Contacts of the helix formed by residues 332 - 345 (chain A) in PDB entry 4IVR
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 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331A GLN* 1.3 80.4 - - - +
333A PRO* 1.3 76.7 - - - +
334A ALA* 3.6 7.6 + - - +
335A GLY* 3.1 19.1 + - - -
336A CYS* 3.1 20.1 + - - -
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Residues in contact with PRO 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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64A THR* 4.3 14.4 - - + -
65A THR* 4.7 4.4 + - - +
68A LEU* 3.3 30.2 - - + +
331A GLN 4.4 1.3 - - - +
332A SER* 1.3 89.3 - - - +
334A ALA* 1.3 60.4 + - - +
336A CYS* 3.6 8.5 + - + +
337A ARG* 3.3 16.5 + - - +
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Residues in contact with ALA 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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68A LEU* 4.1 4.6 - - + +
332A SER* 3.3 7.6 + - - +
333A PRO* 1.3 76.2 - - - +
335A GLY* 1.3 64.2 + - - +
337A ARG* 3.3 26.4 + - - +
338A ASP* 3.1 31.4 + - - +
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Residues in contact with GLY 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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331A GLN* 3.6 20.5 - - - +
332A SER* 3.1 19.4 + - - -
334A ALA* 1.3 77.5 - - - +
336A CYS* 1.3 57.0 + - - +
337A ARG 3.2 0.3 + - - -
338A ASP* 3.2 5.6 + - - +
339A ALA* 2.9 29.5 + - - +
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Residues in contact with CYS 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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65A THR* 3.4 26.9 - - + +
327A LEU* 3.7 5.1 - - + +
328A ASP 3.9 1.6 - - - +
329A TYR* 3.7 34.3 - - + -
331A GLN* 3.6 29.8 - - - +
332A SER 3.1 21.2 + - - -
333A PRO* 3.9 5.8 - - - +
335A GLY* 1.3 73.9 - - - +
337A ARG* 1.3 52.3 + - - +
339A ALA* 3.5 2.7 - - - +
340A LEU* 2.8 36.2 + - - +
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Residues in contact with ARG 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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65A THR* 3.7 11.2 - - - +
68A LEU* 3.5 51.7 + - + +
69A LEU* 3.9 11.5 - - + +
72A LEU* 3.5 32.4 - - + +
333A PRO 3.3 12.6 + - - +
334A ALA* 3.4 23.4 - - - +
336A CYS* 1.3 80.8 - - - +
338A ASP* 1.3 88.2 + - - +
340A LEU* 3.3 5.1 + - - +
341A LEU* 2.9 26.2 + - - +
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Residues in contact with ASP 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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72A LEU* 4.5 5.4 - - - +
334A ALA* 3.1 19.5 + - - +
335A GLY* 3.9 4.0 - - - +
337A ARG* 1.3 106.4 + - - +
339A ALA* 1.3 67.4 + - - +
341A LEU* 3.5 14.5 - - + +
342A GLN* 3.0 23.9 + - - +
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Residues in contact with ALA 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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327A LEU* 3.6 17.5 - - + -
328A ASP* 5.6 0.4 - - + +
331A GLN* 3.8 15.9 - - - +
335A GLY 2.9 17.9 + - - +
336A CYS 3.5 5.2 - - - +
338A ASP* 1.3 78.9 - - - +
340A LEU* 1.3 62.0 + - - +
342A GLN* 3.2 7.4 + - - +
343A LEU* 3.0 22.2 + - - +
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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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52A VAL* 5.0 1.8 - - + -
54A ILE* 4.1 21.5 - - + -
65A THR* 3.9 24.0 - - + +
66A THR* 4.8 2.9 - - - +
69A LEU* 3.5 33.0 - - + -
204A VAL* 4.1 26.5 - - + -
327A LEU* 3.8 19.0 - - + +
336A CYS 2.8 20.4 + - - +
337A ARG 3.5 4.3 - - - +
338A ASP 3.2 0.2 - - - -
339A ALA* 1.3 73.8 - - - +
341A LEU* 1.3 62.1 + - - +
343A LEU* 3.1 10.7 + - + +
344A THR* 3.1 33.1 + - + +
347A MET* 4.8 2.9 - - + -
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Residues in contact with LEU 341 (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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69A LEU* 4.2 22.9 - - + +
72A LEU* 4.7 14.8 - - + -
337A ARG 2.9 15.5 + - - +
338A ASP* 3.5 20.0 - - + +
340A LEU* 1.3 77.6 - - - +
342A GLN* 1.3 60.2 + - - +
344A THR* 2.7 31.9 + - + +
345A SER* 4.1 1.9 + - - -
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Residues in contact with GLN 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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338A ASP 3.0 17.1 + - - +
339A ALA* 3.7 5.7 - - - +
341A LEU* 1.3 75.7 - - - +
343A LEU* 1.3 73.3 + - - +
345A SER* 2.6 34.5 + - - +
346A GLY 4.5 0.3 + - - -
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Residues in contact with LEU 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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204A VAL* 4.7 9.0 - - + -
325A PHE* 3.9 35.3 - - + -
326A ILE 3.6 28.3 - - - +
327A LEU* 4.5 16.4 - - + -
339A ALA 3.0 13.0 + - - +
340A LEU* 3.1 13.4 + - + +
342A GLN* 1.3 89.1 + - - +
344A THR* 1.3 60.1 + - - +
345A SER 3.5 0.2 + - - -
346A GLY* 3.6 8.2 + - - -
347A MET* 3.5 16.3 - - + +
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Residues in contact with THR 344 (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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50A LEU* 4.5 17.9 - - + +
52A VAL* 5.0 5.8 - - + -
69A LEU* 5.2 9.2 - - + -
158A THR* 6.4 0.4 - - + -
340A LEU* 3.1 24.7 + - + +
341A LEU* 2.7 26.3 + - + +
342A GLN 3.1 0.2 - - - -
343A LEU* 1.3 77.3 - - - +
345A SER* 1.3 58.2 + - - +
347A MET* 2.9 49.8 + - + +
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Residues in contact with SER 345 (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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341A LEU 4.1 1.0 + - - -
342A GLN* 2.6 34.4 + - - +
344A THR* 1.3 79.0 + - - +
346A GLY* 1.3 55.8 + - - +
347A MET 3.3 5.1 + - - +
349A GLN* 5.9 1.2 + - - -
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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