Contacts of the helix formed by residues 216 - 228 (chain A) in PDB entry 1PVS
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 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A GLN* 4.6 1.2 - - - +
210A GLN* 3.9 4.7 - - - -
214A GLY 3.9 3.4 + - - -
215A ILE* 1.3 76.2 - - - +
217A ARG* 1.3 59.9 + - - -
218A TRP 3.3 2.9 - - - -
219A THR* 4.0 10.0 + - - -
220A ALA* 2.9 30.8 + - - +
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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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203A GLU* 4.0 19.6 + - - -
206A MET* 4.0 16.4 - - - +
207A LYS* 5.2 1.4 - - - +
210A GLN* 2.9 39.7 + - - +
216A GLY* 1.3 68.2 - - - -
218A TRP* 1.3 60.2 + - - +
220A ALA* 3.4 1.2 + - - +
221A ASN* 2.9 65.0 + - - +
236A PRO* 6.0 1.1 - - + -
237A ASP* 3.6 20.4 - - - +
254A ARG* 5.3 13.5 - - - +
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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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120A ALA 3.6 22.0 - - - -
123A GLY* 3.7 20.0 - - - -
124A GLN* 4.0 2.2 - - + -
216A GLY 3.3 0.4 - - - -
217A ARG* 1.3 79.2 - - - +
219A THR* 1.3 78.9 + - - +
221A ASN* 3.7 4.6 - - - +
222A TYR* 2.8 64.5 + + + +
235A LEU* 3.8 16.2 - - + +
237A ASP* 4.2 14.8 + - + -
238A ASP* 3.2 36.2 + - + -
272A TRP* 5.6 1.6 - + - -
800A 7HP 3.4 65.8 + + + +
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Residues in contact with THR 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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117A GLY 5.2 0.2 - - - +
120A ALA* 3.9 20.3 - - + +
121A ILE* 4.1 14.1 - - + +
124A GLN* 2.9 41.1 + - - +
215A ILE* 4.2 13.2 - - + -
216A GLY* 3.5 15.4 + - - -
218A TRP* 1.3 89.3 - - - +
220A ALA* 1.3 54.2 - - - +
222A TYR* 3.8 1.7 - - - +
223A PHE* 2.7 40.5 + - + +
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Residues in contact with ALA 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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206A MET* 3.9 18.0 - - + +
209A LEU* 4.5 10.5 - - + +
210A GLN* 3.6 28.0 - - + +
215A ILE* 4.2 9.6 - - + +
216A GLY 2.9 19.2 + - - +
217A ARG 3.5 4.5 - - - +
219A THR* 1.3 76.4 - - - +
221A ASN* 1.3 60.2 - - - +
223A PHE* 3.8 4.5 - - - +
224A ALA* 2.9 28.4 + - - +
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Residues in contact with ASN 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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206A MET* 3.7 18.8 - - - +
217A ARG* 2.9 62.8 + - - +
218A TRP* 3.8 3.8 - - - +
220A ALA* 1.3 76.5 - - - +
222A TYR* 1.3 58.8 + - - +
224A ALA* 3.2 3.1 + - - +
225A LEU* 3.0 29.1 + - - +
233A VAL* 3.9 10.0 - - + +
234A PHE 3.2 17.7 - - - +
235A LEU* 3.6 19.8 - - + -
236A PRO* 4.1 11.3 - - - +
237A ASP* 4.9 1.0 - - - +
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Residues in contact with TYR 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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18A PHE* 4.6 1.4 - - - -
22A ARG* 3.7 15.9 + - - -
116A GLN* 4.7 7.6 - - + -
119A ARG* 5.7 1.8 - - + -
120A ALA* 4.1 22.9 - - + -
123A GLY* 6.3 1.1 - - - -
218A TRP* 2.8 44.9 + + + +
219A THR* 3.8 4.3 - - - +
221A ASN* 1.3 72.6 - - - +
223A PHE* 1.4 66.9 + - - +
225A LEU* 3.1 11.7 + - + +
226A ARG* 2.9 67.6 + - + +
235A LEU* 3.8 24.4 - - + +
272A TRP* 3.8 25.4 - + - -
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Residues in contact with PHE 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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113A ALA* 3.7 22.9 - - + -
116A GLN* 4.6 2.9 - - - -
117A GLY* 3.7 24.0 - - - -
120A ALA* 4.3 13.4 - - + +
194A LEU* 3.9 21.1 - - + -
195A PRO 4.2 3.4 - - - -
209A LEU* 3.0 36.8 - - + -
219A THR* 2.7 25.5 + - + +
220A ALA 3.8 1.3 - - - +
222A TYR* 1.4 75.5 - - - +
224A ALA* 1.4 59.1 + - - +
226A ARG* 5.3 0.9 - - - -
227A GLY* 2.5 45.8 + - - +
228A TRP* 3.2 43.0 + + - -
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Residues in contact with ALA 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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202A VAL* 4.2 7.4 - - + -
206A MET* 3.8 19.3 - - + -
220A ALA 2.9 17.6 + - - +
221A ASN 3.2 4.9 + - - +
223A PHE* 1.4 80.3 - - - +
225A LEU* 1.3 63.1 + - - +
228A TRP* 3.0 48.2 + - + +
229A GLN 3.0 7.3 + - - -
230A ALA* 3.1 11.7 + - + -
233A VAL* 4.6 2.7 - - + -
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Residues in contact with LEU 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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107A LEU* 3.2 36.6 - - + +
221A ASN 3.0 8.1 + - - +
222A TYR* 3.4 13.2 - - + +
224A ALA* 1.3 78.7 - - - +
226A ARG* 1.3 81.1 + - + +
229A GLN* 3.0 24.4 - - - -
230A ALA 3.6 4.8 + - - -
233A VAL* 3.4 29.4 - - + +
235A LEU* 4.3 8.1 - - + -
265A SER* 4.0 8.5 - - - +
268A LEU* 3.1 35.9 - - + -
269A LEU* 5.3 5.6 - - + -
272A TRP* 5.7 1.6 - - + -
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Residues in contact with ARG 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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18A PHE* 3.4 21.7 - - - -
19A LEU* 5.3 6.1 - - - +
22A ARG* 3.3 32.9 - - - +
108A PRO* 3.0 26.6 + - - +
109A GLY* 2.6 43.8 + - - -
110A CYS* 3.7 1.0 - - - -
116A GLN* 3.2 37.7 + - + +
119A ARG* 5.8 4.2 - - - +
222A TYR* 2.9 46.9 + - + +
225A LEU* 1.3 91.2 - - + +
227A GLY* 1.3 58.1 + - - +
228A TRP 3.4 0.2 - - - -
229A GLN* 2.6 26.0 + - - -
269A LEU* 6.4 0.2 - - - -
272A TRP* 6.3 0.2 - - - -
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Residues in contact with GLY 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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110A CYS* 3.9 11.8 - - - -
113A ALA* 4.1 9.2 - - - +
116A GLN* 3.8 17.1 - - - +
196A MET 4.6 2.8 - - - +
197A THR* 5.7 0.2 - - - -
223A PHE* 2.5 31.8 + - - -
226A ARG* 1.3 70.1 - - - +
228A TRP* 1.3 67.4 + - - -
229A GLN* 3.0 14.9 + - - +
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Residues in contact with TRP 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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113A ALA* 4.9 0.7 - - + -
195A PRO* 2.7 48.6 + - + +
196A MET 4.7 0.7 - - - -
197A THR 4.0 14.1 - - - -
198A ILE* 3.4 39.4 + - + +
199A PRO* 3.6 17.0 - - + -
202A VAL* 4.1 14.4 - - + -
205A ALA* 3.5 36.3 - - + -
206A MET* 4.1 6.5 - - + -
209A LEU* 4.5 7.0 - - + -
223A PHE* 3.2 31.9 + + - -
224A ALA* 3.0 36.1 + - + +
227A GLY* 1.3 83.3 - - - +
229A GLN* 1.3 80.9 + - - +
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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