Contacts of the helix formed by residues 76 - 91 (chain d) in PDB entry 5GJQ
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 76 (chain d).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D GLU* 3.0 24.7 + - - -
141D LYS* 3.7 19.9 - - - +
42d ILE* 4.1 0.9 - - - -
74d GLU 3.8 1.6 + - - -
75d LEU* 1.3 76.7 - - - +
77d PRO* 1.3 69.7 - - - +
78d THR* 3.2 6.3 + - - -
79d ALA* 3.2 14.6 + - - +
80d ALA* 2.8 26.9 + - - +
108d ASP* 4.5 15.3 - - - -
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Residues in contact with PRO 77 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41d LYS* 6.0 0.4 - - + -
42d ILE* 3.9 19.1 - - + -
75d LEU 4.2 3.1 - - - +
76d SER* 1.3 87.4 - - - +
78d THR* 1.3 56.4 + - - +
80d ALA* 3.6 2.2 - - + +
81d ALA* 2.9 29.1 + - - +
104d LEU* 3.8 13.0 - - + +
106d GLY* 3.6 33.0 - - - -
107d TYR 3.8 12.1 - - - +
108d ASP* 4.1 19.5 - - + +
114d ALA* 4.2 17.7 - - + -
116d TYR* 3.9 3.3 - - + -
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Residues in contact with THR 78 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D TYR 5.2 2.0 - - - +
102D GLN 5.5 4.7 - - - +
103D GLU* 5.0 6.1 - - + +
76d SER* 3.1 7.8 + - - -
77d PRO* 1.3 77.2 - - - +
79d ALA* 1.3 66.7 + - - +
81d ALA* 3.2 3.1 + - - +
82d ASN* 3.0 42.0 + - - +
111d GLU* 6.2 0.2 - - - +
116d TYR* 2.9 29.5 + - + +
126d LYS* 5.4 1.7 + - - -
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Residues in contact with ALA 79 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D TYR* 5.8 0.2 - - - +
101D TYR* 3.5 30.0 - - + +
103D GLU* 3.8 20.1 + - - +
75d LEU* 3.8 20.2 - - + -
76d SER* 3.2 20.7 + - - +
78d THR* 1.3 80.2 - - - +
80d ALA* 1.3 61.8 + - - +
82d ASN* 3.4 1.2 + - - +
83d PHE* 3.0 23.6 + - - +
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Residues in contact with ALA 80 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38d MET* 4.6 11.7 - - + -
42d ILE* 4.0 19.7 - - + -
64d VAL* 5.1 2.2 - - + -
75d LEU* 4.5 14.3 - - + +
76d SER 2.8 17.5 + - - +
77d PRO 3.6 5.2 - - - +
79d ALA* 1.3 73.6 - - - +
81d ALA* 1.3 65.3 + - - +
83d PHE* 2.9 18.0 + - - +
84d THR* 2.9 19.7 + - + +
104d LEU* 4.1 11.9 - - + -
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Residues in contact with ALA 81 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77d PRO 2.9 18.7 + - - +
78d THR 3.2 5.1 + - - +
80d ALA* 1.3 77.1 - - - +
82d ASN* 1.3 61.4 + - - +
84d THR* 3.4 4.7 + - - -
85d ARG* 3.0 25.6 + - - +
104d LEU* 3.7 14.5 - - + +
116d TYR* 3.7 31.2 - - + -
118d MET* 4.2 2.0 - - - +
124d LEU* 3.9 16.8 - - + +
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Residues in contact with ASN 82 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D LEU 5.3 1.1 - - - +
100D GLN 3.5 10.7 - - - +
101D TYR 3.7 16.1 + - - +
102D GLN* 3.0 36.9 - - + +
65c GLN* 3.6 9.2 + - - -
78d THR* 3.0 39.1 + - - +
79d ALA 4.0 0.7 - - - +
81d ALA* 1.3 77.6 - - - +
83d PHE* 1.3 58.6 + - - +
85d ARG* 3.5 8.2 + - - +
86d ARG* 3.0 26.3 + - - +
116d TYR* 5.9 0.8 - - - -
124d LEU* 3.9 20.6 - - - +
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Residues in contact with PHE 83 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D GLN* 3.3 37.2 + - + -
101D TYR* 3.3 31.2 - + + -
59d TYR* 5.2 1.6 - + - -
60d ILE* 4.1 22.4 - - + -
63d ASN* 3.7 42.0 - - + -
64d VAL* 5.1 6.7 - - + -
75d LEU* 5.4 1.6 - - + -
79d ALA 3.0 14.3 + - - +
80d ALA* 2.9 11.8 + - - +
82d ASN* 1.3 75.7 - - - +
84d THR* 1.3 67.2 + - - +
86d ARG* 3.2 4.7 + - - +
87d ASN* 3.0 48.4 + - - -
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Residues in contact with THR 84 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38d MET* 5.0 0.4 - - + -
44d LEU* 5.4 1.6 - - + -
56d PHE* 3.4 13.6 - - - -
60d ILE* 3.8 42.0 - - + -
80d ALA* 2.9 21.1 + - - +
81d ALA* 3.4 2.8 + - - -
83d PHE* 1.3 76.5 - - + +
85d ARG* 1.3 60.6 + - - +
87d ASN* 3.3 0.3 + - - +
88d LEU* 3.0 30.5 + - - +
102d LEU* 3.9 7.9 - - + +
104d LEU* 4.0 15.3 - - + +
118d MET* 3.1 21.5 - - - -
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Residues in contact with ARG 85 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58c THR 2.9 19.4 + - - -
61c GLN* 3.6 17.4 + - - +
62c THR* 2.7 30.3 + - - +
65c GLN* 3.0 25.7 + - - +
81d ALA 3.0 16.7 + - - +
82d ASN* 3.7 11.8 + - - +
84d THR* 1.3 79.1 + - - +
86d ARG* 1.3 82.7 + - - +
89d ALA* 3.0 40.1 + - - +
118d MET* 3.6 22.9 - - + -
122d ALA* 3.0 27.8 + - - +
124d LEU* 3.9 24.5 - - + -
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Residues in contact with ARG 86 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D LEU* 3.4 42.0 + - + +
100D GLN* 3.1 34.3 - - + +
62c THR* 3.8 28.1 + - - +
65c GLN* 3.1 29.9 + - - +
66c ARG* 4.3 7.8 - - - +
82d ASN 3.0 14.7 + - - +
83d PHE* 3.5 8.5 - - - +
85d ARG* 1.3 94.1 - - - +
87d ASN* 1.3 64.9 + - - +
89d ALA* 3.2 7.8 + - - +
90d ASP* 3.1 58.9 + - - +
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Residues in contact with ASN 87 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D GLN* 3.9 11.0 + - - +
56d PHE* 4.5 5.8 - - + -
59d TYR* 3.8 30.3 + - + -
60d ILE* 3.9 10.0 - - + +
83d PHE* 3.0 57.4 + - - +
84d THR 3.8 3.8 - - - +
86d ARG* 1.3 83.1 - - - +
88d LEU* 1.3 62.4 + - - +
89d ALA 3.4 0.2 + - - -
90d ASP* 3.5 10.9 + - - +
91d CYS* 3.5 22.2 + - - -
98d TYR* 5.5 0.6 - - - -
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Residues in contact with LEU 88 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56d PHE* 3.7 15.8 - - + -
84d THR 3.0 17.2 + - - +
85d ARG 3.9 0.7 - - - +
87d ASN* 1.3 78.3 - - - +
89d ALA* 1.3 61.4 + - - +
91d CYS* 3.6 3.4 + - - +
92d LEU* 3.4 19.4 + - - +
98d TYR* 3.7 37.7 + - + +
100d VAL* 3.7 24.0 - - + +
102d LEU* 4.3 4.5 - - + -
118d MET* 3.7 24.0 - - + -
119d ASP 3.7 15.7 - - - +
120d TYR 4.1 9.2 - - - +
122d ALA* 3.8 14.4 - - + +
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Residues in contact with ALA 89 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58c THR* 4.5 5.8 - - + -
62c THR* 4.2 5.4 - - + +
85d ARG* 3.0 39.7 + - - +
86d ARG* 3.7 15.9 - - - +
87d ASN 3.2 0.4 - - - -
88d LEU* 1.3 75.5 - - - +
90d ASP* 1.3 65.0 + - - +
92d LEU* 3.3 21.1 - - - +
93d ARG* 4.6 3.1 + - - +
122d ALA* 3.8 14.4 - - + -
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Residues in contact with ASP 90 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66c ARG* 4.6 7.1 + - - -
86d ARG* 3.1 56.4 + - - +
87d ASN* 4.0 7.1 - - - +
88d LEU 3.4 0.2 - - - -
89d ALA* 1.3 78.6 - - - +
91d CYS* 1.3 64.6 + - - +
92d LEU 3.6 0.3 + - - -
93d ARG* 4.4 5.4 + - - +
94d SER* 4.4 7.6 - - - -
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Residues in contact with CYS 91 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87d ASN 3.5 17.3 + - - +
88d LEU 3.6 2.7 + - - +
89d ALA 3.2 0.4 - - - -
90d ASP* 1.3 81.5 - - - +
92d LEU* 1.3 63.4 + - - +
93d ARG 3.3 0.9 - - - -
94d SER* 2.6 27.9 + - - +
96d THR* 3.7 19.3 - - - +
97d PRO* 3.2 13.7 - - - +
98d TYR* 3.9 27.8 - - + -
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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