Contacts of the helix formed by residues 51 - 58 (chain E) in PDB entry 4PEI
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 TYR 51 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B LYS* 3.3 48.7 - - + +
321B TYR* 3.7 31.0 - + - +
343B TYR* 3.2 30.5 - + + +
49E LEU 3.5 0.6 - - - -
50E ARG* 1.3 123.5 + - + +
52E GLU* 1.3 67.5 + - - +
53E ALA* 3.3 6.3 - - + -
54E ASP* 3.0 29.0 + - - +
67E MET* 3.5 15.9 - - - +
74E TYR* 4.0 19.8 + + - -
402E SO4 4.6 3.2 + - - -
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Residues in contact with GLU 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B TYR 3.3 7.8 + - - +
322B ILE* 4.1 12.8 - - - +
327B ILE* 3.8 7.4 - - + +
329B ASP* 4.7 15.7 - - - +
336B GLN 5.2 0.3 - - - +
339B SER* 2.8 30.7 + - - +
340B ARG* 2.7 51.0 + - - +
343B TYR* 3.7 16.0 + - + -
51E TYR* 1.3 73.7 - - - +
53E ALA* 1.3 63.4 + - - +
55E LEU* 3.0 29.1 + - + +
67E MET* 3.9 19.0 - - + +
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Residues in contact with ALA 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B GLU 4.1 3.6 - - - +
320B LYS 3.2 28.3 - - - +
321B TYR 2.8 17.2 + - - +
322B ILE 3.5 17.9 + - - +
323B GLY* 4.1 4.5 - - - +
327B ILE* 4.9 1.8 - - - -
51E TYR* 3.2 4.9 + - + -
52E GLU* 1.3 73.2 - - - +
54E ASP* 1.3 63.5 + - - +
55E LEU 3.2 0.9 + - - -
56E VAL* 3.5 22.5 + - - +
57E TYR* 4.9 2.4 - - - -
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Residues in contact with ASP 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E LEU* 4.1 12.4 - - + +
50E ARG* 2.8 64.6 + - - +
51E TYR* 3.0 20.2 + - - +
53E ALA* 1.3 75.0 - - - +
55E LEU* 1.3 54.0 + - - +
56E VAL 3.0 3.1 - - - -
57E TYR* 2.8 33.8 + - - +
58E LEU 3.8 2.3 + - - -
93E SER* 3.3 23.8 + - - +
95E ASN* 3.1 12.3 + - - +
96E VAL* 4.0 0.3 - - - +
402E SO4 4.4 2.1 + - - -
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Residues in contact with LEU 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ILE* 3.9 16.4 - - + -
328B TYR 4.8 2.7 - - - +
329B ASP* 4.2 30.3 - - + +
49E LEU* 3.3 28.8 - - + +
51E TYR 4.2 0.2 + - - -
52E GLU* 3.0 23.9 + - + +
54E ASP* 1.3 76.0 - - - +
56E VAL* 1.3 57.9 + - - +
57E TYR 3.0 1.8 + - - -
58E LEU* 3.1 12.7 + - + +
65E LYS* 2.9 39.3 + - + +
66E GLN 3.6 31.4 - - - +
67E MET* 4.0 14.6 - - + -
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Residues in contact with VAL 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B LYS* 6.2 1.8 - - + -
327B ILE* 4.2 28.2 - - + +
53E ALA* 3.5 15.9 + - - +
54E ASP 3.0 0.2 - - - -
55E LEU* 1.3 77.9 - - - +
57E TYR* 1.3 75.7 + - + +
58E LEU 3.4 0.2 - - - -
65E LYS* 4.2 7.1 + - - +
148E PRO* 3.8 32.5 - - + -
151E VAL* 3.5 20.3 - - - +
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Residues in contact with TYR 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E ALA 4.9 1.3 - - - -
54E ASP* 2.8 12.7 + - - +
56E VAL* 1.3 95.9 - - + +
58E LEU* 1.3 61.5 + - - +
59E LYS* 3.6 2.9 + - - +
92E GLU 2.9 14.7 - - - +
93E SER* 4.4 0.9 - - - -
94E SER* 3.5 19.1 + - - +
95E ASN* 3.3 53.2 - - + +
146E PRO* 3.1 36.2 + - + +
147E SER* 3.3 30.9 - - - -
148E PRO* 3.4 13.2 - - + +
151E VAL* 3.7 15.6 - - - +
154E LEU* 4.4 11.2 - - + -
402E SO4 4.1 10.7 + - - -
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Residues in contact with LEU 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E GLN* 4.2 15.3 - - + +
49E LEU* 4.1 18.8 - - + -
54E ASP 3.8 1.2 + - - -
55E LEU* 3.1 17.1 + - + +
57E TYR* 1.3 79.8 - - - +
59E LYS* 1.3 58.2 + - - +
60E VAL* 3.1 19.4 + - + -
64E TYR 4.1 16.2 - - - +
65E LYS* 2.7 29.0 + - + -
66E GLN 4.0 20.2 - - - +
91E HIS* 3.9 20.4 - - + +
92E GLU* 3.4 32.5 - - - +
151E VAL* 4.0 2.1 - - - +
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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