Contacts of the helix formed by residues 58 - 65 (chain C) in PDB entry 1GC1
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C GLU* 4.1 15.9 + - - -
57C SER* 1.3 82.1 + - - +
59C ARG* 1.3 51.1 + - - +
60C SER* 2.7 33.0 + - - +
61C LEU* 2.8 35.1 + - + +
62C TRP* 3.5 10.3 - - - -
66C ASN 4.4 0.5 - - - +
68C PRO* 3.9 19.6 - - + +
70C ILE* 3.1 25.1 - - + +
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Residues in contact with ARG 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C SER 3.1 25.4 + - - -
43C PHE* 3.6 3.6 - - - +
44C LEU* 3.6 19.9 - - + +
56C ASP* 5.6 1.6 + - - -
57C SER* 5.1 3.8 - - - -
58C ARG* 1.3 71.7 - - - +
60C SER* 1.3 62.6 + - - +
61C LEU 3.2 0.2 - - - -
62C TRP* 3.2 47.8 + - + +
63C ASP* 4.5 2.3 + - - +
123G THR* 4.8 0.4 + - - -
368G ASP* 2.5 46.1 + - - -
425G ASN* 4.3 13.5 + - - +
430G VAL* 3.6 31.3 - - + +
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Residues in contact with SER 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ARG* 2.7 18.3 + - - +
59C ARG* 1.3 78.6 + - - +
61C LEU* 1.3 59.0 - - - -
62C TRP 3.7 0.7 + - - -
63C ASP* 4.5 2.3 + - - +
64C GLN* 3.8 5.9 - - - +
123G THR* 4.1 22.3 + - - +
125G LEU* 2.9 48.8 - - - +
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Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLU* 5.3 4.5 - - - +
58C ARG* 2.8 35.0 + - + +
60C SER* 1.3 75.2 - - - +
62C TRP* 1.3 62.9 + - - +
63C ASP 3.3 2.5 - - - -
64C GLN* 3.2 17.4 + - + +
66C ASN* 2.9 66.0 + - + +
68C PRO* 4.6 2.7 - - + -
125G LEU* 3.7 31.6 - - + -
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Residues in contact with TRP 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C SER* 3.0 31.9 + - - +
26C PHE* 3.9 11.0 - + - -
39C ASN* 3.7 30.1 - - + +
41C GLY 4.3 3.1 - - - -
42C SER 3.5 27.1 - - - -
44C LEU* 3.5 40.2 - - + -
57C SER* 3.2 22.6 + - - -
58C ARG 3.5 10.7 + - - -
59C ARG* 3.2 33.1 + - + +
60C SER 3.4 0.2 - - - -
61C LEU* 1.3 77.6 - - - +
63C ASP* 1.3 59.2 + - - +
65C GLY* 2.9 18.4 + - - -
66C ASN 3.8 7.0 - - - -
67C PHE* 3.7 28.0 - + + +
430G VAL* 3.4 20.9 - - + -
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Residues in contact with ASP 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LYS* 3.7 17.7 - - - +
23C SER* 3.1 26.6 + - - +
59C ARG 5.1 2.0 - - - +
60C SER 4.5 2.7 + - - +
61C LEU 3.3 0.8 - - - -
62C TRP* 1.3 76.4 - - - +
64C GLN* 1.3 80.0 + - - +
65C GLY 3.4 1.6 - - - -
123G THR 4.0 15.8 - - - +
124G PRO* 6.3 0.2 - - + -
429G LYS* 5.8 2.6 - - - +
430G VAL* 4.3 26.9 + - - +
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Residues in contact with GLN 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C THR* 5.0 5.0 - - - +
21C LYS 4.5 0.3 - - - +
22C LYS* 3.9 16.8 - - - +
60C SER 3.8 5.0 - - - +
61C LEU* 3.2 17.2 + - + +
62C TRP 3.1 1.0 - - - -
63C ASP* 1.3 103.8 + - - +
65C GLY* 1.3 60.5 + - - +
66C ASN* 3.4 4.3 + - + +
123G THR 5.0 0.7 - - - +
124G PRO* 5.1 1.1 - - - +
125G LEU* 3.6 42.0 + - + +
126G CYS 6.0 0.4 - - - +
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Residues in contact with GLY 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C THR* 3.3 6.4 - - - -
18C ALA 2.9 27.3 + - - -
21C LYS 3.6 20.2 - - - -
22C LYS* 3.9 9.3 - - - +
61C LEU 3.9 0.2 - - - -
62C TRP 2.9 11.8 + - - -
63C ASP 3.4 1.2 - - - -
64C GLN* 1.3 79.8 - - - +
66C ASN* 1.3 57.9 + - - +
67C PHE* 3.4 11.9 - - - -
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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