Contacts of the helix formed by residues 58 - 65 (chain L) in PDB entry 4R2G
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 ARG 58 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73D THR* 3.6 22.6 + - - -
74D SER* 5.1 10.3 + - - +
13L GLU* 4.3 15.3 + - - +
57L SER* 1.3 77.3 + - - +
59L ARG* 1.3 55.0 + - - +
60L SER* 2.8 28.8 + - - +
61L LEU* 3.1 54.9 + - + +
62L TRP* 3.8 3.3 + - - -
68L PRO* 4.0 11.2 - - + +
70L ILE* 4.3 7.2 - - + +
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Residues in contact with ARG 59 (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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368A ASP* 2.4 45.4 + - - -
425A ASN* 4.2 14.8 + - - +
430A VAL* 3.7 27.0 - - + +
431A GLY* 5.5 4.9 - - - +
42L SER 3.8 15.7 + - - -
43L PHE* 4.5 0.2 - - - +
44L LEU* 3.3 26.7 - - - +
57L SER 3.8 5.9 + - - -
58L ARG* 1.3 70.4 - - - +
60L SER* 1.3 68.3 + - - +
61L LEU 3.1 0.9 - - - -
62L TRP* 3.0 55.2 + - + +
63L ASP* 4.2 0.9 - - - +
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Residues in contact with SER 60 (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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197A GLY* 5.0 19.7 + - - +
430A VAL* 5.3 2.9 - - - -
74D SER* 6.2 0.2 - - - -
58L ARG* 2.8 17.6 + - - +
59L ARG* 1.3 84.2 + - - +
61L LEU* 1.3 67.5 + - - +
63L ASP* 4.2 12.0 + - - +
64L GLN* 5.5 0.9 - - - +
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Residues in contact with LEU 61 (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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13L GLU* 4.4 5.8 - - - +
58L ARG* 3.5 50.9 - - + +
59L ARG 3.1 0.6 - - - -
60L SER* 1.3 79.0 - - - +
62L TRP* 1.3 63.7 + - - +
63L ASP 3.1 3.4 - - - -
64L GLN* 2.9 41.6 + - - +
66L ASN* 3.5 33.0 + - + +
68L PRO* 4.0 15.5 - - + -
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Residues in contact with TRP 62 (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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430A VAL* 4.0 14.8 - - + -
23L SER* 3.1 31.2 - - - +
26L PHE* 3.6 21.6 - + - -
39L ASN* 3.7 36.6 - - + -
41L GLY 4.8 0.4 - - - -
42L SER 3.7 19.1 - - - -
43L PHE 3.9 3.4 - - - -
44L LEU* 3.7 29.6 - - + -
57L SER* 2.9 28.6 + - - -
58L ARG 3.8 3.1 - - - -
59L ARG* 3.0 40.5 + - + +
61L LEU* 1.3 76.8 - - - +
63L ASP* 1.3 63.9 + - - +
64L GLN 3.1 1.1 - - - -
65L GLY 3.2 10.3 + - - -
66L ASN 3.2 19.0 + - - -
67L PHE* 3.6 17.2 - + + +
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Residues in contact with ASP 63 (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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123A THR* 6.1 0.7 - - - -
429A GLU* 5.7 3.1 - - - +
430A VAL* 3.5 39.5 + - - +
21L LYS 2.9 16.7 - - - +
22L LYS* 3.8 4.6 - - - -
23L SER* 4.6 7.2 - - - +
59L ARG 4.2 2.6 - - - +
60L SER* 4.2 8.6 + - - +
61L LEU 3.0 1.6 + - - -
62L TRP* 1.3 78.1 - - - +
64L GLN* 1.3 57.5 + - + +
65L GLY 3.5 0.7 - - - -
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Residues in contact with GLN 64 (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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17L THR* 5.5 1.0 - - - +
21L LYS* 3.6 29.6 - - + +
60L SER 5.5 0.9 - - - +
61L LEU* 2.9 39.6 + - - +
63L ASP* 1.3 79.7 - - + +
65L GLY* 1.3 61.0 + - - +
66L ASN* 3.1 23.9 + - - +
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Residues in contact with GLY 65 (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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17L THR* 3.4 10.0 - - - +
18L ALA* 3.4 22.4 + - - -
20L GLN 4.0 13.2 - - - -
21L LYS 3.9 3.6 - - - -
22L LYS 3.7 16.8 - - - -
62L TRP 3.2 8.8 + - - -
63L ASP 3.5 0.8 - - - -
64L GLN* 1.3 77.7 - - - +
66L ASN* 1.3 62.1 + - - +
67L PHE* 3.9 12.6 - - - -
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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