Contacts of the helix formed by residues 355 - 367 (chain I) in PDB entry 5U07
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 355 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338I ALA* 4.1 5.2 - - - +
353I TYR* 3.3 1.3 - - - +
354I ASP* 1.3 94.8 + - - +
356I TYR* 1.3 68.9 + - - +
357I PRO* 4.0 9.5 - - - +
358I ALA* 3.3 16.1 + - - +
359I LEU* 3.0 23.4 + - - +
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Residues in contact with TYR 356 (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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264I LEU* 4.4 22.9 - - + -
280I LEU* 4.0 41.2 - - + +
281I PRO* 2.3 36.9 + - + -
282I ASP 4.4 2.1 + - - -
284I VAL* 4.3 16.4 - - + -
338I ALA* 3.8 35.0 - - + -
339I THR* 4.9 3.4 - - - -
340I VAL* 4.4 15.9 - - + +
355I SER* 1.3 71.8 - - - +
357I PRO* 1.3 72.7 - - + +
359I LEU* 3.3 4.4 + - + +
360I ILE* 3.0 32.6 + - + +
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Residues in contact with PRO 357 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261I ARG* 3.9 34.3 - - - +
355I SER* 3.7 11.7 - - - +
356I TYR* 1.3 95.9 - - + +
358I ALA* 1.3 56.1 + - - +
360I ILE* 4.6 3.6 - - + +
361I ASP* 2.9 40.2 + - - +
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Residues in contact with ALA 358 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353I TYR* 4.4 10.7 - - + -
354I ASP* 3.8 12.6 - - - +
355I SER* 3.3 23.0 + - - +
356I TYR 3.3 0.8 - - - -
357I PRO* 1.3 77.4 - - - +
359I LEU* 1.3 58.1 + - - +
361I ASP* 3.9 4.2 - - - +
362I ALA* 2.9 32.8 + - - +
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Residues in contact with LEU 359 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264I LEU* 6.1 0.2 - - + -
284I VAL* 4.1 7.0 - - + +
286I ILE* 3.4 26.9 - - + -
336I GLY 3.6 12.8 - - - +
337I TYR* 3.5 3.6 - - - -
338I ALA* 3.5 34.3 - - + +
353I TYR* 3.4 36.0 - - + +
355I SER 3.0 15.9 + - - +
356I TYR* 3.6 6.3 - - + +
358I ALA* 1.3 73.4 - - - +
360I ILE* 1.3 65.9 + - + +
362I ALA* 3.2 1.9 + - - +
363I MET* 3.0 56.4 + - + +
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Residues in contact with ILE 360 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257I ALA* 4.4 14.4 - - + +
260I LEU* 4.0 23.3 - - + -
261I ARG* 4.1 32.8 - - + +
264I LEU* 3.7 29.2 - - + -
286I ILE* 4.6 9.9 - - + -
356I TYR* 3.0 20.8 + - + +
357I PRO* 4.1 5.4 - - + +
359I LEU* 1.3 74.6 - - + +
361I ASP* 1.3 65.9 + - - +
363I MET* 4.5 4.5 - - - -
364I VAL* 2.9 50.6 + - + +
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Residues in contact with ASP 361 (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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257I ALA* 5.2 6.9 - - - +
261I ARG* 4.2 17.5 + - - -
357I PRO* 2.9 29.0 + - - +
358I ALA* 3.9 4.6 - - - +
360I ILE* 1.3 81.2 - - - +
362I ALA* 1.3 56.7 + - - +
364I VAL* 4.8 2.2 - - - -
365I ALA* 2.9 33.6 + - - +
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Residues in contact with ALA 362 (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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353I TYR* 3.4 35.9 - - + +
358I ALA 2.9 18.1 + - - +
359I LEU 3.9 0.7 - - - +
361I ASP* 1.3 78.5 - - - +
363I MET* 1.3 58.9 + - - +
365I ALA* 3.7 4.2 - - - +
366I ALA* 2.9 25.8 + - - +
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Residues in contact with MET 363 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286I ILE* 3.3 48.2 - - + +
288I VAL* 4.3 17.7 - - + +
334I ILE* 4.7 11.0 - - + +
335I ARG 3.4 26.5 - - - +
336I GLY* 3.5 4.5 - - - -
353I TYR* 4.0 13.5 - - + +
359I LEU* 3.0 39.1 + - + +
360I ILE* 4.1 4.0 - - - +
362I ALA* 1.3 75.7 - - - +
364I VAL* 1.3 66.4 + - + +
366I ALA* 3.0 24.0 + - + +
367I ALA* 3.2 12.8 + - - +
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Residues in contact with VAL 364 (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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4I VAL* 5.5 7.2 - - + -
253I ARG* 4.1 37.7 + - + +
256I VAL* 4.2 15.7 - - + -
257I ALA* 4.3 13.7 - - + +
260I LEU* 3.9 27.1 - - + -
360I ILE* 2.9 28.5 + - + +
361I ASP* 4.4 2.5 - - - +
363I MET* 1.3 77.5 - - + +
365I ALA* 1.3 61.6 + - - +
367I ALA* 3.1 22.2 + - + +
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Residues in contact with ALA 365 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361I ASP 2.9 21.9 + - - +
362I ALA* 3.8 4.7 - - - +
364I VAL* 1.3 78.4 - - - +
366I ALA* 1.3 59.7 + - - +
367I ALA 3.4 4.2 + - - -
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Residues in contact with ALA 366 (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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288I VAL* 5.9 2.6 - - + +
290I PHE* 6.1 0.7 - - - -
334I ILE* 5.0 17.2 - - + +
362I ALA 2.9 15.5 + - - +
363I MET* 3.0 17.4 + - + +
365I ALA* 1.3 77.2 - - - +
367I ALA* 1.3 55.9 + - - +
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Residues in contact with ALA 367 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I VAL* 4.7 8.1 - - + -
239I LEU* 4.0 25.9 - - + +
253I ARG* 2.3 45.9 + - - +
288I VAL* 4.7 15.7 - - + -
290I PHE* 6.6 0.2 - - - -
363I MET 3.2 8.1 + - - +
364I VAL* 3.1 14.6 + - + +
365I ALA 4.4 3.8 - - - -
366I ALA* 1.3 80.8 - - - +
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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