Contacts of the helix formed by residues 329 - 340 (chain A) in PDB entry 3P0G
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 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A LEU* 4.3 2.6 - - - +
69A ASN* 5.6 0.6 + - - -
326A TYR 5.0 1.7 + - - -
327A CYS 3.5 1.0 - - - -
328A ARG* 1.4 78.4 - - - +
330A PRO* 1.4 67.4 - - - +
331A ASP* 3.3 15.1 + - - +
332A PHE* 3.0 35.0 + - - +
333A ARG* 2.9 25.5 + - - +
105B TYR* 4.0 28.1 - - - -
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Residues in contact with PRO 330 (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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328A ARG 3.6 2.0 - - - +
329A SER* 1.4 82.9 - - - +
331A ASP* 1.3 63.4 - - - +
333A ARG* 3.4 10.5 - - + +
334A ILE* 2.9 42.4 + - + +
105B TYR* 3.5 26.0 - - + +
107B TYR* 5.4 15.5 - - + -
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Residues in contact with ASP 331 (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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61A PHE* 5.7 0.2 - - - +
63A ARG* 3.1 54.9 + - + +
64A LEU* 4.1 15.3 - - + +
329A SER* 3.6 11.3 + - - +
330A PRO* 1.3 84.8 - - - +
332A PHE* 1.4 54.4 + - - +
334A ILE* 3.6 10.9 + - - +
335A ALA* 2.9 33.1 + - - +
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Residues in contact with PHE 332 (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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54A VAL* 4.4 3.1 - - + -
57A ALA* 4.4 2.5 - - + -
58A ILE* 3.8 36.6 - - + -
64A LEU* 3.7 22.2 - - + +
69A ASN* 3.5 22.2 - - - -
72A ILE* 4.4 3.8 - - + -
326A TYR 4.1 6.7 - - - -
327A CYS* 3.4 48.7 - - + +
329A SER* 3.0 34.0 + - - +
331A ASP* 1.4 73.1 - - - +
333A ARG* 1.4 57.7 + - - +
335A ALA* 2.9 4.7 + - - -
336A PHE* 2.7 63.9 + + + -
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Residues in contact with ARG 333 (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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327A CYS 5.2 2.2 - - - -
328A ARG* 4.3 51.9 + - - +
329A SER 2.9 10.4 + - - +
330A PRO* 3.4 15.3 - - + +
332A PHE* 1.4 77.1 - - - +
334A ILE* 1.4 49.8 + - + +
336A PHE* 4.1 8.4 - - - +
337A GLN* 2.8 43.0 + - - +
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Residues in contact with ILE 334 (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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61A PHE* 5.9 3.1 - - + -
63A ARG* 6.2 1.8 - - - +
330A PRO* 2.9 24.4 + - + +
331A ASP* 3.9 9.2 - - - +
333A ARG* 1.4 74.0 - - - +
335A ALA* 1.4 66.1 + - - +
337A GLN* 3.3 19.1 - - - +
338A GLU* 3.4 25.6 + - - +
343A ARG* 3.4 39.0 - - - +
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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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57A ALA* 4.2 6.3 - - + -
61A PHE* 3.4 38.4 - - + -
64A LEU* 3.6 19.5 - - + -
331A ASP 2.9 22.6 + - - +
332A PHE* 2.9 4.5 + - - +
334A ILE* 1.4 73.8 - - - +
336A PHE* 1.3 61.5 + - - +
338A GLU* 3.3 2.6 + - - +
339A LEU* 3.2 27.5 + - - +
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Residues in contact with PHE 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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53A LEU* 3.3 52.9 - - + -
54A VAL* 3.6 22.2 - - + -
57A ALA* 3.7 8.7 - - + -
323A PRO 6.4 0.2 - - - -
327A CYS* 3.7 15.0 - - + -
332A PHE* 2.7 61.7 + + + +
333A ARG* 4.1 8.5 - - - +
335A ALA* 1.3 72.9 - - - +
337A GLN* 1.3 56.9 + - - +
339A LEU* 3.4 7.5 + - + +
340A LEU* 2.9 42.4 + - + +
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Residues in contact with GLN 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 ARG* 2.8 35.3 + - - +
334A ILE* 3.3 16.2 - - - +
336A PHE* 1.3 73.5 - - - +
338A GLU* 1.3 56.1 + - - +
340A LEU* 3.2 3.4 + - - +
341A CYS 3.1 6.1 + - - -
342A LEU* 2.8 56.8 + - + +
343A ARG* 3.3 47.1 + - + +
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Residues in contact with GLU 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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61A PHE* 3.2 32.5 - - + -
334A ILE* 3.4 20.6 + - - +
335A ALA 3.3 10.2 + - - +
337A GLN* 1.3 75.7 - - - +
339A LEU* 1.4 60.4 + - - +
341A CYS* 3.3 14.7 + - - -
342A LEU 4.3 0.2 + - - -
343A ARG* 3.6 25.1 + - + +
344A ARG* 3.0 54.7 + - + +
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Residues in contact with LEU 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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53A LEU* 4.0 16.4 - - + +
56A THR* 3.9 24.2 - - + -
57A ALA* 3.7 35.0 - - + +
60A LYS* 4.4 14.8 - - + -
61A PHE* 3.6 17.9 - - + -
335A ALA 3.2 18.1 + - - +
336A PHE* 3.5 10.3 - - + +
338A GLU* 1.4 72.1 - - - +
340A LEU* 1.4 60.5 + - + +
341A CYS* 3.0 22.3 + - - -
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Residues in contact with LEU 340 (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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49A PHE* 3.7 29.4 - - + -
53A LEU* 3.7 27.1 - - + -
336A PHE* 2.9 27.0 + - + +
337A GLN* 3.2 7.6 + - - +
339A LEU* 1.4 73.1 - - - +
341A CYS* 1.3 67.3 + - - +
342A LEU* 3.3 26.6 - - + +
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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