Contacts of the helix formed by residues 219 - 228 (chain A) in PDB entry 6S1M
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 LEU 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A LEU 3.8 21.8 - - - +
183A THR* 5.0 7.5 - - - +
186A ALA* 4.6 17.5 - - + -
214A VAL* 3.7 15.8 - - + +
215A ALA* 5.0 1.8 - - + -
216A LEU* 3.7 42.4 - - + +
217A PRO 3.2 1.2 - - - -
218A ARG* 1.3 85.9 - - - +
220A VAL* 1.3 65.1 - - - +
221A ALA 3.3 1.8 - - - -
222A PRO* 3.6 13.4 - - + +
223A ALA* 3.4 22.5 + - - +
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Residues in contact with VAL 220 (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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146A PRO* 5.9 6.1 - - + -
147A TYR 5.5 2.2 - - - +
148A PHE* 3.8 33.1 - - + -
214A VAL* 4.5 11.0 - - + +
216A LEU 4.2 3.4 + - - +
217A PRO* 3.4 20.4 + - + +
219A LEU* 1.3 77.7 - - - +
221A ALA* 1.3 61.8 + - + +
223A ALA* 4.1 4.6 - - - +
224A ARG* 3.2 30.8 + - + +
247A ASN* 4.1 27.4 - - - +
248A VAL 6.1 0.2 - - - +
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Residues in contact with ALA 221 (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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218A ARG* 5.1 2.7 - - - -
219A LEU* 4.2 0.6 - - - +
220A VAL* 1.3 81.0 - - + +
222A PRO* 1.3 70.7 - - + +
224A ARG* 3.5 25.6 + - - +
225A ARG* 3.1 38.9 + - - +
-3T T 5.0 6.7 - - - +
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Residues in contact with PRO 222 (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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182A LEU* 4.3 41.3 - - + +
183A THR* 4.5 1.8 - - + -
218A ARG 4.5 4.5 - - - +
219A LEU* 3.6 25.4 - - + +
221A ALA* 1.3 89.2 - - + +
223A ALA* 1.3 59.7 + - - +
225A ARG* 3.0 15.9 + - + +
226A LEU* 2.9 32.2 + - + +
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Residues in contact with ALA 223 (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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148A PHE* 5.2 14.6 - - + -
183A THR* 3.7 24.1 - - + +
188A LEU* 6.5 1.1 - - + -
214A VAL* 5.5 5.2 - - + -
219A LEU 3.4 19.8 + - - +
220A VAL* 4.1 5.4 - - - +
221A ALA 3.3 1.0 - - - -
222A PRO* 1.3 77.2 - - - +
224A ARG* 1.3 55.2 + - - +
226A LEU 3.0 0.7 + - - +
227A LEU* 2.8 42.6 + - + +
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Residues in contact with ARG 224 (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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148A PHE* 5.7 6.0 - - + -
220A VAL* 3.2 21.5 + - + +
221A ALA* 3.6 28.2 + - - +
223A ALA* 1.3 78.9 - - - +
225A ARG* 1.3 67.2 + - - +
226A LEU 3.2 0.6 + - - -
227A LEU* 5.1 0.2 - - - -
228A GLU* 2.8 21.3 - - - +
229A GLN* 3.0 13.0 + - - +
244A TYR* 3.6 51.8 + - + -
247A ASN* 3.0 32.6 - - - +
-3T T 3.5 35.1 + - - -
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Residues in contact with ARG 225 (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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221A ALA* 3.1 24.4 + - - +
222A PRO* 3.0 17.5 + - + +
224A ARG* 1.3 85.7 - - + +
226A LEU* 1.3 68.0 + - + +
229A GLN* 3.3 40.8 - - - +
230A GLY* 3.8 2.8 + - - -
-3T T 4.5 14.1 + - - -
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Residues in contact with LEU 226 (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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178A GLY 3.4 26.9 - - - +
179A GLY* 3.7 16.0 - - - +
182A LEU* 4.4 20.4 - - + +
183A THR* 3.7 43.1 - - + +
222A PRO* 2.9 17.1 + - + +
223A ALA 3.0 3.5 + - - +
225A ARG* 1.3 91.6 - - + +
227A LEU* 1.3 59.7 + - - +
228A GLU 3.7 0.7 - - - -
230A GLY* 3.4 22.4 - - - -
231A ILE* 3.5 15.2 + - - +
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Residues in contact with LEU 227 (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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148A PHE* 5.2 10.5 - - + -
150A THR* 4.7 8.3 - - + +
167A GLU* 5.5 1.6 - - - +
212A ILE* 4.4 18.2 - - + -
223A ALA* 2.8 17.8 + - + +
224A ARG* 5.1 0.2 - - - -
226A LEU* 1.3 78.5 - - - +
228A GLU* 1.3 85.2 + - - +
230A GLY 4.5 2.4 - - - +
231A ILE 5.0 1.6 - - - -
232A ARG* 3.4 61.9 + - + +
240A SER* 4.3 6.8 + - - -
241A PHE* 5.3 2.3 - - - +
242A ALA 3.9 6.8 - - - +
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Residues in contact with GLU 228 (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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148A PHE* 5.5 0.9 - - - -
224A ARG* 2.8 29.9 - - - +
227A LEU* 1.3 104.4 - - - +
229A GLN* 1.3 67.6 + - - +
230A GLY 3.5 3.6 - - - +
240A SER* 4.4 9.7 + - - -
241A PHE* 4.5 24.8 - - + +
242A ALA 3.5 15.1 - - - +
243A PRO* 5.0 1.3 - - + -
244A TYR* 3.2 42.7 + - + +
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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