Contacts of the helix formed by residues 186 - 197 (chain A) in PDB entry 6BSL
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 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A ASP* 2.6 27.9 + - - -
147A ASP* 3.4 42.2 - - - -
148A SER* 3.7 0.2 - - - -
181A GLN* 4.3 0.2 - - - +
184A ARG* 3.4 4.4 + - - +
185A LEU* 1.3 77.2 - - - +
187A LYS* 1.3 65.3 + - - +
188A GLY 3.3 1.3 + - - -
189A ASP* 2.9 21.6 + - - -
190A ILE* 3.1 24.6 + - - +
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Residues in contact with LYS 187 (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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147A ASP* 5.0 0.8 + - - -
186A SER* 1.3 73.6 - - - +
188A GLY* 1.3 57.1 + - - +
190A ILE* 3.4 9.1 + - - +
191A ALA* 3.0 30.3 + - - +
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Residues in contact with GLY 188 (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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142A GLU* 4.3 6.4 - - - +
145A ASP* 3.3 21.6 + - - -
186A SER* 3.1 3.8 + - - -
187A LYS* 1.3 77.1 - - - +
189A ASP* 1.3 58.4 + - - +
191A ALA* 3.9 5.7 - - - +
192A GLN* 2.9 35.7 + - - +
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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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38A TRP* 4.9 4.2 - - + -
101A PHE* 4.4 7.2 - - + -
104A GLU* 5.1 0.5 - - - +
145A ASP* 3.4 0.5 + - - +
148A SER* 2.6 28.4 + - - -
149A ILE* 2.8 37.7 + - - +
150A MET* 4.6 3.4 - - - +
185A LEU* 3.8 16.3 - - + -
186A SER* 2.9 39.4 + - - +
188A GLY* 1.3 72.4 - - - +
190A ILE* 1.3 58.8 + - - +
192A GLN* 3.8 6.6 - - - +
193A ALA* 2.9 32.2 + - - +
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Residues in contact with ILE 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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41A HIS* 3.4 62.8 - - + +
42A THR* 4.4 3.1 - - + +
185A LEU* 3.9 26.7 - - + +
186A SER 3.1 18.5 + - - +
187A LYS* 3.7 7.4 - - - +
189A ASP* 1.3 74.0 - - - +
191A ALA* 1.3 65.3 + - - +
193A ALA* 3.4 4.6 + - - +
194A ARG* 3.0 46.7 + - - +
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Residues in contact with ALA 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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142A GLU* 3.7 21.8 - - - +
187A LYS 3.0 17.0 + - - +
188A GLY* 3.9 3.4 - - - +
190A ILE* 1.3 78.8 - - - +
192A GLN* 1.3 61.4 + - - +
194A ARG* 3.5 9.4 + - - +
195A LYS* 3.2 26.8 + - - +
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Residues in contact with GLN 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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-1A ACE 3.0 28.8 + - - +
2A ALA* 4.5 1.4 - - + +
101A PHE* 3.6 24.7 - - + -
107A ARG* 3.9 0.8 - - - +
139A SER* 2.9 24.8 + - - +
140A LEU* 3.9 9.5 - - + +
142A GLU* 3.6 28.2 + - + +
188A GLY 2.9 17.1 + - - +
189A ASP* 4.0 3.3 - - - +
191A ALA* 1.3 75.8 - - - +
193A ALA* 1.3 59.7 + - - +
195A LYS* 3.3 4.3 + - - +
196A LEU* 2.9 28.1 + - - +
303A ZN 2.3 29.8 - - - -
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Residues in contact with ALA 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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38A TRP* 3.7 26.7 - - + -
42A THR* 3.9 13.5 - - + -
44A VAL* 5.7 1.3 - - + +
99A VAL* 5.4 0.7 - - + -
101A PHE* 3.8 15.6 - - + -
189A ASP 2.9 18.9 + - - +
190A ILE 3.9 3.4 - - - +
192A GLN* 1.3 74.8 - - - +
194A ARG* 1.3 56.6 + - - +
196A LEU* 3.3 2.9 + - - -
197A TYR* 2.9 40.7 + - + +
199A CYS* 4.9 0.9 - - - -
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Residues in contact with ARG 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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40A LYS 5.4 0.4 + - - -
41A HIS* 2.8 38.4 + - - +
42A THR* 4.5 5.3 - - - +
190A ILE* 3.0 36.0 + - - +
191A ALA* 3.7 9.3 - - - +
193A ALA* 1.3 77.2 - - - +
195A LYS* 1.3 56.6 + - + +
197A TYR 3.6 0.2 + - - -
198A LYS* 2.9 24.1 + - - -
199A CYS* 2.9 39.2 + - + +
200A PRO 5.9 1.8 - - - -
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Residues in contact with LYS 195 (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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140A LEU* 2.9 47.2 + - + +
141A GLY* 4.2 7.3 + - - -
142A GLU* 2.8 32.7 + - + +
191A ALA* 3.2 11.6 + - - +
192A GLN 3.6 7.4 - - - +
194A ARG* 1.3 76.9 - - + +
196A LEU* 1.3 64.1 + - - +
198A LYS* 3.2 19.4 + - - +
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Residues in contact with LEU 196 (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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2A ALA* 4.4 11.2 - - + -
3A THR* 4.2 18.6 - - + +
9A VAL* 3.8 32.9 - - + +
99A VAL 3.9 11.4 - - - +
100A GLY* 4.6 8.5 - - - +
101A PHE* 4.2 20.9 - - + -
138A GLU 6.0 0.2 - - - +
140A LEU* 3.5 20.1 - - + +
192A GLN 2.9 17.4 + - - +
193A ALA 3.6 5.4 - - - +
195A LYS* 1.3 77.4 - - - +
197A TYR* 1.3 80.2 + - + +
198A LYS* 3.4 7.5 + - - +
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Residues in contact with TYR 197 (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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9A VAL* 3.5 18.5 - - + -
10A TRP* 3.2 49.6 + - + -
12A ASP 6.1 0.5 - - - -
13A GLY* 3.7 25.4 - - - -
15A ILE* 5.4 1.1 - - + -
43A CYS* 3.7 23.7 - - - -
44A VAL* 4.1 16.6 - - + -
99A VAL* 2.7 43.0 + - + -
193A ALA* 2.9 22.6 + - + +
194A ARG 3.6 0.2 - - - -
196A LEU* 1.3 90.8 - - + +
198A LYS* 1.3 72.3 + - - +
199A CYS* 3.2 3.4 + - - -
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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