Contacts of the helix formed by residues 302 - 312 (chain C) in PDB entry 1PL8
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 THR 302 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C TYR* 4.7 0.6 + - - -
158C SER* 2.7 45.1 + - - +
161C ILE* 3.7 27.3 - - + +
162C HIS* 4.3 4.7 - - + +
165C ARG* 3.7 8.5 - - - +
299C TYR* 4.0 11.2 - - + +
300C CYS 3.5 15.4 - - - +
301C ASN* 1.3 75.8 - - - +
303C TRP* 1.3 73.7 + - - +
304C PRO* 3.5 2.0 - - - -
305C VAL* 3.5 4.1 + - - +
306C ALA* 2.8 31.2 + - - +
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Residues in contact with TRP 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ALA* 3.8 21.3 - - + +
93C ILE 3.7 17.9 + - - +
94C GLU* 3.4 42.1 + - + +
95C PRO* 3.8 4.5 - - + -
140C TYR* 3.5 39.3 - + + -
151C GLY 4.8 1.0 + - - -
154C ILE* 3.4 24.0 - - + +
155C GLU* 3.7 30.7 - - + -
158C SER* 3.3 12.3 - - - -
299C TYR* 3.5 35.2 - + - -
302C THR* 1.3 100.7 + - - +
304C PRO* 1.3 74.0 - - + +
306C ALA* 3.2 1.4 + - - +
307C ILE* 2.9 30.1 + - - +
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Residues in contact with PRO 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C GLU* 5.5 0.2 - - - +
140C TYR* 3.7 25.8 - - + +
301C ASN* 4.7 6.5 - - - -
302C THR 3.8 5.2 - - - +
303C TRP* 1.3 96.1 - - + +
305C VAL* 1.3 59.0 - - + +
307C ILE* 3.4 9.7 + - + +
308C SER* 2.9 31.9 + - - -
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Residues in contact with VAL 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ILE* 4.3 11.7 - - + -
165C ARG* 3.5 28.7 - - - +
301C ASN 4.6 2.2 - - - +
302C THR 3.5 6.9 + - - +
303C TRP 3.2 0.6 - - - -
304C PRO* 1.3 79.2 - - + +
306C ALA* 1.3 66.4 + - - +
308C SER* 3.1 8.2 + - - +
309C MET* 2.9 22.8 + - + +
171D LEU* 3.5 47.1 - - + +
172D GLY* 4.5 4.9 - - - -
173D HIS* 5.8 3.1 - - + -
244D GLU* 5.9 2.0 - - - +
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Residues in contact with ALA 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ILE* 3.5 30.1 - - + -
157C LEU* 4.0 15.0 - - + +
158C SER* 4.6 0.4 - - - +
161C ILE* 3.9 17.7 - - + -
302C THR 2.8 23.4 + - - +
303C TRP 3.6 0.4 - - - +
305C VAL* 1.3 72.4 - - - +
307C ILE* 1.3 56.7 + - - +
309C MET* 3.2 5.6 + - - +
310C LEU* 2.9 35.9 + - - +
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Residues in contact with ILE 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ALA* 4.7 1.6 - - + -
140C TYR* 3.5 35.2 - - + +
141C LYS 3.7 15.0 - - - +
142C LEU* 4.3 9.6 - - + -
143C PRO* 3.5 30.7 - - + -
146C VAL* 4.7 1.5 - - + +
154C ILE* 3.6 20.9 - - + -
303C TRP* 2.9 20.8 + - + +
304C PRO* 3.6 7.2 - - + +
306C ALA* 1.3 77.2 - - - +
308C SER* 1.3 58.6 + - - +
310C LEU* 3.8 6.5 - - - +
311C ALA* 2.8 28.5 + - + +
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Residues in contact with SER 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C PRO 2.9 16.7 + - - -
305C VAL* 3.1 9.3 + - - -
307C ILE* 1.3 79.0 - - - +
309C MET* 1.3 59.8 + - - +
311C ALA* 4.0 5.3 - - - +
312C SER* 2.7 29.5 + - - -
172D GLY* 3.7 22.0 + - - -
174D LYS* 3.6 21.3 + - - +
197D ALA* 3.7 10.7 - - - +
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Residues in contact with MET 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C LEU* 5.7 1.1 - - + -
161C ILE* 6.0 0.7 - - + -
193C ALA* 5.2 2.2 - - + -
305C VAL* 2.9 16.7 + - + +
306C ALA* 3.6 9.6 - - - +
308C SER* 1.3 76.3 - - - +
310C LEU* 1.3 58.1 + - - +
312C SER* 3.2 0.7 + - - -
313C LYS 3.1 5.0 + - - -
314C SER* 2.8 51.3 + - - +
315C VAL* 3.7 21.0 + - + -
171D LEU* 3.6 31.4 - - + -
172D GLY* 3.2 9.0 - - - +
195D GLY* 3.1 24.0 - - - +
197D ALA* 3.1 45.8 - - + -
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Residues in contact with LEU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C VAL* 4.0 17.8 - - + +
150C GLU* 3.8 36.9 - - + +
154C ILE* 3.7 33.0 - - + -
157C LEU* 4.7 7.0 - - + -
306C ALA 2.9 22.4 + - - +
307C ILE* 3.8 3.6 - - - +
309C MET* 1.3 75.7 - - - +
311C ALA* 1.3 64.6 - - - +
313C LYS* 3.1 27.5 + - - +
315C VAL* 3.8 28.4 - - + +
317C VAL* 4.1 21.5 - - + +
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Residues in contact with ALA 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C PRO* 3.8 25.4 - - + -
145C ASN* 2.8 28.8 + - - +
146C VAL* 3.7 9.1 - - + +
307C ILE* 2.8 22.3 + - + +
308C SER* 4.0 5.4 - - - +
310C LEU* 1.3 74.1 - - - +
312C SER* 1.3 59.0 + - - +
313C LYS* 3.2 2.8 + - - +
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Residues in contact with SER 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C SER 2.7 22.5 + - - -
309C MET* 3.2 3.6 + - - -
311C ALA* 1.3 75.4 - - - +
313C LYS* 1.3 71.8 + - - +
314C SER* 2.6 26.9 + - - -
197D ALA* 3.3 28.8 + - - -
198D GLN* 4.8 6.5 - - - -
218D ASP* 5.9 0.7 - - - -
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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