Contacts of the helix formed by residues 216 - 228 (chain A) in PDB entry 3S3J
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 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A PHE* 4.0 2.0 - - - -
213A ARG* 2.9 24.3 + - - -
215A SER* 1.3 82.7 + - - +
217A PRO* 1.3 62.8 - - - +
218A VAL* 3.2 14.6 + - - +
219A TYR* 3.1 22.5 + - - +
220A VAL* 3.0 31.0 + - - +
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Residues in contact with PRO 217 (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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35A ARG* 4.4 1.6 - - - +
139A PHE* 3.7 9.8 - - + -
147A ALA* 4.2 18.6 - - + -
148A VAL* 3.6 26.2 - - + -
215A SER 3.7 8.1 - - - +
216A SER* 1.3 83.7 - - - +
218A VAL* 1.3 64.1 + - + +
219A TYR 3.3 0.2 - - - -
220A VAL* 3.9 0.7 - - + -
221A GLY* 2.9 26.0 + - - -
293A ILE* 3.6 28.6 - - + +
342A MET* 3.7 27.9 - - + +
343A THR 5.4 0.7 - - - +
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Residues in contact with VAL 218 (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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216A SER* 3.2 9.3 + - - +
217A PRO* 1.3 81.5 - - + +
219A TYR* 1.3 57.8 + - - +
222A ARG* 3.0 28.9 + - + +
342A MET* 3.5 16.2 - - - -
343A THR 4.0 6.7 - - - +
344A ARG* 3.4 38.1 - - - +
345A PRO* 5.7 1.1 - - + -
346A ASP* 4.2 11.0 - - - +
373A PRO* 3.6 19.8 - - + +
388A TYR* 4.1 23.1 - - + +
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Residues in contact with TYR 219 (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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202A LYS* 3.4 42.3 - - + +
210A ASP* 2.5 43.9 + - - -
213A ARG* 3.5 69.3 - - + +
214A ARG* 4.0 7.6 - - + -
216A SER* 3.1 13.9 + - - +
218A VAL* 1.3 76.2 - - - +
220A VAL* 1.3 63.7 + - + +
222A ARG* 3.2 7.8 + - + +
223A VAL* 2.9 41.4 + - + +
702A SO4 3.9 11.0 + - - -
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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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112A ILE* 4.5 3.6 - - + -
139A PHE* 3.5 23.3 - - + -
197A LEU* 4.6 8.7 - - + -
214A ARG* 4.0 26.7 - - + +
216A SER 3.0 21.4 + - - +
217A PRO* 4.1 3.1 - - + +
219A TYR* 1.3 75.3 - - + +
221A GLY* 1.3 68.4 + - - +
223A VAL* 3.1 6.5 + - - +
224A VAL* 2.9 29.0 + - + +
288A LEU* 4.7 1.1 - - + -
291A LEU* 3.9 27.6 - - + -
293A ILE* 4.1 12.1 - - + -
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Residues in contact with GLY 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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217A PRO 2.9 18.7 + - - -
218A VAL* 4.0 0.7 - - - -
220A VAL* 1.3 77.2 - - - +
222A ARG* 1.3 61.7 + - - +
224A VAL* 3.1 4.2 + - - +
225A SER* 3.0 22.7 + - - -
288A LEU* 4.0 13.9 - - - -
293A ILE* 4.5 1.5 - - - +
342A MET* 5.8 1.3 - - - -
357A LEU* 3.8 27.8 - - - +
373A PRO* 5.3 0.4 - - - -
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Residues in contact with ARG 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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202A LYS* 5.2 4.7 - - - +
218A VAL* 3.0 19.0 + - - +
219A TYR* 3.2 9.2 + - + +
221A GLY* 1.3 74.2 - - - +
223A VAL* 1.3 64.2 + - + +
225A SER* 2.9 21.2 + - - -
226A GLY 3.3 3.8 + - - -
357A LEU* 4.3 0.4 - - - -
367A GLY 4.5 3.0 + - - -
368A THR* 4.1 16.4 - - - +
370A CYS* 3.3 26.8 + - + +
372A GLY 2.8 41.8 + - - +
373A PRO* 3.8 4.0 - - + +
388A TYR* 3.6 33.0 - - - +
389A ASP* 3.0 27.9 + - - -
701A SO4 2.8 43.5 + - - +
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Residues in contact with VAL 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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196A LEU* 4.9 0.4 - - + -
197A LEU* 4.2 18.8 - - + -
200A ASN* 3.5 45.8 - - + +
202A LYS* 4.6 8.5 - - + +
219A TYR* 2.9 47.9 + - + +
220A VAL* 3.1 6.5 + - - +
222A ARG* 1.3 77.9 - - + +
224A VAL* 1.3 63.2 + - - +
226A GLY* 3.2 2.9 + - - -
227A MET* 3.2 24.5 + - + +
370A CYS* 4.6 6.2 - - - -
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Residues in contact with VAL 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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196A LEU* 4.6 5.8 - - + -
197A LEU* 4.4 11.7 - - + -
220A VAL* 2.9 26.8 + - + +
221A GLY 3.1 7.1 + - - +
223A VAL* 1.3 76.2 - - - +
225A SER* 1.3 62.2 + - - +
226A GLY 3.3 0.7 + - - -
227A MET* 3.3 13.2 + - - +
228A VAL* 3.3 19.5 + - + +
284A ALA* 4.1 22.9 - - + -
287A VAL* 3.8 28.5 - - + -
288A LEU* 3.9 31.2 - - + -
291A LEU* 4.7 0.7 - - + -
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Residues in contact with SER 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 GLY 3.0 12.1 + - - -
222A ARG* 2.9 17.3 + - - -
224A VAL* 1.3 78.2 - - - +
226A GLY* 1.3 59.3 + - - +
228A VAL 4.4 1.2 + - - -
229A ASN* 5.1 1.2 + - - +
284A ALA* 5.9 0.9 - - - -
357A LEU* 4.2 15.7 - - - -
358A ASP 4.4 6.1 - - - +
359A PRO* 3.4 32.3 - - - +
369A TYR 4.0 6.6 - - - +
370A CYS* 3.5 1.4 - - - +
371A CYS 3.0 38.3 + - - -
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Residues in contact with GLY 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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222A ARG 3.3 2.4 + - - -
223A VAL 3.2 4.9 + - - -
224A VAL 3.1 0.4 - - - -
225A SER* 1.3 83.3 + - - +
227A MET* 1.3 64.2 + - - +
228A VAL 3.4 1.1 + - - -
229A ASN* 3.8 14.0 + - - +
230A CYS 5.3 0.7 - - - +
231A ASN* 5.7 1.9 - - - +
369A TYR* 3.9 23.3 - - - +
370A CYS* 3.6 23.1 - - - -
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Residues in contact with MET 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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196A LEU* 3.5 35.7 - - + +
199A VAL* 3.5 34.3 - - + +
200A ASN* 3.8 32.5 - - + -
201A PRO* 4.0 10.1 - - + -
223A VAL 3.2 15.0 + - - +
224A VAL 3.3 2.4 + - - +
226A GLY* 1.3 81.2 - - - +
228A VAL* 1.3 62.6 + - - +
229A ASN 3.5 3.1 - - - -
234A GLN* 4.0 26.5 - - + +
235A GLY* 3.5 6.6 - - - -
236A VAL* 3.2 26.0 + - - +
264A TRP* 4.8 1.8 - - + -
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Residues in contact with VAL 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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196A LEU* 5.3 6.1 - - + -
224A VAL* 3.3 20.5 + - + +
226A GLY 3.4 1.0 - - - -
227A MET* 1.3 80.4 - - - +
229A ASN* 1.3 57.8 + - - +
236A VAL* 3.4 6.6 + - - +
237A LEU* 3.0 33.2 + - + +
280A PHE* 3.3 43.7 - - + +
283A VAL* 4.4 11.9 - - + -
284A ALA* 3.8 30.7 - - + +
287A VAL* 5.6 0.7 - - + -
359A PRO* 3.8 13.0 - - + -
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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