Contacts of the helix formed by residues 212 - 223 (chain A) in PDB entry 1DWQ
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 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A SER* 3.9 28.5 + - - +
125A PHE* 3.8 22.2 - - + -
208A ASP 3.6 16.4 - - - +
209A LYS* 3.7 23.8 - - + +
210A ILE 3.2 8.0 + - - +
211A PHE* 1.3 74.1 - - - +
213A PRO* 1.3 67.8 - - + +
214A ASP* 3.1 4.7 - - + +
215A PHE* 2.8 28.4 + - - +
216A GLN* 2.9 10.4 + - - +
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Residues in contact with PRO 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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204A TRP* 3.8 16.8 - - + -
205A THR 5.3 0.2 - - - +
206A ASP* 3.4 36.3 - - + +
208A ASP 4.4 4.0 - - - +
211A PHE 4.6 0.2 - - - +
212A LEU* 1.3 92.6 - - + +
214A ASP* 1.3 62.1 + - - +
217A ARG* 2.9 55.6 + - - +
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Residues in contact with ASP 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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124A SER* 5.9 0.7 - - - +
212A LEU* 3.0 3.7 + - + +
213A PRO* 1.3 87.5 - - - +
215A PHE* 1.3 60.3 + - - +
217A ARG* 4.1 17.6 + - - +
218A TRP* 3.3 21.0 + - - +
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Residues in contact with PHE 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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106A LEU* 3.9 5.4 - - + -
117A THR 3.5 17.7 - - - -
120A LYS* 3.7 10.8 - - + -
121A LEU* 3.4 52.3 - - + -
124A SER* 3.4 24.3 + - - +
211A PHE* 4.0 22.0 - + + -
212A LEU* 2.8 17.2 + - - +
214A ASP* 1.3 71.2 - - - +
216A GLN* 1.3 68.1 + - - +
218A TRP* 3.2 28.3 + + - +
219A GLN* 2.9 54.6 + - - +
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Residues in contact with GLN 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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104A ASN* 3.1 30.3 + - - +
202A TYR* 2.7 32.0 + - + +
204A TRP* 3.2 43.7 - - + +
205A THR 3.9 6.3 + - - -
208A ASP* 3.2 9.5 + - - -
211A PHE* 3.0 43.4 + - + +
212A LEU 2.9 9.4 + - - +
213A PRO 3.9 0.2 - - - +
215A PHE* 1.3 76.8 - - + +
217A ARG* 1.3 59.8 + - - +
219A GLN* 2.8 22.3 + - - +
220A ILE* 3.1 16.3 + - - +
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Residues in contact with ARG 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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204A TRP* 3.7 35.2 - - + -
206A ASP* 4.7 7.3 + - - +
213A PRO* 2.9 32.7 + - - +
214A ASP* 4.1 15.9 + - - +
216A GLN* 1.3 74.7 - - - +
218A TRP* 1.3 64.0 + - - +
220A ILE* 3.1 13.0 + - + +
221A ALA* 2.9 24.4 + - - +
230A GLN* 4.6 10.5 + - - +
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Residues in contact with TRP 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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116A TYR* 3.3 47.1 + + - -
117A THR* 4.0 13.9 - - + -
120A LYS* 3.5 36.3 - - + +
214A ASP 3.3 18.9 + - - +
215A PHE* 3.2 21.9 + + - +
217A ARG* 1.3 77.9 - - - +
219A GLN* 1.3 75.4 + - + +
221A ALA* 3.1 8.0 + - + +
222A ASN* 2.7 51.2 + - + +
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Residues in contact with GLN 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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105A SER 2.7 27.3 + - - -
106A LEU* 3.3 4.7 - - - -
107A LEU* 2.8 39.4 + - + +
117A THR* 3.7 10.6 - - + +
202A TYR* 2.8 26.1 + - + +
211A PHE* 5.3 0.4 - - - -
215A PHE* 2.9 45.9 + - + +
216A GLN 2.8 8.4 + - - +
218A TRP* 1.3 94.9 - - + +
220A ILE* 1.3 60.3 + - - +
222A ASN* 3.2 3.9 + - - +
223A TYR* 3.0 20.4 + - - +
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Residues in contact with ILE 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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107A LEU* 4.5 0.7 - - - -
202A TYR* 3.7 42.2 - - + -
204A TRP* 4.1 13.5 - - + +
216A GLN 3.1 10.4 + - - +
217A ARG* 3.5 13.7 - - + +
219A GLN* 1.3 74.8 - - - +
221A ALA* 1.3 63.7 + - - +
223A TYR 4.5 0.2 - - - -
224A LYS* 3.3 26.6 + - + +
225A PRO* 3.8 20.6 - - + -
228A VAL* 4.0 26.0 - - + -
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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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217A ARG 2.9 12.1 + - - +
218A TRP* 3.4 13.7 - - + +
220A ILE* 1.3 80.7 - - - +
222A ASN* 1.3 61.0 + - - +
223A TYR* 3.4 0.3 + - - -
224A LYS* 4.6 2.6 + - - +
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Residues in contact with ASN 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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107A LEU 4.9 1.6 + - - -
109A ASP* 3.0 34.3 + - - +
111A VAL* 6.1 0.9 - - - +
112A HIS* 3.7 16.6 - - - -
116A TYR* 3.9 11.3 + - - -
117A THR* 4.8 5.7 - - - +
218A TRP* 2.7 47.7 + - + +
219A GLN* 3.2 6.7 + - - +
221A ALA* 1.3 74.3 - - - +
223A TYR* 1.3 64.0 + - - +
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Residues in contact with TYR 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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107A LEU* 3.3 29.9 - - + +
108A PRO 3.5 17.7 - - - +
109A ASP* 3.5 24.0 - - + -
110A THR* 3.7 22.9 + - - +
111A VAL* 5.2 6.3 - - + -
192A GLU* 4.3 4.2 + - - -
195A TYR* 4.2 2.4 - + - -
196A GLY* 3.6 28.6 + - - -
200A LYS* 3.4 32.9 + - + -
219A GLN 3.0 7.9 + - - +
220A ILE 3.4 2.7 - - - -
222A ASN* 1.3 90.6 - - - +
224A LYS* 1.3 69.9 + - - +
225A PRO* 3.1 9.2 - - - +
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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