Contacts of the helix formed by residues 95 - 105 (chain C) in PDB entry 2GD4
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 CYS 95 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C MET* 4.8 13.2 - - - -
21C CYS* 2.0 46.4 - - - -
94C ALA* 1.3 74.0 - - - +
96C ASN* 1.3 84.5 + - - +
98C THR 3.5 1.0 + - - -
99C LEU* 3.5 5.8 + - - -
350C ALA* 2.8 25.8 + - + +
352C PRO* 3.4 34.3 - - + -
353C GLY* 5.7 0.4 - - - -
501C NAG 5.2 3.4 - - + -
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Residues in contact with ASN 96 (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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21C CYS* 4.5 4.7 - - - -
95C CYS* 1.3 88.9 - - - +
97C ASP* 1.3 62.8 + - + +
98C THR 2.4 12.9 + - - -
99C LEU* 2.7 15.1 + - - +
100C GLN* 3.8 3.5 + - - -
350C ALA* 4.8 5.8 - - + +
501C NAG 1.5 83.3 + - - +
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Residues in contact with ASP 97 (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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96C ASN* 1.3 77.4 - - + +
98C THR* 1.3 65.2 + - - +
99C LEU 3.5 0.2 + - - -
100C GLN* 3.5 22.9 + - - +
101C GLN* 3.5 20.1 + - - +
342C ASP* 3.5 17.7 - - - +
349C SER 5.7 2.2 - - - +
204I SER* 3.9 29.7 - - - +
205I GLU* 5.2 2.9 - - - +
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Residues in contact with THR 98 (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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94C ALA* 4.1 8.7 - - + -
95C CYS 3.5 0.2 + - - -
96C ASN 2.4 8.7 + - - -
97C ASP* 1.3 77.1 - - - +
99C LEU* 1.3 69.1 + - - +
101C GLN* 3.2 16.5 + - - +
102C LEU* 3.4 7.8 + - + +
340C LEU* 4.8 0.9 - - - +
342C ASP* 3.2 23.0 - - - +
343C LEU* 4.4 26.2 + - + -
349C SER* 3.0 27.8 + - - -
350C ALA* 3.2 29.5 - - - +
351C LEU* 5.1 3.1 - - + -
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Residues in contact with LEU 99 (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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21C CYS* 4.3 11.4 - - + +
23C TYR* 3.4 34.1 - - + +
91C LYS* 3.4 49.4 - - + +
94C ALA* 3.8 27.4 - - + +
95C CYS* 3.5 6.7 + - - +
96C ASN 2.7 13.9 + - - +
98C THR* 1.3 73.4 - - - +
100C GLN* 1.3 70.2 + - - +
102C LEU* 2.6 21.0 + - + +
103C MET* 2.9 21.5 + - + -
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Residues in contact with GLN 100 (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 TYR* 3.3 40.1 + - + +
26C PRO* 6.3 0.6 - - - +
96C ASN 3.8 3.3 + - - +
97C ASP* 3.5 21.0 + - - +
98C THR 3.4 0.6 - - - -
99C LEU* 1.3 77.0 - - - +
101C GLN* 1.3 66.8 + - + +
103C MET* 2.8 14.2 + - - +
104C GLU* 2.9 37.5 + - - +
205I GLU* 2.7 48.2 + - - +
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Residues in contact with GLN 101 (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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97C ASP* 3.5 14.1 + - - +
98C THR 3.2 6.7 + - - +
99C LEU 2.7 3.4 + - - -
100C GLN* 1.3 72.6 - - + +
102C LEU* 1.3 55.1 + - - +
103C MET 2.5 16.5 + - - -
104C GLU* 2.7 20.4 + - - +
105C VAL* 3.0 19.6 + - + +
339C GLY 3.0 15.7 - - - +
340C LEU* 3.5 11.2 - - + +
341C VAL* 2.5 37.8 + - - +
342C ASP* 2.8 38.6 + - - -
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Residues in contact with LEU 102 (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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87C PHE* 3.7 8.3 - - + +
90C THR* 3.5 23.8 - - + +
91C LYS* 3.5 34.3 - - + +
94C ALA* 4.8 6.3 - - + -
98C THR* 3.4 6.8 + - + +
99C LEU* 2.6 19.7 + - + +
101C GLN* 1.3 73.5 - - - +
103C MET* 1.3 59.0 + - - +
106C PHE* 3.3 43.5 - - + +
108C PHE* 3.5 13.2 - - - -
340C LEU* 3.2 24.8 - - + +
343C LEU* 3.5 22.0 - - + -
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Residues in contact with MET 103 (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 TYR* 3.7 39.7 - - + -
91C LYS* 3.6 29.6 - - - -
99C LEU* 2.9 27.5 + - + +
100C GLN* 2.8 12.8 + - - +
101C GLN 2.5 6.5 + - - -
102C LEU* 1.3 75.6 - - - +
104C GLU* 1.3 57.4 + - + +
107C LYS 3.4 2.4 + - - -
108C PHE* 2.8 65.8 + - + +
109C ASP* 3.2 10.1 + - + +
116C SER* 4.4 21.5 - - - +
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Residues in contact with GLU 104 (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 TYR* 4.2 10.8 + - - +
100C GLN* 2.9 37.9 + - - +
101C GLN* 2.7 14.3 + - - +
103C MET* 1.3 74.8 - - + +
105C VAL* 1.3 61.7 + - + -
106C PHE 3.5 0.4 - - - -
107C LYS* 3.6 22.9 + - - +
109C ASP* 3.8 24.8 - - + +
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Residues in contact with VAL 105 (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 PHE* 2.9 24.8 - - + -
101C GLN* 3.0 23.2 + - + +
104C GLU* 1.3 80.5 - - + +
106C PHE* 1.3 67.6 + - + +
107C LYS* 3.2 12.9 + - - +
335C LEU* 4.7 8.7 - - + +
338C MET* 3.5 46.6 - - + +
339C GLY* 4.1 6.3 - - - -
340C LEU* 4.0 27.1 - - + +
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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