Contacts of the helix formed by residues 212 - 221 (chain A) in PDB entry 4WNC
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 GLY 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A THR* 1.3 72.8 + - - +
213A ALA* 1.3 58.8 + - - +
214A ALA 3.4 2.4 + - - -
215A LYS* 3.4 17.0 + - - +
216A ALA* 2.9 30.4 + - - +
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Residues in contact with ALA 213 (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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151A SER* 3.9 5.2 - - - +
153A THR* 3.5 34.8 - - + -
154A THR* 3.1 30.5 + - - +
157A LEU* 5.0 1.1 - - - -
175A MET* 5.0 1.1 - - + -
211A THR* 3.0 18.9 + - + +
212A GLY* 1.3 79.0 - - - +
214A ALA* 1.3 61.5 + - - +
216A ALA* 3.3 8.0 + - - -
217A VAL* 3.4 12.9 + - - +
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Residues in contact with ALA 214 (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 LEU* 3.9 24.0 - - + +
175A MET* 4.2 11.4 - - + +
211A THR 4.9 1.4 + - - +
212A GLY 3.4 0.4 - - - -
213A ALA* 1.3 75.6 - - - +
215A LYS* 1.3 67.6 + - - +
217A VAL* 3.1 19.8 + - - +
218A GLY 3.9 1.0 + - - -
228A LEU* 3.7 14.7 - - + +
229A THR* 3.3 38.1 - - - +
230A GLY* 3.7 4.5 - - - +
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Residues in contact with LYS 215 (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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211A THR 5.6 0.4 + - - +
212A GLY* 3.4 16.3 + - - +
214A ALA* 1.3 78.1 - - - +
216A ALA* 1.3 56.5 - - - +
218A GLY* 3.0 21.1 + - - -
219A LYS* 3.9 11.3 + - - +
225A ASN* 5.3 6.8 + - - +
226A GLY* 5.7 4.6 + - - +
228A LEU* 3.7 14.4 + - - +
229A THR* 4.3 21.4 + - - +
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Residues in contact with ALA 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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124A PRO* 6.3 2.0 - - + -
130A MET* 3.7 25.1 - - + +
150A ALA* 5.8 0.2 - - + -
154A THR* 3.7 15.5 - - + +
212A GLY 2.9 19.0 + - - +
213A ALA* 3.4 8.7 - - - +
214A ALA 3.1 0.4 - - - -
215A LYS* 1.3 72.4 - - - +
217A VAL* 1.3 59.0 + - - +
218A GLY 3.0 2.0 - - - -
219A LYS* 2.9 29.6 + - - +
220A VAL* 3.3 13.3 + - - +
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Residues in contact with VAL 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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154A THR* 4.3 5.4 - - + -
157A LEU* 3.6 31.2 - - + -
158A ALA* 4.2 13.7 - - + +
161A ALA* 4.2 7.6 - - + -
213A ALA 3.5 14.8 - - - +
214A ALA 3.1 10.9 + - - +
216A ALA* 1.3 78.6 - - - +
218A GLY* 1.3 52.4 + - - +
220A VAL* 3.2 7.0 + - - +
221A ILE* 2.7 56.3 + - + +
224A LEU* 4.1 5.6 - - + -
228A LEU* 3.7 20.6 - - + -
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Residues in contact with GLY 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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214A ALA 3.9 1.6 + - - -
215A LYS 3.0 13.8 + - - -
217A VAL* 1.3 79.1 - - - +
219A LYS* 1.3 57.2 + - - +
221A ILE 3.3 19.0 - - - +
222A PRO* 3.4 12.3 - - - +
224A LEU* 3.8 8.9 + - - +
225A ASN* 3.7 33.7 + - - +
226A GLY 5.1 0.2 - - - -
228A LEU* 5.2 0.8 - - - +
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Residues in contact with LYS 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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125A SER 5.3 6.5 - - - -
126A ALA 5.7 4.0 - - - -
130A MET* 4.2 30.5 - - + +
136A ASN* 4.7 2.8 + - - -
215A LYS* 3.9 9.8 + - - +
216A ALA* 2.9 18.4 + - - +
218A GLY* 1.3 78.7 - - - +
220A VAL* 1.3 63.9 + - + +
221A ILE 3.3 0.4 - - - -
222A PRO* 4.1 10.7 - - - +
225A ASN* 5.5 5.2 - - - +
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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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130A MET* 4.0 35.0 - - + +
132A VAL* 4.0 19.7 - - + -
135A VAL* 3.9 6.7 - - + +
136A ASN* 3.6 36.7 - - - +
154A THR* 4.8 3.4 - - + -
158A ALA* 3.9 23.6 - - + -
216A ALA 3.3 6.9 + - - +
217A VAL* 3.4 20.4 - - - +
219A LYS* 1.3 78.4 - - - +
221A ILE* 1.3 66.5 + - + +
222A PRO* 3.6 7.0 - - - +
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Residues in contact with ILE 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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135A VAL* 3.5 17.7 - - + -
158A ALA* 3.6 24.7 - - - +
162A LYS* 3.8 24.2 - - + +
165A HIS* 4.8 11.7 - - + -
217A VAL* 2.7 30.2 + - + +
218A GLY 3.3 8.8 - - - +
220A VAL* 1.3 81.6 - - + +
222A PRO* 1.3 59.6 - - + +
223A GLU* 4.5 4.5 - - + +
224A LEU* 2.8 47.4 + - + +
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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