Contacts of the helix formed by residues 303 - 312 (chain A) in PDB entry 1PG0
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 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A LEU* 3.8 15.2 - - + +
201A LEU* 3.5 25.4 - - + +
218A MET* 3.4 26.5 - - + -
221A TRP* 4.1 11.4 - - + -
222A PHE* 4.6 11.0 - - + -
226A LEU* 3.8 17.3 - - + -
299A TYR* 3.0 54.1 + - + +
302A SER* 1.3 84.8 - - - +
304A PHE* 1.3 68.9 + - - +
305A TRP 3.4 0.7 - - - -
306A PRO* 3.1 10.7 - - - +
307A ALA* 3.2 15.2 + - - +
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Residues in contact with PHE 304 (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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192A PHE* 4.0 2.6 - + - -
194A LEU* 3.4 34.8 - - + -
227A GLN 4.9 1.8 - - - -
229A TRP* 3.4 75.8 - + + -
299A TYR* 3.7 30.0 + + - -
300A PHE* 3.7 40.8 - + - +
303A LEU* 1.3 80.0 - - - +
305A TRP* 1.3 55.3 + - - +
307A ALA* 3.2 2.5 + - - +
308A MET* 2.8 40.5 + - - +
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Residues in contact with TRP 305 (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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109A ILE* 5.1 1.8 - - + -
257A PRO* 3.4 57.0 - - + -
258A ILE* 4.0 12.6 - - + -
260A TYR* 4.2 4.4 - + - -
261A MET* 3.9 15.0 - - - -
281A TRP* 3.9 18.8 - + - -
291A HIS* 2.8 33.9 - + - -
300A PHE 2.9 24.0 + - - +
301A HIS* 3.8 18.8 - + - +
304A PHE* 1.3 72.4 - - - +
306A PRO* 1.3 65.7 - - + +
308A MET* 3.2 15.8 + - + -
309A LEU* 3.1 56.7 + - + +
317A PRO* 3.6 17.0 - - + +
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Residues in contact with PRO 306 (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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200A MET* 4.5 0.4 - - - -
201A LEU* 3.8 16.2 - - + -
204A TRP* 3.8 18.4 - - + -
301A HIS 3.2 25.1 - - - +
302A SER 3.4 13.2 - - - +
303A LEU 3.1 20.0 - - - +
305A TRP* 1.3 85.1 - - + +
307A ALA* 1.3 56.1 + - - +
309A LEU* 3.3 8.3 + - + +
310A GLU* 2.9 29.7 + - - +
316A LYS* 3.7 25.0 - - + +
317A PRO* 4.4 6.7 - - + -
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Residues in contact with ALA 307 (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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192A PHE* 3.5 21.3 - - + -
194A LEU* 3.6 14.4 - - + -
197A PHE* 3.4 32.5 - - + -
200A MET* 4.4 2.9 - - - -
201A LEU* 4.4 2.8 - - + +
303A LEU 3.2 10.8 + - - +
304A PHE 3.2 9.9 + - - +
306A PRO* 1.3 77.9 - - - +
308A MET* 1.3 64.6 + - - +
310A GLU* 3.2 1.4 + - - -
311A GLY 2.9 20.8 + - - -
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Residues in contact with MET 308 (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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109A ILE* 4.2 13.8 - - + +
113A LEU* 3.7 11.6 - - + +
192A PHE* 3.8 24.2 - - + -
229A TRP* 4.0 14.1 - - - -
254A LEU* 3.3 50.9 - - + +
257A PRO* 4.7 4.7 - - + -
258A ILE* 4.0 19.7 - - + -
304A PHE* 2.8 30.4 + - - +
305A TRP* 3.6 21.8 - - + +
307A ALA* 1.3 72.3 - - - +
309A LEU* 1.3 54.6 + - - +
311A GLY 3.6 0.2 + - - -
312A SER* 2.7 33.7 + - - -
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Residues in contact with LEU 309 (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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109A ILE* 5.1 2.0 - - + -
261A MET* 4.0 13.7 - - - -
281A TRP* 4.0 9.0 - - + -
289A LEU* 5.2 0.2 - - + -
305A TRP* 3.1 64.4 + - + +
306A PRO* 3.6 5.4 - - + +
308A MET* 1.3 75.1 - - - +
310A GLU* 1.3 66.1 + - - +
312A SER* 3.1 9.5 + - - +
314A PHE* 2.9 49.5 + - + +
315A ARG 3.2 25.6 - - - +
316A LYS* 3.9 0.7 - - + -
317A PRO* 3.9 17.9 - - + -
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Residues in contact with GLU 310 (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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197A PHE* 3.8 11.9 - - + -
200A MET* 3.4 39.9 - - + +
283A LYS* 4.9 16.4 - - - +
306A PRO 2.9 17.2 + - - +
307A ALA 3.2 4.2 + - - +
309A LEU* 1.3 77.9 - - - +
311A GLY* 1.3 62.6 + - - +
312A SER 3.1 0.7 + - - -
313A ASN* 3.2 11.3 + - - -
314A PHE 4.0 6.9 + - - +
316A LYS* 3.1 26.0 + - + +
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Residues in contact with GLY 311 (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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112A ARG 4.0 1.6 - - - +
113A LEU* 3.8 14.9 - - - +
116A ASN* 2.8 27.9 - - - +
118A PHE* 3.7 15.3 - - - -
197A PHE* 3.5 18.0 - - - -
307A ALA 2.9 13.3 + - - -
310A GLU* 1.3 76.6 - - - +
312A SER* 1.3 57.2 + - - +
313A ASN 3.5 1.1 - - - -
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Residues in contact with SER 312 (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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109A ILE* 3.9 24.7 - - - +
112A ARG* 3.0 44.6 + - - -
113A LEU* 4.5 0.7 - - - -
116A ASN* 5.2 1.1 - - - -
308A MET 2.7 22.0 + - - -
309A LEU* 3.1 6.3 + - - -
311A GLY* 1.3 76.9 - - - +
313A ASN* 1.3 68.0 + - - +
314A PHE* 3.2 21.9 - - - -
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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