Contacts of the helix formed by residues 336 - 345 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C LEU* 4.2 30.7 + - - +
113C GLU* 4.6 7.3 - - - +
305C ALA* 3.4 27.2 - - + +
306C GLU* 3.3 28.3 + - - +
307C PRO* 4.1 6.1 - - + -
334C ASP* 3.2 26.8 + - - +
335C LEU* 1.3 79.9 - - - +
337C PRO* 1.3 76.8 - - + +
338C TYR 4.6 1.8 - - - +
339C GLY 2.7 17.1 + - - +
340C LEU* 3.1 8.4 + - - +
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Residues in contact with PRO 337 (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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114C GLN 3.1 20.0 - - - +
115C GLY 4.0 4.7 - - - +
116C ALA* 3.5 24.0 - - - +
268C SER* 5.6 5.2 - - - +
270C VAL* 5.2 4.9 - - + -
300C TYR* 4.1 10.8 - - + -
305C ALA* 2.7 29.6 - - + +
335C LEU 3.6 3.5 - - - +
336C ARG* 1.3 78.4 - - + +
338C TYR* 1.3 76.2 + - + +
339C GLY 3.1 2.8 + - - -
340C LEU* 3.0 25.1 + - + +
341C ILE* 3.2 16.3 - - - +
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Residues in contact with TYR 338 (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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36C LYS* 6.3 3.1 - - + -
38C ARG* 3.1 28.7 + - - -
106C VAL* 3.3 11.1 - - - +
107C ASP* 3.1 9.5 + - - -
111C PRO* 3.2 20.6 - - + +
112C LEU* 4.1 18.2 + - + +
114C GLN* 3.0 63.9 + - + -
115C GLY 3.9 5.8 - - - -
268C SER* 3.8 10.9 - - - -
336C ARG* 3.2 3.7 - - - +
337C PRO* 1.3 85.2 - - + +
339C GLY* 1.3 56.0 + - - +
341C ILE* 4.6 16.4 - - + -
342C GLN* 3.9 18.6 - - - +
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Residues in contact with GLY 339 (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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334C ASP* 3.5 34.4 - - - +
336C ARG* 2.7 16.5 + - - +
338C TYR* 1.3 74.1 - - - +
340C LEU* 1.3 58.1 + - - +
341C ILE 3.3 1.1 - - - -
342C GLN* 3.5 5.2 + - - +
343C MET* 2.9 27.9 + - - +
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Residues in contact with LEU 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C PRO 5.3 0.4 - - - +
270C VAL* 5.0 3.8 - - + -
273C SER* 4.0 29.8 - - - +
274C ALA* 4.2 7.0 - - - +
277C ALA* 3.8 30.7 - - + -
300C TYR* 3.5 10.5 - - - +
334C ASP 3.4 4.6 + - - +
335C LEU* 3.2 34.1 - - + +
336C ARG 3.1 6.7 + - - +
337C PRO* 3.0 33.7 - - + +
339C GLY* 1.3 76.3 - - - +
341C ILE* 1.3 59.5 + - + +
343C MET* 3.4 9.4 - - + +
344C LEU* 2.9 35.4 + - + +
346C LEU* 4.0 1.9 - - - +
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Residues in contact with ILE 341 (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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38C ARG* 6.0 0.9 - - - +
267C PRO* 3.3 42.6 - - + +
268C SER* 3.8 9.9 - - - +
337C PRO 3.2 20.8 + - - +
338C TYR* 4.6 17.7 - - + -
339C GLY 3.3 0.6 - - - -
340C LEU* 1.3 80.3 - - + +
342C GLN* 1.3 55.3 + - + +
345C ASP* 2.7 34.0 + - - -
346C LEU* 3.0 19.9 + - + -
347C LEU* 3.2 40.9 - - + +
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Residues in contact with GLN 342 (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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338C TYR 3.9 18.2 - - - +
339C GLY* 3.5 6.8 + - - +
340C LEU 3.2 0.4 - - - -
341C ILE* 1.3 76.9 - - + +
343C MET* 1.3 70.3 + - - +
344C LEU 3.1 1.3 + - - -
345C ASP* 3.2 12.1 + - - +
347C LEU* 3.8 19.9 - - - +
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Residues in contact with MET 343 (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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277C ALA* 3.3 35.7 - - + +
280C TYR* 3.3 45.4 + - + +
333C PHE* 4.4 17.3 - - + -
334C ASP* 4.2 19.1 - - + +
335C LEU* 5.0 1.8 - - + -
339C GLY 2.9 19.1 + - - +
340C LEU* 3.4 6.5 - - + +
342C GLN* 1.3 79.3 - - - +
344C LEU* 1.3 75.8 + - + +
372C LYS* 6.1 0.4 - - + -
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Residues in contact with LEU 344 (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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273C SER 4.4 1.1 - - - +
276C TYR* 4.3 8.1 - - + -
277C ALA* 3.9 21.5 - - + +
280C TYR* 4.0 11.4 - - + -
340C LEU 2.9 16.8 + - - +
343C MET* 1.3 112.1 - - + +
345C ASP* 1.3 74.1 + - - +
346C LEU* 3.4 25.8 + - + +
366C PRO* 3.5 33.2 - - + +
367C TRP* 3.8 29.8 - - + -
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Residues in contact with ASP 345 (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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341C ILE 2.7 17.6 + - - -
342C GLN* 3.2 10.5 + - - +
344C LEU* 1.3 76.7 - - - +
346C LEU* 1.3 60.2 + - - +
347C LEU* 3.5 11.1 + - - +
348C HIS* 3.0 37.0 + - - -
350C ILE* 4.5 8.3 - - - +
366C PRO* 5.2 1.9 - - + +
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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