Contacts of the helix formed by residues 186 - 198 (chain A) in PDB entry 5SY1
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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164A LEU* 4.7 14.7 - - - +
168A LYS* 4.7 9.5 + - - +
182A ALA* 3.1 19.6 + - - +
183A LEU 3.4 5.1 + - - -
184A PHE 3.2 0.6 - - - -
185A GLY* 1.3 76.3 - - - +
187A LEU* 1.3 57.8 + - - +
188A PRO 3.5 2.0 - - - -
189A GLN* 3.2 19.4 + - - -
190A ILE* 2.9 43.6 + - - +
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Residues in contact with LEU 187 (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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183A LEU* 3.5 22.4 - - + +
184A PHE* 3.6 33.9 - - + +
185A GLY 3.4 0.2 - - - -
186A SER* 1.3 75.3 - - - +
188A PRO* 1.3 73.1 - - + +
190A ILE* 4.2 12.5 - - + +
191A ALA* 3.5 22.5 + - - +
287A TYR* 3.4 22.4 - - + +
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Residues in contact with PRO 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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95A GLY 5.6 0.2 - - - -
99A CYS* 4.1 15.3 - - - -
185A GLY 4.2 2.7 - - - +
186A SER 3.9 1.1 - - - -
187A LEU* 1.3 93.4 - - + +
189A GLN* 1.3 58.1 + - - +
191A ALA* 3.3 2.5 + - + +
192A CYS* 2.9 35.6 + - + +
284A ILE* 4.4 24.2 - - + -
287A TYR* 3.6 32.8 - - + -
288A GLN* 3.8 14.4 - - - +
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Residues in contact with GLN 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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95A GLY 5.3 0.2 - - - -
96A VAL* 4.4 23.6 + - + +
99A CYS* 4.1 32.1 - - + +
100A LYS* 5.1 10.4 - - - +
131A TYR* 6.1 0.6 - - - -
135A TYR* 4.1 17.6 + - - -
164A LEU* 4.0 20.3 - - + +
185A GLY 5.5 0.7 - - - +
186A SER* 3.2 22.0 + - - +
188A PRO* 1.3 80.0 - - - +
190A ILE* 1.3 63.1 + - - +
192A CYS* 4.5 3.7 - - - +
193A LEU* 3.5 26.7 + - + +
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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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161A PHE* 4.1 20.6 - - + -
164A LEU* 3.7 25.1 - - + +
165A VAL* 4.5 13.0 - - + -
168A LYS* 4.8 16.8 - - + -
183A LEU* 5.3 8.1 - - + -
186A SER* 2.9 30.6 + - - +
187A LEU* 4.2 15.0 - - + +
189A GLN* 1.3 77.3 - - - +
191A ALA* 1.3 66.6 + - + +
192A CYS 3.2 1.2 + - - -
193A LEU* 3.2 14.4 + - - +
194A ALA* 3.3 10.1 + - + +
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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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187A LEU 3.5 14.4 + - - +
188A PRO* 3.3 4.2 + - + +
190A ILE* 1.3 81.9 - - + +
192A CYS* 1.3 59.7 + - - +
194A ALA* 3.4 18.7 + - + +
195A PHE* 3.5 10.6 + - - +
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Residues in contact with CYS 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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91A VAL 4.6 0.9 - - - -
92A ALA* 3.2 45.8 - - - +
95A GLY* 4.4 12.3 - - - -
96A VAL* 4.1 12.5 - - + +
188A PRO* 2.9 19.6 + - + +
189A GLN* 4.5 0.4 - - - +
191A ALA* 1.3 77.2 - - - +
193A LEU* 1.3 63.5 + - - +
194A ALA 3.2 0.2 - - - -
195A PHE* 3.4 18.2 + - - +
196A LEU* 3.7 5.4 + - - +
284A ILE* 5.4 5.6 - - + -
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Residues in contact with LEU 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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96A VAL* 4.1 21.8 - - + -
135A TYR* 4.8 9.2 - - + +
138A LEU* 5.2 2.0 - - + -
157A SER* 4.7 7.7 - - - +
160A HIS* 3.7 43.5 - - + +
161A PHE* 4.0 16.5 - - + +
164A LEU* 4.3 12.8 - - + -
189A GLN* 3.5 19.9 + - + +
190A ILE 3.2 7.4 + - - +
192A CYS* 1.3 74.6 - - - +
194A ALA* 1.3 60.7 + - - +
195A PHE 3.2 0.7 - - - -
196A LEU* 3.1 41.0 + - + +
197A SER* 3.1 12.0 + - - -
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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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161A PHE* 4.2 18.3 - - + -
190A ILE* 3.3 11.5 + - + +
191A ALA* 3.5 15.5 - - + +
192A CYS 3.2 0.6 - - - -
193A LEU* 1.3 78.7 - - - +
195A PHE* 1.3 59.3 + - - +
197A SER* 2.6 26.0 + - - +
198A PHE* 3.2 18.0 + - + +
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Residues in contact with PHE 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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86A HIS* 4.9 4.3 - + - -
88A GLY* 3.2 42.6 - - - -
89A LEU* 5.2 0.2 - - - -
92A ALA* 4.2 9.9 - - + -
191A ALA 3.5 7.7 + - - +
192A CYS* 3.4 13.3 + - - +
193A LEU 3.2 0.4 - - - -
194A ALA* 1.3 77.4 - - - +
196A LEU* 1.3 65.1 + - + +
198A PHE* 3.4 9.2 + - + +
199A GLN* 3.3 44.6 + - + +
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Residues in contact with LEU 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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89A LEU* 4.8 8.5 - - + +
92A ALA* 4.2 18.4 - - + -
93A VAL* 4.5 17.3 - - + -
96A VAL* 5.5 3.6 - - + -
138A LEU* 4.2 21.5 - - + -
157A SER* 3.6 24.6 + - - -
192A CYS 4.2 7.9 - - - +
193A LEU* 3.1 36.3 + - + +
195A PHE* 1.3 79.6 - - + +
197A SER* 1.3 60.1 + - - +
199A GLN* 4.6 3.4 - - + -
200A TYR* 3.4 52.2 + - + +
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Residues in contact with SER 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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157A SER* 4.1 15.9 + - - -
158A TRP* 4.6 27.9 - - - -
161A PHE* 5.2 10.2 - - - -
193A LEU 3.1 10.6 + - - -
194A ALA* 2.6 29.0 + - - +
196A LEU* 1.3 78.3 - - - +
198A PHE* 1.3 73.0 + - - +
199A GLN 3.4 0.2 - - - -
201A PRO* 3.3 24.2 - - - +
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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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158A TRP* 5.7 7.4 - + - -
194A ALA* 3.2 15.2 + - + +
195A PHE* 3.4 9.2 + - + +
196A LEU 3.3 0.4 - - - -
197A SER* 1.3 94.7 + - - +
199A GLN* 1.3 61.0 + - - +
201A PRO* 4.8 0.2 - - - -
202A LEU* 3.3 29.5 - - - +
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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