Contacts of the helix formed by residues 187 - 199 (chain A) in PDB entry 1SHC
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 ALA 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A GLY 4.3 9.0 - - - +
156A GLY* 5.5 2.7 - - - -
162A GLU* 4.8 15.7 - - - +
163A TYR 5.8 0.2 - - - -
164A VAL* 4.9 4.9 - - - +
183A PRO* 4.6 5.8 - - + +
186A LEU* 1.3 75.6 - - - +
188A GLN* 1.3 66.0 + - + +
190A VAL* 2.9 21.9 - - - +
191A ILE* 2.9 19.6 - - - +
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Residues in contact with GLN 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 6.5 0.2 - - + -
156A GLY* 6.0 3.8 - - - -
186A LEU 2.6 5.1 + - - -
187A ALA* 1.3 81.1 - - + +
189A ASP* 1.3 69.3 + - - +
191A ILE* 3.1 9.3 + - - +
192A SER* 3.1 20.3 + - - -
483B HIS* 4.5 26.9 + - + +
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Residues in contact with ASP 189 (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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39A LEU* 2.8 37.3 - - - +
40A HIS* 3.2 23.5 + - + +
41A PRO* 2.8 41.9 - - + +
52A TYR* 5.0 0.2 - - - -
185A GLY 5.0 0.9 - - - +
186A LEU* 2.8 16.3 + - - +
188A GLN* 1.3 77.6 - - - +
190A VAL* 1.3 61.6 + - - +
192A SER* 3.0 13.3 + - - -
193A THR* 2.9 11.3 + - - -
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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
----------------------------------------------------------
52A TYR* 4.4 2.9 + - + -
124A LEU* 3.8 16.8 - - + -
164A VAL* 3.8 20.2 - - + -
186A LEU* 3.2 38.2 + - + +
187A ALA* 2.9 44.4 - - - +
189A ASP* 1.3 79.4 - - - +
191A ILE* 1.3 66.4 + - - +
193A THR* 2.7 21.1 + - - +
194A ILE* 3.1 29.0 + - + +
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Residues in contact with ILE 191 (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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154A SER* 3.4 11.0 - - - +
155A GLY* 3.2 44.6 - - - +
156A GLY* 4.3 4.7 - - - +
164A VAL* 5.2 1.3 - - + -
187A ALA 2.9 20.0 - - - +
188A GLN* 3.1 9.8 + - - +
190A VAL* 1.3 86.0 - - + +
192A SER* 1.3 64.4 + - - +
194A ILE* 4.6 5.8 - - + -
195A GLY* 3.2 17.2 + - - -
483B HIS* 3.4 37.7 - - + +
485B ILE* 3.2 28.0 - - + +
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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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38A TRP* 4.6 18.1 - - - -
39A LEU* 5.6 5.0 - - - +
41A PRO* 4.4 7.8 - - - +
42A ASN* 5.1 3.1 - - - +
188A GLN 3.1 9.8 + - - -
189A ASP* 3.0 15.0 + - - -
191A ILE* 1.3 79.8 - - - +
193A THR* 1.3 59.5 + - - +
195A GLY* 4.0 1.2 - - - -
196A GLN* 2.8 40.3 + - - +
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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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41A PRO* 3.0 30.7 - - + +
45A VAL* 3.5 7.1 - - + +
50A VAL* 3.0 35.9 - - + -
52A TYR* 3.3 5.1 + - - +
126A VAL* 3.7 15.6 - - + +
189A ASP 2.9 11.9 + - - -
190A VAL* 2.7 19.7 + - - -
192A SER* 1.3 73.0 - - - +
194A ILE* 1.3 66.6 + - - -
195A GLY 3.0 0.9 - - - -
196A GLN* 2.8 17.4 + - - +
197A ALA 3.1 11.6 + - - -
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Residues in contact with ILE 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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124A LEU* 4.9 8.3 - - + -
126A VAL* 4.2 2.7 - - + -
131A LEU* 3.6 30.1 - - + -
153A ALA* 4.0 7.9 - - + -
154A SER 5.6 3.6 - - - +
164A VAL* 5.6 6.3 - - + -
166A TYR* 5.8 9.6 - - + -
190A VAL* 3.1 37.1 + - + +
191A ILE* 4.6 8.5 - - + -
193A THR* 1.3 75.5 - - - +
195A GLY* 1.3 62.3 + - - +
197A ALA 4.0 0.3 - - - -
198A PHE* 2.7 61.0 + - + -
485B ILE* 3.4 17.9 - - + -
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Residues in contact with GLY 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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191A ILE 3.2 10.1 + - - -
192A SER* 4.1 1.8 - - - -
193A THR 3.0 0.8 - - - -
194A ILE* 1.3 79.1 - - - +
196A GLN* 1.3 64.7 + - - +
198A PHE* 3.1 13.5 - - - +
199A GLU* 3.2 9.4 + - - +
485B ILE* 3.3 27.7 - - - +
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Residues in contact with GLN 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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38A TRP* 6.2 1.6 - - - -
42A ASN* 2.5 41.0 + - + +
45A VAL* 3.8 21.4 - - + +
46A MET* 5.4 2.9 - - - +
192A SER* 2.8 30.9 + - - +
193A THR* 2.8 15.4 + - - +
195A GLY* 1.3 74.1 - - - +
197A ALA* 1.3 65.9 + - - +
198A PHE 2.8 1.7 + - - -
199A GLU* 2.9 8.2 + - - +
200A LEU* 2.9 20.0 - - - +
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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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45A VAL* 4.3 2.3 - - + +
126A VAL* 3.7 15.5 - - + -
127A SER 2.9 27.1 - - - +
128A THR* 4.6 0.4 - - - +
129A SER* 3.5 10.5 + - - +
147A MET* 3.2 32.9 - - + +
193A THR 3.1 3.2 + - - +
196A GLN* 1.3 79.1 - - - +
198A PHE* 1.3 61.1 + - - +
200A LEU* 3.2 26.3 + - - +
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Residues in contact with PHE 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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131A LEU* 4.4 1.3 - - + -
147A MET* 3.5 19.5 - - + +
150A ILE* 4.3 22.4 - - + -
151A SER 5.8 1.1 - - - -
152A PHE* 5.0 1.8 - - - -
153A ALA* 3.2 22.9 - - + -
166A TYR* 6.5 0.7 - + - -
194A ILE* 2.7 44.9 + - + +
195A GLY* 3.1 10.8 - - - +
196A GLN 2.8 2.0 + - - -
197A ALA* 1.3 78.5 - - - +
199A GLU* 1.3 58.4 + - + +
200A LEU 3.2 4.2 + - - -
201A ARG 4.7 0.2 + - - -
202A PHE* 4.4 13.9 - - - +
485B ILE* 3.1 29.8 - - + -
486B GLU* 3.4 17.0 - - - +
487B ASN* 2.8 51.3 - - - +
488B PRO* 4.5 2.2 - - - +
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Residues in contact with GLU 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 GLY 3.2 5.5 + - - +
196A GLN 2.9 7.8 + - - +
198A PHE* 1.3 78.6 - - + +
200A LEU* 1.3 67.7 + - + +
201A ARG 5.4 0.2 - - - -
204A GLN* 4.6 22.7 + - - +
486B GLU 5.8 2.5 - - - +
488B PRO* 4.6 15.7 - - + +
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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
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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