Contacts of the helix formed by residues 371 - 381 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B PHE* 4.5 4.9 - - - -
62B ARG* 3.7 14.4 - - - +
309B LEU* 4.1 6.1 - - - +
312B GLU* 2.3 43.7 + - - -
367B SER 4.7 0.6 + - - -
368B ALA 4.3 1.0 + - - -
369B LEU 3.4 0.2 - - - -
370B ALA* 1.3 74.6 - - - +
372B LEU* 1.3 65.6 + - - +
373B PRO* 3.4 0.9 - - - -
374B LEU* 3.0 9.1 + - - +
375B SER* 2.9 24.1 + - - -
394B MSE 3.3 21.3 - - - +
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Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ARG* 3.2 42.4 - - - +
166B THR* 4.7 6.1 - - + -
167B LEU* 4.7 13.0 - - + -
170B ILE* 4.0 23.8 - - + -
369B LEU* 3.3 32.8 - - + +
371B SER* 1.3 75.4 - - - +
373B PRO* 1.3 60.6 - - + +
375B SER* 4.0 3.7 - - - -
376B LEU* 2.9 48.0 + - + +
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Residues in contact with PRO 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B LEU* 4.2 21.5 - - + -
125B ILE* 4.3 7.9 - - + -
166B THR* 6.1 0.7 - - + -
170B ILE* 5.0 7.9 - - + -
369B LEU 3.2 15.3 - - - +
370B ALA 3.2 13.0 - - - +
372B LEU* 1.3 93.2 - - + +
374B LEU* 1.3 57.1 + - - +
376B LEU* 3.8 5.1 - - + +
377B ALA* 2.9 30.0 + - - +
385B LEU* 4.2 9.7 - - + +
390B GLY* 4.8 10.2 - - - +
393B ILE* 3.6 26.9 - - + -
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ARG* 3.2 27.6 - - - +
55B HIS* 3.6 23.3 - - + +
312B GLU* 4.9 0.7 - - - +
371B SER* 3.0 12.4 + - - +
373B PRO* 1.3 78.8 - - + +
375B SER* 1.3 66.6 + - - +
377B ALA* 3.0 7.4 + - - +
378B LEU* 2.9 36.5 + - + +
387B VAL* 3.8 28.0 - - + +
390B GLY* 4.3 13.4 - - - +
391B GLU* 3.3 28.7 - - + +
394B MSE 4.1 14.1 - - + -
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Residues in contact with SER 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B HIS* 5.0 15.4 + - - +
59B ASP* 3.4 31.7 + - - -
62B ARG* 5.4 1.8 - - - -
371B SER* 2.9 20.3 + - - -
372B LEU* 4.0 6.7 - - - -
374B LEU* 1.3 75.2 - - - +
376B LEU* 1.3 58.1 + - - +
378B LEU* 3.3 11.6 + - - +
379B LYS* 2.9 41.1 + - - +
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Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ILE* 3.5 41.7 - - + -
174B VAL* 6.2 3.8 - - + -
372B LEU* 2.9 31.1 + - + +
373B PRO* 3.8 4.9 - - + +
375B SER* 1.3 76.8 - - - +
377B ALA* 1.3 57.9 + - - +
379B LYS* 4.5 8.5 - - + +
380B TYR* 2.9 69.2 + - + +
385B LEU* 4.9 7.3 - - + +
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Residues in contact with ALA 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B PRO 2.9 19.5 + - - +
374B LEU* 3.0 6.7 + - - +
376B LEU* 1.3 75.4 - - - +
378B LEU* 1.3 59.3 + - - +
381B LYS* 2.9 31.9 + - - +
382B SER 4.3 2.2 + - - +
385B LEU* 3.6 25.3 - - + +
386B THR 4.5 2.2 - - - +
387B VAL* 4.3 32.5 - - + +
390B GLY* 5.6 0.7 - - - -
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Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ASP* 5.4 2.7 - - - +
55B HIS* 4.3 27.8 - - + +
374B LEU* 2.9 26.4 + - + +
375B SER* 3.3 10.7 + - - +
377B ALA* 1.3 77.0 - - - +
379B LYS* 1.3 65.8 + - + +
381B LYS* 4.2 9.9 + - - +
387B VAL* 3.7 36.8 - - + -
391B GLU* 5.9 0.2 - - - +
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Residues in contact with LYS 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B GLU* 3.8 13.2 + - - -
59B ASP* 2.5 34.5 + - - +
375B SER* 2.9 27.5 + - - +
376B LEU* 4.0 9.4 - - + +
377B ALA 3.2 0.2 - - - -
378B LEU* 1.3 79.9 - - + +
380B TYR* 1.3 75.7 + - + +
381B LYS* 3.3 5.2 + - - +
1425B TAM 5.2 12.7 + - - -
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Residues in contact with TYR 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B VAL* 4.6 16.8 - - + -
176B GLY* 4.4 19.2 - - - -
177B TYR* 3.7 29.7 - - + +
376B LEU* 2.9 45.3 + - + +
379B LYS* 1.3 82.8 - - + +
381B LYS* 1.3 68.8 + - - +
382B SER* 3.4 16.1 + - - +
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Residues in contact with LYS 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B ALA 2.9 21.2 + - - +
378B LEU 4.3 7.0 - - - +
379B LYS 3.9 6.7 - - - +
380B TYR* 1.3 80.9 - - - +
382B SER* 1.3 59.0 + - - +
383B PRO* 4.2 2.3 - - - +
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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