Contacts of the helix formed by residues 32 - 37 (chain H) in PDB entry 5PRC
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 LEU 32 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H VAL* 2.9 16.1 + - + +
28H VAL* 3.7 12.3 - - - +
31H TYR* 1.3 93.4 - - + +
33H ARG* 1.3 59.7 + - - +
34H ARG 2.9 5.9 + - - -
35H GLU* 3.1 8.2 + - + +
36H ASP* 2.9 27.8 + - - +
262M SER 5.7 0.2 - - - -
265M ARG* 3.7 34.1 - - + +
266M TRP* 3.8 44.6 - - + +
269M PHE* 3.7 35.7 - - + -
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Residues in contact with ARG 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H VAL* 2.8 27.1 + - + +
29H LEU* 3.6 20.0 - - + +
31H TYR 3.3 0.4 - - - -
32H LEU* 1.3 75.7 - - - +
34H ARG* 1.3 58.3 + - - +
36H ASP* 2.9 39.9 + - - +
37H ARG* 2.7 61.0 + - - +
41H TYR* 5.2 1.2 + - - -
701H LDA 3.3 34.6 + - - +
801H SO4 3.6 12.3 + - - -
256M PHE* 3.3 35.2 - - - +
257M ASN 3.4 18.2 + - - +
266M TRP* 4.0 13.7 - - + -
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Residues in contact with ARG 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H LEU 4.1 8.6 + - - +
30H LEU* 3.1 51.0 + - - +
31H TYR 2.8 8.7 + - - +
33H ARG* 1.3 80.5 - - - +
35H GLU* 1.3 61.6 + - - +
36H ASP 3.0 1.1 - - - -
37H ARG* 2.9 23.9 + - - +
60H TYR* 2.9 27.0 + - - +
61H GLU* 3.3 26.7 + - - +
62H LEU 3.8 9.2 - - - -
63H PRO* 3.3 28.2 - - + +
703H LDA 3.9 22.5 - - - -
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Residues in contact with GLU 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H TYR* 2.9 52.8 + - + +
32H LEU* 3.3 10.8 - - - +
34H ARG* 1.3 76.6 - - - +
36H ASP* 1.3 56.4 + - - +
37H ARG 3.0 5.5 + - - -
38H ARG* 3.0 60.2 + - - +
63H PRO* 4.3 4.2 - - - +
66H LYS* 4.9 5.2 + - - +
259M THR* 3.9 4.5 + - - -
261M GLU* 5.1 2.4 - - - +
262M SER* 3.8 22.0 - - - -
265M ARG* 4.0 19.3 + - - -
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Residues in contact with ASP 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H LEU 2.9 17.0 + - - +
33H ARG* 2.9 38.3 + - - +
34H ARG 3.0 0.6 - - - -
35H GLU* 1.3 74.3 - - - +
37H ARG* 1.3 58.9 + - - +
38H ARG 3.5 1.3 - - - -
39H GLU 4.7 1.2 - - - +
41H TYR* 4.4 4.2 + - - -
256M PHE* 5.1 0.7 - - - -
257M ASN* 3.3 26.9 + - - +
258M ALA* 3.5 10.3 - - - -
259M THR* 3.5 16.9 - - - +
262M SER* 2.6 32.6 + - - -
266M TRP* 3.0 29.2 + - - -
501M MQ7 5.5 0.2 - - - +
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Residues in contact with ARG 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H LEU 5.4 0.4 + - - -
33H ARG* 2.7 55.7 + - - +
34H ARG* 2.9 16.1 + - - +
36H ASP* 1.3 78.9 - - + +
38H ARG* 1.3 58.1 + - - +
39H GLU 3.2 8.4 + - - -
41H TYR* 3.4 48.7 + - + +
61H GLU* 3.3 47.0 + - - +
62H LEU* 3.8 17.1 - - + +
63H PRO* 4.5 1.1 - - + -
79H PRO* 4.2 2.8 - - - +
801H SO4 2.7 40.6 + - - -
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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