Contacts of the helix formed by residues 35 - 41 (chain F) in PDB entry 4Q9U
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 35 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34F SER* 1.3 87.1 + - - +
36F LEU* 1.3 60.7 + - - +
37F VAL 3.5 1.1 - - - -
38F LEU* 3.2 32.5 + - - +
39F ARG* 3.3 10.4 + - - +
133F ASN* 5.4 5.5 + - - -
164F ALA* 4.3 7.8 - - - +
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Residues in contact with LEU 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F LEU* 5.3 3.8 - - + -
34F SER 3.6 4.4 - - - +
35F SER* 1.3 76.1 + - - +
37F VAL* 1.3 71.3 + - + +
38F LEU 3.2 4.7 + - - -
39F ARG 3.8 0.3 + - - -
40F PHE* 3.8 2.8 + - - +
97F ILE* 4.9 9.4 - - + -
99F VAL* 3.6 40.4 - - + -
131F SER* 3.7 13.9 - - - +
133F ASN* 4.4 21.5 - - - +
162F THR* 4.7 8.7 - - - +
164F ALA* 4.4 13.9 - - + -
170F VAL* 3.7 26.1 - - + +
173F ILE* 6.4 2.2 - - + -
174F PHE* 5.0 9.9 - - + -
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Residues in contact with VAL 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F LEU* 3.8 28.7 - - + -
34F SER* 4.7 9.9 - - - +
36F LEU* 1.3 82.7 - - + +
38F LEU* 1.3 63.1 + - - +
39F ARG 3.4 0.2 - - - -
40F PHE* 3.9 4.5 - - - -
41F VAL* 3.4 25.6 + - + +
55F ALA 4.7 8.1 - - - +
56F ALA 5.6 0.4 - - - +
58F LEU* 3.6 41.9 - - + +
73F ILE* 4.4 0.9 - - + -
75F ASP* 5.5 3.1 - - + +
174F PHE* 3.7 27.6 - - + -
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Residues in contact with LEU 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309E PRO* 5.7 12.8 - - + -
34F SER 3.9 8.7 - - - +
35F SER* 3.2 28.0 - - - +
36F LEU 3.2 0.6 - - - -
37F VAL* 1.3 79.3 - - + +
39F ARG* 1.3 61.0 + - - +
41F VAL 4.4 10.3 - - - -
58F LEU* 5.5 2.5 - - - -
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Residues in contact with ARG 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F SER 3.3 4.5 + - - +
36F LEU 3.8 0.4 + - - +
37F VAL 3.4 0.2 - - - -
38F LEU* 1.3 80.4 - - - +
40F PHE* 1.3 65.6 + - - +
41F VAL 4.6 1.9 - - - +
164F ALA* 3.3 37.1 + - + +
165F LYS 5.5 1.4 + - - -
167F SER* 3.1 34.9 + - - -
170F VAL* 3.6 17.5 - - + +
171F ASN* 5.6 5.9 + - - -
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Residues in contact with PHE 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F LEU 3.8 3.0 + - - +
37F VAL 3.6 5.5 + - - +
38F LEU 3.4 0.6 - - - -
39F ARG* 1.3 83.3 + - - +
41F VAL* 1.3 85.2 + - + +
60F GLN* 3.5 37.7 + - + -
71F PHE* 3.9 16.8 - + - -
73F ILE* 4.4 1.8 - - + -
170F VAL* 3.4 23.9 - - + +
171F ASN* 3.7 30.7 - - - +
174F PHE* 3.3 66.9 - + + -
175F MET* 4.8 9.2 - - + -
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Residues in contact with VAL 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F VAL* 3.4 12.1 + - + +
38F LEU* 4.4 11.2 - - - -
39F ARG 4.6 2.0 - - - +
40F PHE* 1.3 101.8 - - + +
58F LEU* 3.7 49.8 - - + +
59F THR 4.4 9.0 - - - +
60F GLN* 3.2 30.0 + - + +
73F ILE* 4.3 3.4 - - + -
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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
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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