Contacts of the helix formed by residues 336 - 345 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A LEU* 4.4 29.0 + - - +
113A GLU* 4.7 6.5 - - - +
305A ALA* 3.5 28.9 + - + +
306A GLU* 3.3 29.7 + - - +
307A PRO* 4.1 6.5 - - + -
334A ASP* 3.1 25.1 + - - +
335A LEU* 1.3 79.1 - - - +
337A PRO* 1.3 75.5 - - + +
338A TYR 3.2 3.6 - - - +
339A GLY 2.7 15.3 + - - +
340A LEU* 3.2 9.1 + - - +
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Residues in contact with PRO 337 (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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114A GLN 3.1 21.1 - - - +
115A GLY 4.1 4.9 - - - +
116A ALA* 3.5 23.1 - - - +
268A SER* 5.5 5.4 - - - +
270A VAL* 5.2 4.7 - - + -
300A TYR* 4.1 11.2 - - + -
305A ALA* 2.8 27.8 - - + +
335A LEU 3.6 4.2 - - - +
336A ARG* 1.3 76.3 - - + +
338A TYR* 1.3 76.9 + - + +
339A GLY 3.1 3.3 + - - -
340A LEU* 3.2 25.6 + - + +
341A ILE* 3.2 16.8 - - - +
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Residues in contact with TYR 338 (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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36A LYS* 6.1 4.3 - - + -
38A ARG* 3.0 28.7 + - - -
106A VAL* 3.4 11.1 - - - +
107A ASP* 3.2 7.8 + - - -
111A PRO* 3.2 20.4 - - + +
112A LEU* 4.0 18.1 + - + +
114A GLN* 2.9 64.1 + - + -
115A GLY 4.0 6.3 - - - -
268A SER* 3.8 11.2 - - - -
336A ARG* 2.9 5.1 + - - +
337A PRO* 1.3 87.6 - - + +
339A GLY* 1.3 55.8 + - - +
341A ILE* 4.7 15.9 - - + -
342A GLN* 3.9 16.6 - - - +
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Residues in contact with GLY 339 (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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334A ASP* 3.4 34.7 - - - +
336A ARG* 2.7 16.7 + - - +
338A TYR* 1.3 74.3 - - - +
340A LEU* 1.3 58.7 + - - +
341A ILE 3.3 1.1 - - - -
342A GLN* 3.6 4.7 + - - +
343A MET* 2.8 28.0 + - - +
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Residues in contact with LEU 340 (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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267A PRO 5.3 0.4 - - - +
270A VAL* 5.0 3.8 - - + -
273A SER* 3.8 32.3 - - - +
274A ALA* 4.2 6.5 - - - +
277A ALA* 3.7 31.9 - - + -
300A TYR* 3.6 10.3 - - - +
334A ASP 3.6 3.9 + - - +
335A LEU* 3.3 33.9 - - + +
336A ARG 3.2 7.5 + - - +
337A PRO* 3.2 31.0 - - + +
339A GLY* 1.3 75.9 - - - +
341A ILE* 1.3 59.5 + - + +
342A GLN 3.2 0.2 - - - -
343A MET* 3.4 10.1 - - + +
344A LEU* 2.8 34.3 + - + +
346A LEU* 4.1 1.5 - - - +
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Residues in contact with ILE 341 (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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38A ARG* 6.0 1.1 - - - +
267A PRO* 3.2 42.6 - - + +
268A SER* 3.8 9.2 - - - +
337A PRO 3.2 20.4 + - - +
338A TYR* 4.8 15.0 - - + -
339A GLY 3.3 0.8 - - - -
340A LEU* 1.3 80.3 - - + +
342A GLN* 1.3 56.2 + - + +
345A ASP* 2.6 30.1 + - - -
346A LEU* 3.0 27.5 + - + -
347A LEU* 3.2 41.3 - - + +
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Residues in contact with GLN 342 (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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338A TYR 3.9 18.6 - - - +
339A GLY* 3.6 6.8 + - - +
340A LEU 3.2 0.2 - - - -
341A ILE* 1.3 76.9 - - + +
343A MET* 1.3 67.9 + - - +
344A LEU 3.1 1.2 + - - -
345A ASP* 3.1 14.0 + - - +
347A LEU* 3.9 18.8 - - - +
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Residues in contact with MET 343 (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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277A ALA* 3.3 35.7 - - + +
280A TYR* 3.5 41.4 + - + +
333A PHE* 4.3 18.2 - - + -
334A ASP* 4.1 17.5 - - + +
335A LEU* 4.9 1.8 - - + -
339A GLY 2.8 20.8 + - - +
340A LEU* 3.4 7.6 - - + +
342A GLN* 1.3 78.4 - - - +
344A LEU* 1.3 77.9 + - + +
372A LYS* 6.1 1.3 - - + -
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Residues in contact with LEU 344 (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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273A SER 4.3 1.3 - - - +
276A TYR* 4.3 7.6 - - + -
277A ALA* 3.9 20.6 - - + +
280A TYR* 3.9 20.6 - - + -
340A LEU 2.8 16.1 + - - +
343A MET* 1.3 102.7 - - + +
345A ASP* 1.3 73.2 + - - +
346A LEU* 3.3 26.1 + - + +
366A PRO* 3.5 47.2 - - + +
367A TRP* 3.7 17.7 - - + -
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Residues in contact with ASP 345 (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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341A ILE 2.6 16.8 + - - -
342A GLN* 3.1 11.3 + - - +
344A LEU* 1.3 77.0 - - - +
346A LEU* 1.3 59.1 + - - +
347A LEU* 3.6 10.7 + - - +
348A HIS* 2.9 41.1 + - - +
350A ILE* 4.5 9.0 - - - +
366A PRO* 5.1 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