Contacts of the helix formed by residues 334 - 343 (chain A) in PDB entry 6E8Z
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 PRO 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A VAL* 4.3 1.1 - - - +
332A GLY 3.4 5.5 - - - +
333A GLN* 1.3 94.7 - - + +
335A VAL* 1.3 66.0 + - - +
336A GLY* 3.1 6.0 + - - +
337A GLU* 3.1 42.1 + - - +
338A PHE 3.9 2.6 + - - -
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Residues in contact with VAL 335 (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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213A PHE* 3.6 44.6 - - + -
217A LEU* 3.3 21.0 - - + +
277A PHE* 3.6 29.3 - - + +
278A ALA* 4.1 21.8 - - + +
328A VAL* 3.8 12.5 - - + +
333A GLN 3.4 3.0 + - - -
334A PRO* 1.3 72.9 - - - +
336A GLY* 1.3 63.3 + - - +
337A GLU 3.1 1.1 + - - -
338A PHE* 3.3 12.2 + - - +
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Residues in contact with GLY 336 (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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217A LEU* 4.0 19.0 - - - +
219A PHE* 4.9 7.4 - - - -
334A PRO* 3.1 5.5 - - - +
335A VAL* 1.3 84.0 - - - +
337A GLU* 1.3 60.0 + - - +
338A PHE 3.5 0.8 + - - -
339A ILE* 5.0 4.7 + - - +
340A HIS* 4.8 4.9 - - - -
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Residues in contact with GLU 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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333A GLN* 4.9 6.4 - - + +
334A PRO* 3.1 40.1 + - + +
336A GLY* 1.3 77.4 - - - +
338A PHE* 1.3 65.9 + - - +
339A ILE 3.1 3.1 - - - -
340A HIS* 2.9 46.1 + - + +
341A CYS* 3.8 8.2 - - - -
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Residues in contact with PHE 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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210A GLY* 3.8 28.0 - - - -
213A PHE* 4.0 31.9 - + + -
214A CYS* 4.6 4.5 - - - -
217A LEU* 5.1 1.3 - - + -
219A PHE* 5.4 4.9 - + - -
227A VAL* 4.1 21.8 - - + -
321A LEU* 3.4 34.5 - - + -
324A ALA* 3.6 23.6 - - + -
325A VAL* 4.5 4.5 - - + -
328A VAL* 4.8 3.6 - - + -
333A GLN* 4.4 4.7 - - - +
334A PRO 3.9 1.6 + - - -
335A VAL* 3.3 21.0 + - - +
336A GLY 3.5 0.6 - - - -
337A GLU* 1.3 75.6 - - - +
339A ILE* 1.3 69.1 + - + +
341A CYS* 3.3 24.3 + - - +
342A LEU* 4.1 12.4 - - + +
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Residues in contact with ILE 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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219A PHE* 4.3 28.9 - - + -
223A THR* 3.9 25.1 - - + -
227A VAL* 4.1 20.4 - - + -
336A GLY 5.0 4.2 + - - +
337A GLU 3.1 1.9 - - - -
338A PHE* 1.3 83.0 - - + +
340A HIS* 1.3 87.5 + - + +
342A LEU* 3.0 22.1 + - + +
343A GLN* 3.6 14.7 - - - +
161B PHE* 3.9 31.6 - - + -
185B ASN* 5.6 1.3 - - - +
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Residues in contact with HIS 340 (chain A).
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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336A GLY 4.8 4.0 - - - -
337A GLU* 2.9 45.1 + - + +
339A ILE* 1.3 87.7 - - + +
341A CYS* 1.3 60.7 + - - +
342A LEU 3.1 1.6 + - - -
343A GLN* 3.2 46.0 + - - +
344A ASN 4.6 1.6 + - - -
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Residues in contact with CYS 341 (chain A).
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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320A PRO* 3.2 30.6 - - + +
324A ALA* 4.1 17.7 - - + -
333A GLN* 3.7 31.4 - - - -
337A GLU 3.8 7.4 - - - -
338A PHE 3.5 15.0 - - - +
339A ILE 3.1 0.8 - - - -
340A HIS* 1.3 75.6 - - - +
342A LEU* 1.3 60.1 + - + +
343A GLN 3.5 0.4 + - - -
344A ASN* 4.6 4.5 + - - +
345A HIS 5.1 0.7 + - - -
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Residues in contact with LEU 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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227A VAL* 3.7 30.3 - - + -
230A LEU* 4.4 14.7 - - + +
320A PRO 4.3 1.1 - - - +
321A LEU* 3.9 41.7 - - + +
338A PHE* 4.1 19.5 - - + +
339A ILE* 3.0 21.3 + - + +
341A CYS* 1.3 84.1 - - + +
343A GLN* 1.3 60.7 + - - +
344A ASN 3.4 3.2 + - - -
345A HIS* 3.8 29.0 - - + +
348A HIS* 4.7 0.2 + - - -
161B PHE* 3.4 25.9 - - + -
187B ARG* 4.5 3.3 - - - +
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Residues in contact with GLN 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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339A ILE* 3.6 16.2 - - - +
340A HIS* 3.2 44.0 + - - +
342A LEU* 1.3 78.2 - - - +
344A ASN* 1.3 57.5 + - - +
345A HIS 3.7 0.9 - - - -
161B PHE* 3.9 10.3 - - + -
184B PRO* 3.4 35.3 + - + +
185B ASN* 3.1 33.7 + - - +
187B ARG* 3.1 28.2 + - - +
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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