Contacts of the helix formed by residues 81 - 103 (chain C) in PDB entry 5GQQ
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 ASN 81 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C PHE* 3.6 3.4 - - - -
41C GLY 3.8 15.7 - - - +
42C VAL* 4.5 3.4 - - + -
75C GLU* 3.7 18.6 + - - +
77C LYS* 3.8 9.6 - - - +
80C VAL* 1.3 74.6 - - - +
82C PHE* 1.3 60.6 + - - +
83C SER* 2.9 11.8 + - - -
84C GLU* 2.8 49.4 + - - +
85C PHE* 2.8 26.2 + - - +
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Residues in contact with PHE 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 3.7 10.5 - - + -
29C TRP* 3.4 58.3 - + + -
32C PHE* 3.4 39.1 - + + -
41C GLY 4.4 0.6 + - - -
81C ASN* 1.3 76.4 - - - +
83C SER* 1.3 67.2 + - - +
85C PHE* 3.0 13.2 + + - +
86C THR* 3.1 37.8 + - + +
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Residues in contact with SER 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ARG* 4.7 11.7 + - - -
81C ASN* 2.9 10.9 + - - -
82C PHE* 1.3 84.0 - - - +
84C GLU* 1.3 61.6 + - - +
86C THR* 2.8 25.2 + - - -
87C GLY* 3.8 2.1 + - - -
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Residues in contact with GLU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C PHE* 3.4 29.0 - - - +
73C ASP* 4.1 0.2 - - - -
74C ARG* 3.2 45.4 + - - +
75C GLU* 3.9 5.7 - - - +
77C LYS* 2.9 22.1 + - - -
79C GLY 3.9 0.5 - - - +
80C VAL* 3.2 13.2 - - + -
81C ASN* 2.8 45.8 + - - +
83C SER* 1.3 75.2 - - - +
85C PHE* 1.3 63.7 + - - +
86C THR 3.1 2.0 - - - -
87C GLY* 3.0 12.9 + - - +
88C VAL* 3.1 13.9 + - - +
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Residues in contact with PHE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE* 3.9 30.1 - + - -
28C LEU* 4.3 8.7 - - + -
31C VAL* 3.9 31.0 - - + -
32C PHE* 3.6 34.1 - + + -
35C VAL* 4.7 3.6 - - + -
43C ILE* 3.6 22.0 - - + -
48C LEU* 4.4 10.8 - - + -
80C VAL* 4.1 11.0 - - + +
81C ASN 2.8 18.6 + - - +
82C PHE* 3.0 12.8 + + - +
84C GLU* 1.3 73.1 - - - +
86C THR* 1.3 62.1 + - + +
88C VAL* 2.9 15.0 + - + +
89C TRP* 2.8 40.0 + + + +
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Residues in contact with THR 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 4.2 21.7 - - + +
82C PHE* 3.3 44.0 - - + +
83C SER* 2.8 19.9 + - - +
84C GLU 3.1 0.2 - - - -
85C PHE* 1.3 78.4 - - + +
87C GLY* 1.3 62.5 + - - +
89C TRP* 3.6 9.2 + - - +
90C LYS* 3.3 22.2 + - - +
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Residues in contact with GLY 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C PHE* 3.6 21.9 - - - -
83C SER 3.8 1.6 + - - -
84C GLU* 3.0 10.5 + - - -
86C THR* 1.3 84.1 + - - +
88C VAL* 1.3 54.4 - - - +
90C LYS* 3.4 5.2 + - - +
91C TYR* 3.0 30.3 + - - +
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Residues in contact with VAL 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 4.3 12.8 - - + -
68C ILE* 3.8 23.6 - - + +
69C ILE* 5.4 0.7 - - - -
72C PHE* 3.7 32.5 - - + -
80C VAL* 4.1 16.8 - - + -
84C GLU 3.1 12.8 + - - +
85C PHE* 2.9 25.2 + - + +
87C GLY* 1.3 72.9 - - - +
89C TRP* 1.3 66.9 + - - +
91C TYR* 3.2 1.2 + - - +
92C ILE* 2.9 39.2 + - + +
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Residues in contact with TRP 89 (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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100A PHE* 3.3 58.7 - + + -
27C PHE* 3.5 33.0 - + - -
28C LEU* 3.6 35.5 - - + +
31C VAL* 4.2 17.0 - - + -
85C PHE* 2.8 24.5 + + + +
86C THR* 3.8 6.1 - - - +
88C VAL* 1.3 74.2 - - - +
90C LYS* 1.3 64.5 + - + +
92C ILE* 3.3 1.4 + - - +
93C THR* 2.8 53.5 + - + +
96C GLN* 6.3 0.7 - - - -
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Residues in contact with LYS 90 (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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86C THR 3.3 15.0 + - - +
87C GLY* 4.0 4.5 - - - +
89C TRP* 1.3 87.3 - - + +
91C TYR* 1.3 57.8 + - - +
93C THR* 3.7 3.5 - - - -
94C ASP* 2.7 64.8 + - - +
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Residues in contact with TYR 91 (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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68C ILE* 4.1 30.5 - - + -
71C MET* 3.7 23.7 - - + +
72C PHE* 3.6 28.7 - + + -
87C GLY 3.0 17.7 + - - +
88C VAL 3.7 2.7 - - - +
90C LYS* 1.3 79.3 - - - +
92C ILE* 1.3 63.6 + - - +
94C ASP* 3.6 6.7 + - + +
95C TRP* 3.1 62.4 + + - -
152C ILE* 4.8 1.1 - - + -
156C ILE* 3.3 27.4 - - + +
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Residues in contact with ILE 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PRO* 4.0 22.2 - - + -
100A PHE* 3.7 36.1 - - + -
52C LEU* 3.8 26.2 - - + -
60C PHE* 5.7 1.3 - - + -
68C ILE* 3.9 25.4 - - + -
88C VAL* 2.9 31.4 + - + +
89C TRP 3.8 2.7 - - - +
91C TYR* 1.3 77.3 - - + +
93C THR* 1.3 64.3 + - - +
95C TRP* 3.4 7.5 + - - +
96C GLN* 3.0 19.4 + - - +
148C PHE* 3.6 13.7 - - + -
152C ILE* 5.6 2.7 - - + -
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Residues in contact with THR 93 (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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99A PRO* 5.7 0.5 - - - +
100A PHE* 5.0 3.5 - - - -
89C TRP* 2.8 51.0 + - + +
90C LYS* 3.8 6.3 - - - -
92C ILE* 1.3 75.5 - - - +
94C ASP* 1.3 67.6 + - - +
96C GLN* 2.9 45.0 + - - +
97C ASN* 3.0 19.0 + - - +
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Residues in contact with ASP 94 (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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90C LYS* 2.7 60.3 + - - +
91C TYR* 3.8 7.5 - - + +
93C THR* 1.3 73.7 - - - +
95C TRP* 1.3 64.1 + - + +
97C ASN* 3.0 24.7 + - - +
98C VAL* 3.0 17.6 + - + +
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Residues in contact with TRP 95 (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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91C TYR* 3.1 64.4 + + - +
92C ILE 3.6 9.0 - - - +
93C THR 3.2 0.2 - - - -
94C ASP* 1.3 79.7 - - + +
96C GLN* 1.3 57.4 + - - +
98C VAL* 3.2 12.6 + - + +
99C PHE* 2.9 27.4 + - - +
122C PHE* 4.1 18.6 - + - -
148C PHE* 3.6 12.1 - - + -
151C PHE* 3.6 31.0 - + - -
152C ILE* 3.8 28.6 - - + +
155C CYS* 3.4 31.0 - - + -
156C ILE* 4.7 9.9 - - + -
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Residues in contact with GLN 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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99A PRO* 3.0 31.9 - - + +
89C TRP* 6.3 0.6 - - - -
92C ILE 3.0 8.5 + - - +
93C THR* 2.9 40.9 + - - +
95C TRP* 1.3 77.4 - - - +
97C ASN* 1.3 59.0 + - - +
99C PHE* 3.5 2.6 - - - +
100C ARG* 2.5 76.6 + - + +
148C PHE* 3.4 26.2 - - + -
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Residues in contact with ASN 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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93C THR* 3.0 29.1 + - - +
94C ASP* 3.0 16.0 + - - +
96C GLN* 1.3 76.2 + - - +
98C VAL* 1.3 65.8 + - + +
100C ARG* 3.4 26.3 + - - +
101C THR* 2.9 29.1 + - - -
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Residues in contact with VAL 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 ASP* 3.0 18.6 + - + +
95C TRP* 3.4 16.4 - - + +
97C ASN* 1.3 79.2 - - + +
99C PHE* 1.3 63.6 + - - +
101C THR* 3.3 4.7 - - - -
102C TYR* 3.2 33.6 + - + -
122C PHE* 3.6 36.8 - - + -
151C PHE* 4.0 14.8 - - + -
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Residues in contact with PHE 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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95C TRP 2.9 16.7 + - - +
96C GLN* 3.5 5.8 - - - +
97C ASN 3.3 0.2 - - - -
98C VAL* 1.3 78.9 - - - +
100C ARG* 1.3 62.5 + - + +
102C TYR* 3.1 4.5 + - - +
103C ASP* 2.9 38.1 + - + +
108C GLY* 3.6 34.1 - - - -
109C MET 4.4 0.2 - - - -
110C ILE* 3.6 32.3 - - + +
146C ILE 3.7 9.9 - - - -
147C ALA 3.8 4.3 - - - -
148C PHE* 3.5 49.4 - + + -
151C PHE* 3.7 25.8 - + + -
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Residues in contact with ARG 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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97A SER 5.2 0.8 + - - -
98A GLY* 4.4 15.0 - - - +
99A PRO* 4.6 0.4 - - - +
96C GLN* 2.5 55.8 + - + +
97C ASN* 3.4 27.0 + - - +
99C PHE* 1.3 81.5 - - + +
101C THR* 1.3 65.3 + - - +
103C ASP* 3.1 26.7 + - - +
106C ASN* 4.9 6.1 - - - +
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Residues in contact with THR 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 ASN* 2.9 16.3 + - - +
98C VAL* 3.3 12.5 - - - -
100C ARG* 1.3 80.4 - - - +
102C TYR* 1.3 85.7 + - + +
103C ASP 4.6 1.0 - - - -
104C ARG* 2.8 35.4 + - - +
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Residues in contact with TYR 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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98C VAL* 3.2 36.9 + - + +
99C PHE 3.1 5.5 + - - +
101C THR* 1.3 94.6 - - + +
103C ASP* 1.3 60.3 + - - +
104C ARG* 3.1 24.9 + - - +
110C ILE* 4.5 7.4 - - + -
114C GLU* 3.2 28.2 - - - +
117C GLN* 3.7 17.3 - - + -
118C ALA* 3.4 52.7 - - + -
121C GLY* 3.6 21.1 + - - -
122C PHE* 4.7 6.0 - + - -
151C PHE* 5.5 0.2 - + - -
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Residues in contact with ASP 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C PHE* 2.9 25.5 + - + +
100C ARG* 3.1 18.3 + - - +
102C TYR* 1.3 75.3 - - - +
104C ARG* 1.3 62.5 + - - +
105C ASP* 2.9 5.9 - - - +
106C ASN* 3.2 19.2 + - - +
107C SER* 3.3 6.6 + - - -
108C GLY* 2.7 31.0 + - - -
109C MET 3.0 9.1 - - - +
110C ILE* 4.5 3.1 - - + -
114C GLU* 3.5 4.3 - - - -
202C CA 2.4 31.4 - - - -
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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