Contacts of the helix formed by residues 215 - 220 (chain A) in PDB entry 4SBV
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 ILE 215 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A ALA* 3.9 20.6 - - + +
211A VAL* 4.2 12.6 - - + -
212A ASN* 3.1 13.6 + - + +
214A ASN* 1.3 79.6 - - - +
216A GLY* 1.3 53.9 + - - +
217A ASN 2.7 16.4 + - - -
218A ILE* 2.8 33.9 + - + +
219A LEU* 2.8 19.1 - - + +
215B ILE* 4.2 17.3 - - + -
218B ILE* 5.5 1.1 - - - -
212C ASN* 4.0 12.8 - - + -
214C ASN* 3.6 19.5 - - - +
215C ILE* 3.4 39.3 - - + -
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Residues in contact with GLY 216 (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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139A MET* 3.8 12.6 - - - -
205A TYR* 3.7 20.6 - - - -
209A VAL* 3.8 14.5 - - - +
213A ALA 4.7 0.2 - - - -
214A ASN 3.2 2.6 - - - +
215A ILE* 1.3 78.0 - - - +
217A ASN* 1.3 53.0 + - - +
219A LEU* 2.7 32.0 + - - +
220A VAL* 2.9 18.7 + - - +
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Residues in contact with ASN 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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137A TYR 3.8 5.2 + - - +
138A ASP* 3.1 20.7 + - - +
139A MET* 2.4 39.3 + - - +
193A SER* 4.7 9.0 + - - -
194A GLU* 4.5 6.2 - - - +
197A TYR* 4.5 5.4 - - - -
214A ASN* 3.2 30.6 + - - +
215A ILE 2.7 4.0 + - - -
216A GLY* 1.3 73.9 - - - +
218A ILE* 1.3 52.6 + - - -
220A VAL 4.2 11.9 - - - +
198B PRO* 4.1 23.2 - - - +
218B ILE* 5.1 9.5 - - + +
219B LEU* 5.0 4.2 - - - +
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Residues in contact with ILE 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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194A GLU* 4.3 17.9 - - - +
196A ARG 5.5 0.2 - - - +
197A TYR* 3.5 16.8 - - - -
198A PRO* 4.1 8.2 - - + +
214A ASN 4.6 0.2 - - - +
215A ILE* 2.8 34.4 + - + +
217A ASN* 1.3 71.9 - - - +
219A LEU* 1.3 70.3 - - + +
220A VAL 3.7 0.4 - - - -
215B ILE* 6.5 0.2 - - + -
218B ILE* 3.3 38.6 - - + -
214C ASN 4.5 7.2 - - - +
215C ILE* 5.2 3.1 - - - +
217C ASN* 4.4 23.1 - - + +
218C ILE* 3.5 27.6 - - + -
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Residues in contact with LEU 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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92A MET* 5.1 1.7 - - - +
110A TYR* 4.8 1.9 + - - -
197A TYR* 3.6 10.5 - - - +
198A PRO* 4.2 19.8 - - + +
200A LYS* 3.2 30.3 - - + +
205A TYR* 4.2 17.7 - - + -
208A ALA* 5.0 8.1 - - + -
215A ILE* 2.8 52.7 - - + +
216A GLY* 2.7 12.3 + - - +
218A ILE* 1.3 90.3 - - + +
220A VAL* 1.3 62.3 + - - +
221A PRO* 4.5 0.5 - - - +
214C ASN* 3.0 33.2 - - - +
217C ASN* 4.9 4.3 - - - +
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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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90A LEU* 4.5 0.7 - - + -
91A VAL 5.1 0.4 - - - +
92A MET* 2.9 39.5 - - + -
137A TYR 5.3 3.3 - - - +
139A MET* 3.5 38.9 - - + +
197A TYR* 3.5 8.6 + - - -
205A TYR* 3.6 16.2 - - + -
216A GLY 2.9 19.6 + - - +
217A ASN* 4.2 8.0 - - - +
218A ILE 3.7 1.2 - - - -
219A LEU* 1.3 80.5 - - + +
221A PRO* 1.3 72.2 - - + +
222A ALA 4.1 9.4 - - - +
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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