Contacts of the helix formed by residues 336 - 345 (chain D) in PDB entry 1P7L
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 ARG 336 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112D LEU* 4.3 29.8 + - - +
113D GLU* 4.6 7.7 - - - +
305D ALA* 3.4 27.4 - - + +
306D GLU* 3.4 28.7 + - - +
307D PRO* 4.2 5.6 - - + -
334D ASP* 3.1 28.0 + - - +
335D LEU* 1.3 78.0 - - - +
337D PRO* 1.3 75.9 - - + +
338D TYR 4.6 2.2 - - - +
339D GLY 2.7 16.6 + - - +
340D LEU* 3.1 8.8 + - - +
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Residues in contact with PRO 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D LEU 5.6 0.2 - - - +
114D GLN 3.1 20.9 - - - +
115D GLY 4.1 5.2 - - - +
116D ALA* 3.6 22.4 - - - +
268D SER* 5.6 4.7 - - - +
270D VAL* 5.2 4.9 - - + -
300D TYR* 4.2 10.8 - - + -
305D ALA* 2.7 30.1 - - + +
335D LEU 3.6 3.5 - - - +
336D ARG* 1.3 78.0 - - + +
338D TYR* 1.3 77.3 + - + +
339D GLY 3.0 2.9 + - - -
340D LEU* 3.1 24.8 + - + +
341D ILE* 3.2 17.2 - - - +
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Residues in contact with TYR 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LYS* 6.2 3.4 - - + -
38D ARG* 3.0 28.8 + - - -
106D VAL* 3.4 10.6 - - - +
107D ASP* 3.1 9.0 + - - -
111D PRO* 3.2 20.0 - - + +
112D LEU* 4.1 18.1 + - + +
114D GLN* 3.0 56.3 + - + -
115D GLY 4.0 5.6 - - - -
268D SER* 3.7 11.8 - - - -
336D ARG* 3.2 3.5 - - - +
337D PRO* 1.3 93.6 - - + +
339D GLY* 1.3 55.8 + - - +
341D ILE* 4.6 15.3 - - + -
342D GLN* 3.9 18.1 - - - +
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Residues in contact with GLY 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334D ASP* 3.5 34.7 - - - +
336D ARG* 2.7 16.5 + - - +
338D TYR* 1.3 74.7 - - - +
340D LEU* 1.3 56.7 + - - +
341D ILE 3.3 1.1 - - - -
342D GLN* 3.5 5.3 + - - +
343D MET* 2.9 28.2 + - - +
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Residues in contact with LEU 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D PRO 5.3 0.2 - - - +
270D VAL* 5.0 3.6 - - + -
273D SER* 3.9 29.6 - - - +
274D ALA* 4.2 6.5 - - - +
277D ALA* 3.8 30.5 - - + -
300D TYR* 3.4 11.0 - - - +
334D ASP 3.5 4.2 + - - +
335D LEU* 3.2 34.1 - - + +
336D ARG 3.1 6.9 + - - +
337D PRO* 3.1 32.8 - - + +
339D GLY* 1.3 75.5 - - - +
341D ILE* 1.3 60.0 + - + +
343D MET* 3.4 10.1 - - + +
344D LEU* 2.9 35.5 + - + +
346D LEU* 4.1 1.7 - - - +
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Residues in contact with ILE 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ARG* 6.1 0.4 - - - +
267D PRO* 3.3 43.5 - - + +
268D SER* 3.7 9.6 - - - +
337D PRO 3.2 20.6 - - - +
338D TYR* 4.6 16.6 - - + -
339D GLY 3.3 0.6 - - - -
340D LEU* 1.3 80.7 - - + +
342D GLN* 1.3 55.5 + - + +
345D ASP* 2.6 34.3 + - - -
346D LEU* 3.0 20.8 + - + -
347D LEU* 3.2 40.8 - - + +
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Residues in contact with GLN 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D TYR 3.9 17.5 - - - +
339D GLY* 3.5 7.0 + - - +
340D LEU 3.2 0.2 - - - -
341D ILE* 1.3 76.2 - - + +
343D MET* 1.3 68.3 + - - +
344D LEU 3.1 1.3 + - - -
345D ASP* 3.2 12.7 + - - +
347D LEU* 3.8 19.8 - - - +
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Residues in contact with MET 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D ALA* 3.2 36.8 - - + +
280D TYR* 3.4 43.5 + - + +
281D VAL* 5.5 0.2 - - + -
333D PHE* 4.3 17.5 - - + -
334D ASP* 4.2 18.4 - - + +
335D LEU* 4.9 1.8 - - + -
339D GLY 2.9 19.7 + - - +
340D LEU* 3.4 7.0 - - + +
342D GLN* 1.3 79.1 - - - +
344D LEU* 1.3 75.8 + - + +
372D LYS* 6.2 0.4 - - + -
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Residues in contact with LEU 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D SER 4.4 0.9 - - - +
276D TYR* 4.3 12.1 - - + -
277D ALA* 3.9 21.8 - - + +
280D TYR* 4.0 13.7 - - + -
340D LEU 2.9 15.5 + - - +
343D MET* 1.3 111.7 - - + +
345D ASP* 1.3 74.4 + - - +
346D LEU* 3.4 23.3 + - + +
366D PRO* 3.5 46.6 - - + +
367D TRP* 3.8 15.0 - - + -
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Residues in contact with ASP 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D ILE 2.6 16.9 + - - -
342D GLN* 3.2 10.5 + - - +
344D LEU* 1.3 77.0 - - - +
346D LEU* 1.3 59.9 + - - +
347D LEU* 3.4 11.2 + - - +
348D HIS* 3.0 39.0 + - - +
350D ILE* 4.6 7.3 - - - +
366D PRO* 5.3 1.5 - - + +
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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