Contacts of the helix formed by residues 371 - 379 (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 ASP 371 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280D TYR* 3.1 31.9 + - - -
369D LYS* 3.9 12.4 - - - +
370D THR* 1.3 70.6 - - - +
372D LYS* 1.3 64.2 + - + +
373D ALA 3.2 5.5 + - - -
374D GLN* 4.1 9.5 + - - +
375D LEU* 4.5 9.4 + - - +
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Residues in contact with LYS 372 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280D TYR* 3.1 35.3 + - + +
284D ASN* 3.2 10.2 + - - +
332D PHE* 3.9 30.5 + - + -
333D PHE* 3.6 28.5 - - + -
343D MET* 6.2 0.4 - - + -
371D ASP* 1.3 79.3 - - + +
373D ALA* 1.3 52.5 + - - +
374D GLN 3.5 0.4 - - - -
375D LEU* 3.3 13.4 + - - +
376D LEU* 2.6 44.6 + - + +
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Residues in contact with ALA 373 (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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284D ASN* 2.9 23.7 + - - +
287D ALA* 3.8 15.0 - - + -
288D ALA* 3.3 32.0 - - - +
370D THR 4.3 10.3 - - - +
371D ASP 3.2 1.2 - - - -
372D LYS* 1.3 75.1 - - - +
374D GLN* 1.3 59.0 + - - +
376D LEU* 2.8 5.6 + - - +
377D ARG* 2.7 32.1 + - - +
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Residues in contact with GLN 374 (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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287D ALA 5.3 3.8 - - - +
288D ALA* 5.8 0.5 - - - -
371D ASP 4.1 6.9 + - - +
372D LYS 3.5 0.2 - - - -
373D ALA* 1.3 82.2 - - - +
375D LEU* 1.3 57.7 + - + +
377D ARG* 3.1 28.9 - - - +
378D ASP* 3.1 23.6 + - - +
382D LEU* 6.5 0.7 - - + -
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Residues in contact with LEU 375 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332D PHE* 3.1 37.6 - - + -
371D ASP 4.5 8.8 + - - +
372D LYS* 3.3 16.9 + - - +
373D ALA 3.1 0.6 - - - -
374D GLN* 1.3 75.8 - - + +
376D LEU* 1.3 60.0 + - - +
377D ARG 3.0 5.9 + - - -
378D ASP* 3.4 28.6 + - + +
379D ALA 3.5 7.1 + - - -
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Residues in contact with LEU 376 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284D ASN* 3.8 28.0 - - + +
285D ILE* 4.2 13.9 - - + +
288D ALA* 3.9 6.3 - - + -
290D LEU* 3.5 22.2 - - + +
328D LEU* 3.3 35.6 - - + +
332D PHE* 3.4 33.0 - - + -
333D PHE* 3.5 29.2 - - + -
372D LYS* 2.6 26.7 + - + +
373D ALA 3.2 6.1 - - - +
375D LEU* 1.3 72.2 - - - +
377D ARG* 1.3 58.7 + - - +
379D ALA* 4.0 5.2 + - - +
380D ALA 4.4 1.2 + - - -
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Residues in contact with ARG 377 (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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287D ALA 5.8 0.2 - - - -
288D ALA* 2.9 39.7 + - - +
289D GLY* 4.1 11.1 + - - -
290D LEU* 5.2 4.4 - - + +
373D ALA 2.7 8.1 + - - +
374D GLN* 3.1 32.1 - - + +
375D LEU 3.0 0.2 - - - -
376D LEU* 1.3 76.1 - - - +
378D ASP* 1.3 54.3 + - - +
379D ALA 3.0 1.8 - - - -
380D ALA 2.6 42.3 + - - +
381D GLY 4.4 5.8 + - - -
382D LEU* 3.5 30.8 + - + +
383D LYS* 3.9 9.9 + - - -
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Residues in contact with ASP 378 (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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374D GLN* 3.1 17.1 - - - +
375D LEU* 3.4 28.4 + - + +
377D ARG* 1.3 75.5 - - - +
379D ALA* 1.3 56.5 + - - +
380D ALA* 3.0 8.0 + - - -
381D GLY 4.6 0.5 + - - -
382D LEU* 3.1 42.6 + - + +
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Residues in contact with ALA 379 (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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324D GLN* 4.4 4.3 - - - +
328D LEU* 3.2 33.2 - - + +
332D PHE* 3.9 23.6 - - + -
375D LEU 3.5 2.2 + - - -
376D LEU 4.1 4.9 - - - +
377D ARG 3.0 0.6 + - - -
378D ASP* 1.3 77.0 - - - +
380D ALA* 1.3 61.5 + - - +
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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