Contacts of the helix formed by residues 376 - 382 (chain I) in PDB entry 4PHZ
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 ARG 376 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B GLY* 4.3 12.9 + - - -
215B LYS* 3.8 20.4 - - - +
32I LYS* 2.3 44.0 + - + +
33I SER* 3.4 11.4 + - - -
34I GLN 3.3 16.6 + - - -
35I GLN* 5.7 2.2 - - - +
36I ALA* 3.7 6.0 - - - +
39I ARG* 3.4 11.0 + - - +
373I ASP 2.7 25.0 + - - +
374I ILE 3.1 6.6 - - - +
375I GLU* 1.3 72.5 - - - +
377I LEU* 1.3 57.9 + - - +
378I SER 3.2 2.0 - - - +
379I ASP* 2.6 66.6 + - - +
382I TYR* 5.2 2.6 - - - -
383I ASP* 5.5 1.6 + - - -
54K PHE* 3.8 30.5 - - + -
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Residues in contact with LEU 377 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I ALA* 3.9 21.9 - - + +
39I ARG* 4.3 9.6 - - - -
40I MET* 3.9 27.1 - - + +
321I ALA* 4.4 13.2 - - + -
322I ALA* 4.4 7.9 - - + -
324I LEU* 3.7 35.7 - - + -
326I PHE* 5.1 0.2 - - + -
372I TRP* 3.0 53.3 + - + +
375I GLU 2.8 9.6 + - - +
376I ARG* 1.3 73.4 - - - +
378I SER* 1.3 60.2 + - - +
379I ASP 3.1 6.1 + - - -
380I LEU* 3.4 20.3 - - - +
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Residues in contact with SER 378 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293I TYR* 4.2 9.8 - - - -
294I LYS 5.0 3.6 - - - -
295I VAL* 4.6 5.4 - - - +
296I PRO* 6.0 1.3 - - - -
297I GLY 3.8 16.8 - - - -
372I TRP* 3.4 20.8 + - - +
373I ASP* 3.0 39.0 + - - -
376I ARG 4.2 0.3 - - - -
377I LEU* 1.3 74.5 - - - +
379I ASP* 1.3 66.8 + - - -
380I LEU* 3.0 10.6 + - - -
381I ALA* 3.6 14.4 + - - +
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Residues in contact with ASP 379 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LYS* 3.4 24.3 - - - +
36I ALA* 4.4 3.3 - - + +
373I ASP 5.2 0.2 - - - +
376I ARG* 2.6 63.8 + - - +
377I LEU 3.1 1.8 - - - -
378I SER* 1.3 88.4 + - - +
380I LEU* 1.3 55.1 + - - +
381I ALA* 3.0 7.2 - - - +
382I TYR* 3.2 22.3 + - - +
383I ASP* 3.3 10.2 - - - +
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Residues in contact with LEU 380 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I ALA* 4.1 6.0 - - + +
37I PHE* 3.8 12.8 - - + -
40I MET* 4.0 7.6 - - + -
293I TYR* 3.6 24.4 + - + +
372I TRP* 4.9 0.7 - - + -
377I LEU 3.4 16.2 + - - +
378I SER 3.0 1.0 - - - -
379I ASP* 1.3 74.0 - - - +
381I ALA* 1.3 63.6 + - - +
382I TYR 3.2 1.1 - - - -
383I ASP* 3.1 23.5 + - - +
385I ASP 3.6 12.6 - - - +
386I SER* 3.6 7.3 + - - +
387I GLN 3.4 29.6 - - - +
388I ILE* 3.6 31.4 - - + -
410I VAL* 3.9 14.6 - - + -
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Residues in contact with ALA 381 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A THR 5.0 2.1 - - - +
258A ILE* 4.0 14.7 - - + +
259A PRO* 3.8 14.2 - - - +
215B LYS* 5.4 3.6 - - - +
293I TYR* 3.6 11.2 + - - +
295I VAL* 4.0 36.1 - - + -
378I SER 3.6 7.8 + - - +
379I ASP* 4.7 1.6 - - - -
380I LEU* 1.3 81.0 - - - +
382I TYR* 1.3 59.0 + - - +
383I ASP 3.5 2.3 + - - +
412I PRO* 5.4 0.9 - - + -
414I PHE* 4.9 9.4 - - + -
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Residues in contact with TYR 382 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A PRO* 3.2 5.4 - - - +
62B ARG* 3.1 50.5 + - - +
206B GLU* 5.1 0.2 - - - -
212B THR* 4.9 0.9 - - + -
214B GLY 3.6 7.9 - - - -
215B LYS* 2.8 74.7 + - + +
217B VAL* 2.8 44.0 + - + +
218B VAL* 4.4 1.6 + - - +
219B PRO* 5.6 0.2 - - - +
35I GLN* 5.1 3.8 - - + -
376I ARG* 5.2 2.2 - - - -
379I ASP* 3.2 13.4 + - + +
380I LEU 3.2 0.2 - - - -
381I ALA* 1.3 79.5 - - - +
383I ASP* 1.3 70.4 + - - +
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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
------------------------------------------------------------
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