3 76.7 - - - +
193A THR* 1.3 60.1 + - - +
195A LEU* 3.2 13.7 + - - +
196A SER* 2.8 26.5 + - - -
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Residues in contact with THR 193 (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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123A ILE* 3.8 20.9 - - + -
183A GLN* 3.6 37.5 - - - +
185A VAL* 3.7 14.9 - - + +
189A GLN* 2.9 26.9 + - - +
190A VAL 3.7 4.0 - - - -
192A SER* 1.3 76.7 + - - +
194A ALA* 1.3 57.3 + - - +
196A SER* 3.3 9.5 + - - +
197A ALA* 2.9 28.4 + - - +
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Residues in contact with ALA 194 (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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53A ILE* 3.9 16.7 - - + +
101A VAL* 4.1 11.5 - - + +
103A ALA* 4.0 20.9 - - + -
123A ILE* 3.4 19.2 - - + +
190A VAL 3.0 17.9 + - - +
191A GLN* 3.6 5.8 - - - +
193A THR* 1.3 76.4 - - - +
195A LEU* 1.3 56.5 + - - +
197A ALA* 3.4 1.0 + - - +
198A ILE* 2.8 31.4 + - - +
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Residues in contact with LEU 195 (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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15A VAL* 5.2 6.7 - - + -
17A VAL* 5.6 4.3 - - + -
53A ILE* 3.8 20.0 - - + -
191A GLN* 3.0 18.2 + - + +
192A SER* 3.2 13.9 + - - +
194A ALA* 1.3 74.5 - - - +
196A SER* 1.3 65.7 + - - +
198A ILE* 3.4 9.9 + - + +
199A ALA* 3.0 24.1 + - - +
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Residues in contact with SER 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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192A SER 2.8 18.6 + - - -
193A THR* 3.4 11.1 + - - +
195A LEU* 1.3 76.1 - - - +
197A ALA* 1.3 62.8 + - - +
199A ALA* 3.4 6.7 + - - +
200A GLN* 3.2 35.4 + - - +
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Residues in contact with ALA 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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101A VAL* 4.7 4.5 - - + -
121A TYR* 3.8 36.3 - - + -
123A ILE* 4.1 4.5 - - + -
183A GLN* 5.3 2.5 - - - +
193A THR 2.9 18.5 + - - +
194A ALA* 3.7 3.8 - - - +
196A SER* 1.3 77.7 - - - +
198A ILE* 1.3 63.2 + - - +
200A GLN* 3.0 19.4 + - - +
201A TRP* 3.1 24.6 + - + -
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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
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15A VAL* 4.3 12.3 - - + -
51A GLY* 3.7 6.3 - - - -
52A VAL 3.5 43.5 - - - +
53A ILE* 3.9 14.4 - - + -
99A VAL* 4.0 10.5 - - + +
101A VAL* 3.8 17.9 - - + +
194A ALA 2.8 16.3 + - - +
195A LEU* 3.5 15.9 - - + +
197A ALA* 1.3 77.3 - - - +
199A ALA* 1.3 65.7 + - - +
201A TRP* 4.4 3.6 - - - +
202A MET* 2.8 55.6 + - + +
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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
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195A LEU 3.0 18.9 + - - +
196A SER* 3.5 8.5 - - - +
197A ALA 3.2 0.2 - - - -
198A ILE* 1.3 78.2 - - - +
200A GLN* 1.3 64.7 + - + +
202A MET* 3.6 6.7 + - - +
203A ALA* 3.3 23.0 + - - +
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Residues in contact with GLN 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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196A SER* 3.2 25.4 - - - +
197A ALA* 3.0 10.7 + - - +
199A ALA* 1.3 80.0 - - + +
201A TRP* 1.3 65.5 + - + +
203A ALA* 3.4 16.6 + - - +
204A ILE* 3.9 11.3 - - - +
162C ARG* 6.0 2.0 - - - +
166C LEU* 3.9 14.6 - - + +
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Residues in contact with TRP 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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99A VAL* 3.5 28.0 - - + -
101A VAL* 5.3 1.1 - - + -
120A ASP* 3.7 39.7 - - + -
121A TYR* 4.0 26.2 - + + -
197A ALA* 3.1 33.7 + - + +
198A ILE* 3.9 2.0 - - - +
200A GLN* 1.3 79.6 - - + +
202A MET* 1.4 62.3 + - - +
203A ALA 3.3 0.9 + - - -
204A ILE* 3.4 18.0 + - - +
209A ARG* 3.8 24.0 + - - -
158C ARG* 5.4 0.7 - - - -
162C ARG* 4.0 28.9 - - + -
165C GLN* 3.6 39.0 - - + -
166C LEU* 3.7 40.0 - - + +
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Residues in contact with MET 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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13A ALA 3.4 25.8 - - - +
14A GLY* 3.9 9.9 - - - +
15A VAL* 3.3 26.2 - - + -
50A ARG* 2.8 50.9 + - + +
51A GLY* 3.9 14.1 - - - +
99A VAL* 4.3 11.9 - - + -
198A ILE* 2.8 47.8 + - + +
199A ALA* 4.1 6.3 - - - +
201A TRP* 1.4 77.2 - - - +
203A ALA* 1.3 61.3 + - - +
204A ILE 3.2 2.4 + - - +
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Residues in contact with ALA 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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199A ALA 3.3 17.0 + - - +
200A GLN* 3.6 9.0 - - - +
201A TRP 3.2 1.0 - - - -
202A MET* 1.3 77.0 - - - +
204A ILE* 1.3 66.0 + - + +
205A PRO* 3.5 5.4 - - - +
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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