Contacts of the helix formed by residues 371 - 381 (chain A) in PDB entry 4CZ8
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 SER 371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A HIS* 4.8 2.1 + - - -
58A PHE* 4.4 2.6 - - - -
62A ARG* 3.9 13.7 - - - -
309A LEU* 4.4 7.4 - - - +
312A GLU* 2.4 44.7 + - - -
367A SER 5.0 0.2 + - - -
368A ALA 4.2 2.0 + - - -
369A LEU 3.3 0.4 - - - -
370A ALA* 1.3 74.5 - - - +
372A LEU* 1.3 64.5 + - - +
373A PRO* 3.5 2.2 - - - -
374A LEU* 3.4 6.7 + - - +
375A SER* 3.1 23.4 + - - -
394A MSE 3.2 21.5 - - - +
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Residues in contact with LEU 372 (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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62A ARG* 4.2 27.3 - - - +
125A ILE* 5.8 0.2 - - + -
166A THR* 4.7 9.6 - - + -
170A ILE* 4.6 18.2 - - + -
177A TYR* 5.9 2.5 - - - +
369A LEU* 3.2 38.9 + - + +
371A SER* 1.3 78.6 - - - +
373A PRO* 1.4 65.5 - - + +
375A SER* 2.6 28.2 + - - +
376A LEU* 3.1 33.8 + - + +
1424A PTY 5.0 6.3 - - - -
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Residues in contact with PRO 373 (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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121A LEU* 3.9 25.4 - - + -
125A ILE* 4.3 5.8 - - + -
170A ILE* 5.0 3.4 - - + -
369A LEU 3.4 13.7 - - - +
370A ALA 3.5 12.3 - - - +
372A LEU* 1.4 93.0 - - + +
374A LEU* 1.3 57.4 + - - +
376A LEU* 3.5 10.8 + - + +
377A ALA* 3.0 28.2 + - - +
385A LEU* 4.1 12.4 - - + +
390A GLY* 4.4 10.2 - - - +
393A ILE* 3.9 30.5 - - + -
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Residues in contact with LEU 374 (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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51A ARG* 4.0 5.6 - - - +
55A HIS* 3.5 29.6 - - + +
371A SER* 3.4 11.9 + - - +
372A LEU 3.2 0.4 - - - -
373A PRO* 1.3 79.2 - - - +
375A SER* 1.3 59.2 - - - +
377A ALA* 3.1 4.9 + - - +
378A LEU* 2.9 43.3 + - + +
387A VAL* 3.5 43.3 - - + +
390A GLY* 4.1 15.8 - - - +
391A GLU* 3.7 29.6 - - + +
394A MSE 4.5 11.2 - - + -
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Residues in contact with SER 375 (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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55A HIS* 5.5 8.9 + - - -
59A ASP* 4.1 22.0 + - - -
62A ARG* 4.6 1.2 + - - -
371A SER 3.1 12.2 + - - -
372A LEU* 2.6 35.5 + - - +
374A LEU* 1.3 75.9 - - - +
376A LEU* 1.3 63.5 + - - +
378A LEU* 3.2 13.4 + - - +
379A LYS* 3.1 34.4 + - - +
1424A PTY 3.9 10.1 + - - -
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Residues in contact with LEU 376 (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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170A ILE* 3.7 44.9 - - + -
174A VAL* 4.6 17.3 - - + -
177A TYR* 4.8 14.1 - - + +
372A LEU* 3.1 28.0 + - + +
373A PRO* 3.8 5.2 - - + +
375A SER* 1.3 81.6 + - - +
377A ALA* 1.3 54.0 + - - +
379A LYS* 4.4 3.6 - - - +
380A TYR* 2.7 58.1 + - + +
381A LYS 4.1 0.3 + - - -
385A LEU* 4.7 4.9 - - + +
1424A PTY 3.6 26.7 - - - +
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Residues in contact with ALA 377 (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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373A PRO 3.0 15.0 + - - +
374A LEU* 3.3 10.8 - - - +
376A LEU* 1.3 76.7 - - - +
378A LEU* 1.3 62.5 + - - +
379A LYS 3.1 1.1 + - - -
381A LYS* 3.5 20.9 + - - +
385A LEU* 3.6 23.1 - - + +
386A THR* 3.7 19.1 - - - +
387A VAL* 3.8 23.2 - - + +
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Residues in contact with LEU 378 (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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55A HIS* 4.5 19.3 - - + +
374A LEU* 2.9 43.2 + - + +
375A SER* 3.2 11.4 + - - +
377A ALA* 1.3 75.2 - - - +
379A LYS* 1.3 62.1 + - + +
387A VAL* 3.7 28.3 - - + -
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Residues in contact with LYS 379 (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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56A GLU* 5.0 10.7 + - - -
59A ASP* 2.8 30.2 + - - +
375A SER* 3.1 19.8 + - - +
376A LEU* 3.9 3.6 - - - +
378A LEU* 1.3 86.1 - - + +
380A TYR* 1.3 82.4 + - + +
381A LYS 3.8 0.9 - - - -
1424A PTY 3.1 40.3 + - - +
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Residues in contact with TYR 380 (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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174A VAL* 5.1 21.3 - - + -
175A PRO* 5.8 7.2 - - + +
176A GLY* 5.5 12.1 - - - -
177A TYR* 5.3 9.2 - + - -
376A LEU* 2.7 43.0 + - + +
379A LYS* 1.3 93.6 - - + +
381A LYS* 1.3 73.4 + - - +
382A SER* 3.6 3.1 - - - -
1424A PTY 5.6 8.4 - - - -
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Residues in contact with LYS 381 (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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376A LEU 4.1 1.0 + - - -
377A ALA 3.5 15.3 + - - +
379A LYS 3.8 0.8 - - - -
380A TYR* 1.3 81.5 - - - +
382A SER* 1.3 63.3 + - - +
383A PRO* 3.9 4.7 - - - +
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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