Contacts of the helix formed by residues 334 - 339 (chain A) in PDB entry 4ZSQ
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 GLY 334 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ASP 3.3 10.3 - - - -
231A THR* 3.3 15.3 - - - -
232A THR 3.7 0.4 - - - -
233A ASN 3.3 22.9 + - - -
332A VAL 3.4 0.6 + - - -
333A MET* 1.3 75.8 - - - +
335A ALA* 1.3 66.9 + - - -
336A VAL 3.2 3.1 - - - -
337A ILE* 3.2 7.0 + - - +
338A MET* 3.0 22.5 + - - +
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Residues in contact with ALA 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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10A SER* 3.8 28.5 - - - +
14A TYR* 4.5 11.7 - - + -
154A LEU* 4.5 7.1 - - + +
228A ASP 4.1 2.0 + - - -
229A SER* 4.5 11.2 - - - +
231A THR 2.8 17.0 + - - +
232A THR* 3.2 5.1 + - - +
334A GLY* 1.3 71.2 - - - -
336A VAL* 1.3 56.2 + - - +
338A MET* 3.2 7.8 + - - +
339A GLU* 2.8 35.9 + - - +
401A 4RX 4.6 2.7 - - + -
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Residues in contact with VAL 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER* 3.8 23.8 - - - +
232A THR* 3.1 23.6 + - + +
234A LEU* 3.7 19.7 - - + +
304A GLN* 3.3 45.6 - - - +
305A TYR* 4.7 3.4 - - - -
307A ARG* 4.4 6.5 - - + -
323A ALA* 3.7 27.6 - - + +
335A ALA* 1.3 77.5 - - - +
337A ILE* 1.3 69.1 + - + +
339A GLU* 3.8 13.8 - - - +
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Residues in contact with ILE 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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234A LEU* 3.7 49.8 - - + -
285A LEU* 5.1 7.0 - - + -
298A ILE* 4.4 3.6 - - + -
300A ILE* 3.2 45.4 - - + +
305A TYR* 5.5 0.9 - - + -
333A MET* 4.1 29.8 - - + -
334A GLY 3.2 11.1 + - - +
336A VAL* 1.3 78.6 - - + +
338A MET* 1.3 65.6 + - + +
339A GLU 3.2 0.4 - - - -
340A GLY 3.2 6.1 + - - -
341A PHE* 3.1 32.5 - - + -
354A PHE* 6.1 0.2 - - + -
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Residues in contact with MET 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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33A THR* 4.8 0.4 - - - -
152A LEU* 3.8 37.2 - - + +
154A LEU* 4.0 24.6 + - + +
227A VAL* 3.9 19.5 - - + -
228A ASP 4.2 2.2 - - - -
229A SER* 3.7 33.4 - - - -
333A MET* 4.1 8.3 - - + +
334A GLY 3.0 16.9 + - - +
335A ALA 3.2 4.5 + - - +
337A ILE* 1.3 77.3 - - + +
339A GLU* 1.3 56.1 + - - +
340A GLY 3.1 0.4 - - - -
341A PHE* 2.7 33.3 + - - +
343A VAL* 4.1 24.2 - - + +
345A PHE* 4.1 9.2 - - + -
354A PHE* 6.1 1.6 - - + -
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Residues in contact with GLU 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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10A SER* 3.3 26.1 + - - -
14A TYR* 2.6 30.4 + - + +
154A LEU* 3.3 24.0 - - + +
156A GLY* 3.6 25.3 + - - +
303A GLN 5.5 1.2 - - - +
304A GLN* 4.7 10.7 + - + +
335A ALA 2.8 23.1 + - - +
336A VAL* 3.8 16.8 - - - +
337A ILE 3.2 0.2 - - - -
338A MET* 1.3 75.7 - - - +
340A GLY* 1.3 57.8 + - - +
341A PHE 3.4 0.6 + - - -
357A SER* 4.1 3.6 + - - -
359A CYS 4.7 1.7 - - - +
360A HIS* 3.7 17.5 - - - +
361A VAL 5.1 0.2 + - - -
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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