Contacts of the helix formed by residues 350 - 359 (chain A) in PDB entry 4Z30
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 LEU 350 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A THR* 5.4 0.9 - - + -
166A LEU* 4.4 15.7 - - + -
347A LEU* 3.0 38.9 + - + +
349A ARG* 1.3 99.1 - - + +
351A ARG* 1.3 64.2 + - - +
352A PRO 3.5 0.7 - - - -
353A HIS* 3.1 12.0 + - - +
354A LEU* 3.0 33.9 + - + +
383A THR* 3.9 35.7 - - + +
384A VAL* 4.1 26.0 - - + +
387A GLY* 4.5 7.0 - - - -
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Residues in contact with ARG 351 (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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331A VAL* 3.9 20.9 - - + +
332A GLN* 3.6 17.6 + - - +
335A THR* 3.3 29.7 + - - +
347A LEU 4.3 0.6 + - - -
348A ASN* 3.1 34.7 + - - +
350A LEU* 1.3 73.3 - - - +
352A PRO* 1.3 76.2 - - + +
354A LEU* 2.9 19.4 + - + +
355A GLU* 2.9 41.0 + - - +
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Residues in contact with PRO 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ASN 4.1 3.8 - - - +
349A ARG* 3.6 17.7 - - - +
351A ARG* 1.3 90.6 - - + +
353A HIS* 1.3 65.6 + - + +
355A GLU* 3.3 8.1 + - + +
356A LEU* 2.9 29.0 + - - +
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Residues in contact with HIS 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ARG 3.9 19.5 + - - -
350A LEU* 3.1 9.4 + - - +
351A ARG 3.1 0.8 - - - -
352A PRO* 1.3 81.5 - - + +
354A LEU* 1.3 64.0 + - - +
356A LEU* 3.4 7.9 + - - +
357A LEU* 3.1 28.3 + - - +
379A VAL* 4.9 9.6 - - + +
380A ALA* 3.8 27.8 - - + +
383A THR* 3.5 34.3 - - + +
384A VAL* 3.9 15.7 - - + -
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Residues in contact with LEU 354 (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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159A GLY* 3.9 14.4 - - - +
162A THR* 5.1 1.1 - - + -
163A VAL* 3.7 31.9 - - + +
166A LEU* 5.5 2.9 - - + -
327A PHE* 3.9 9.4 - - + -
331A VAL* 4.1 22.2 - - + -
334A LEU* 4.8 13.7 - - + -
350A LEU* 3.0 33.7 + - + +
351A ARG* 2.9 14.6 + - + +
353A HIS* 1.3 71.9 - - - +
355A GLU* 1.3 58.2 + - - +
357A LEU* 3.2 6.1 + - + +
358A ALA* 2.8 31.1 + - - +
384A VAL* 3.7 25.8 - - + -
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Residues in contact with GLU 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ALA* 5.2 7.8 - - - +
331A VAL* 3.4 28.8 - - - +
351A ARG* 2.9 45.7 + - + +
352A PRO* 3.5 9.9 - - + +
354A LEU* 1.3 73.6 - - - +
356A LEU* 1.3 64.5 + - - +
358A ALA* 3.3 9.0 + - - +
359A ASN* 3.1 34.4 + - - +
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Residues in contact with LEU 356 (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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152A MET* 5.9 0.9 - - + -
352A PRO 2.9 14.8 + - - +
353A HIS* 3.5 14.4 - - - +
354A LEU 3.3 0.2 - - - -
355A GLU* 1.3 78.0 - - - +
357A LEU* 1.3 65.3 + - - +
359A ASN* 3.4 14.2 + - - +
360A ILE* 3.6 13.5 + - + +
373A GLN 5.1 2.0 - - - +
376A ASN* 4.1 27.6 - - + +
377A ALA* 4.0 31.0 - - + +
380A ALA* 4.6 6.3 - - + -
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Residues in contact with LEU 357 (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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155A ALA* 3.9 28.9 - - + +
156A ARG* 3.3 19.0 - - - +
159A GLY* 4.0 16.4 - - - -
327A PHE* 3.9 12.1 - - + -
353A HIS 3.1 19.4 + - - +
354A LEU* 3.6 8.5 - - - +
356A LEU* 1.3 76.9 - - + +
358A ALA* 1.3 65.0 + - - +
360A ILE* 3.2 33.2 + - + +
377A ALA* 3.8 24.0 - - - +
380A ALA* 4.1 9.0 - - + +
381A VAL* 4.1 20.9 - - - +
384A VAL* 4.7 6.5 - - + -
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Residues in contact with ALA 358 (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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156A ARG* 2.8 26.8 + - - +
327A PHE* 3.6 37.4 - - + -
328A ALA* 4.4 12.6 - - + +
331A VAL* 5.5 0.9 - - + -
354A LEU 2.8 20.5 + - - +
355A GLU* 3.3 13.4 + - - +
357A LEU* 1.3 73.3 - - - +
359A ASN* 1.3 60.2 + - - +
360A ILE 3.2 0.9 - - - +
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Residues in contact with ASN 359 (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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355A GLU* 3.1 26.5 + - - +
356A LEU* 3.7 7.9 - - - +
357A LEU 3.2 0.4 - - - -
358A ALA* 1.3 76.1 - - - +
360A ILE* 1.3 62.7 + - - +
361A ASP* 3.3 4.0 + - - +
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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