Contacts of the helix formed by residues 41 - 46 (chain L) in PDB entry 5G04
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 GLY 41 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1350A TYR* 4.0 27.6 - - - -
33L LEU* 4.6 3.4 - - - -
37L LYS 4.4 2.0 - - - -
39L GLY* 3.6 0.6 - - - -
40L PHE* 1.3 81.1 - - - +
42L VAL* 1.3 60.3 + - - -
43L ASP* 3.3 4.5 - - - -
44L GLN* 2.9 29.0 + - - +
45L LEU* 3.0 14.6 + - - +
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Residues in contact with VAL 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1349A SER 6.0 0.2 - - - +
1350A TYR* 3.1 21.7 + - - +
1351A GLN 3.1 30.5 - - - +
1352A ILE 4.4 2.0 - - - +
1353A LYS* 3.7 26.7 - - + -
31L TRP* 3.6 30.3 - - + +
33L LEU* 3.4 24.8 - - + +
41L GLY* 1.3 67.2 - - - -
43L ASP* 1.3 67.1 + - - +
45L LEU* 3.4 7.8 + - + +
46L ARG* 3.2 24.7 + - + +
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Residues in contact with ASP 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1347A SER* 6.1 0.2 - - - -
1348A PRO* 5.0 12.5 - - - +
1349A SER 5.2 7.1 - - - +
1350A TYR* 6.6 0.4 - - + -
1353A LYS* 3.4 30.3 - - - +
41L GLY* 4.9 1.8 - - - -
42L VAL* 1.3 78.2 - - - +
44L GLN* 1.3 64.4 + - + +
46L ARG* 3.3 4.4 + - - +
47L ASP* 2.9 29.9 + - - +
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Residues in contact with GLN 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1350A TYR* 5.8 1.2 - - - -
39L GLY* 3.0 27.6 + - - +
40L PHE* 2.9 23.4 - - - -
41L GLY* 2.9 20.0 + - - +
43L ASP* 1.3 74.4 - - + +
45L LEU* 1.3 66.0 + - - +
47L ASP* 3.0 23.0 + - - +
49L ASN 4.6 0.3 - - - +
52L THR* 3.1 39.8 + - + +
53L TYR 4.1 9.7 + - - +
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Residues in contact with LEU 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L TRP* 4.2 26.0 - - + -
33L LEU* 4.3 12.3 - - + -
41L GLY 3.0 11.2 + - - +
42L VAL* 3.6 11.4 - - + +
44L GLN* 1.3 75.4 - - - +
46L ARG* 1.3 67.3 - - + +
53L TYR* 5.0 0.2 - - - +
54L TRP* 3.6 42.4 - - + +
64L VAL* 5.1 0.2 - - + -
153L MET 4.1 13.7 - - - +
154L ARG 3.3 14.1 - - - +
155L GLN* 2.2 32.3 - - - +
156L ILE* 3.9 31.0 - - + +
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Residues in contact with ARG 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1353A LYS* 5.1 17.7 - - + +
24L GLU* 3.3 26.7 + - - +
26L GLY* 3.4 32.3 - - - +
31L TRP* 3.2 37.3 - - + +
42L VAL* 3.2 16.4 + - + +
43L ASP* 3.6 5.8 - - - +
45L LEU* 1.3 83.8 - - + +
47L ASP* 1.3 61.6 + - - +
48L ASP* 3.3 16.7 + - - +
155L GLN* 3.7 6.5 - - - +
156L ILE 2.6 32.0 + - - -
157L LYS* 3.5 15.1 - - - +
158L ILE 4.2 1.4 - - - +
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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