Contacts of the helix formed by residues 83 - 97 (chain c) 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 LYS 83 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C GLU* 4.3 18.4 - - - +
49c LEU* 4.3 0.9 - - - -
74c TYR* 5.4 1.5 + - - +
80c ARG* 4.5 17.9 - - - +
81c GLN 5.0 2.7 - - - +
82c ILE* 1.3 79.2 - - - +
84c PRO* 1.3 74.6 - - + +
85c TYR* 3.4 9.4 - - + +
86c THR* 3.1 23.0 + - - +
87c LEU* 3.0 18.0 + - - +
113c ASP* 4.0 20.5 + - - +
114c PRO* 4.2 14.1 - - + -
115c LYS* 6.0 1.4 - - - +
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Residues in contact with PRO 84 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49c LEU* 4.0 32.1 - - + -
82c ILE 4.1 1.6 - - - +
83c LYS* 1.3 87.8 - - + +
85c TYR* 1.3 63.4 + - + +
87c LEU* 3.0 4.1 + - + +
88c MET* 2.9 22.5 + - - +
109c ILE* 5.1 1.2 - - - +
111c GLY 4.3 7.0 - - - +
112c LEU 4.1 17.7 - - - +
113c ASP* 4.2 7.4 - - + +
114c PRO* 3.9 15.0 - - + -
120c PHE* 3.5 35.0 - - + -
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Residues in contact with TYR 85 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83c LYS* 3.4 8.4 - - + +
84c PRO* 1.3 79.4 - - + +
86c THR* 1.3 61.5 + - - +
88c MET* 3.1 30.6 + - + +
89c SER* 3.0 33.0 + - - -
120c PHE* 3.4 34.2 - + - -
132c VAL* 4.5 16.4 - - + +
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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
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100C TYR* 3.8 30.9 - - + -
102C GLU* 2.8 37.2 + - - +
74c TYR* 3.9 8.5 + - + +
82c ILE* 3.6 22.2 - - + -
83c LYS* 3.1 24.7 + - - +
84c PRO 3.1 0.4 - - - -
85c TYR* 1.3 77.2 - - - +
87c LEU* 1.3 58.9 + - - +
89c SER* 3.3 2.4 + - - -
90c MET* 2.9 28.1 + - - +
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Residues in contact with LEU 87 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45c MET* 3.9 26.0 - - + -
49c LEU* 3.9 30.1 - - + -
51c ILE* 5.1 2.5 - - + -
67c LEU* 4.1 29.2 - - + -
71c LEU* 4.3 22.4 - - + -
82c ILE* 3.7 8.9 - - + +
83c LYS 3.0 12.8 + - - +
84c PRO* 3.4 10.8 - - + +
86c THR* 1.3 76.2 - - - +
88c MET* 1.3 57.8 + - - +
90c MET* 3.2 7.5 + - - +
91c VAL* 2.9 29.6 + - + +
109c ILE* 4.0 19.7 - - + -
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Residues in contact with MET 88 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84c PRO 2.9 12.2 + - - +
85c TYR* 3.3 39.9 - - + +
87c LEU* 1.3 80.1 - - - +
89c SER* 1.3 65.8 + - - +
91c VAL* 3.4 2.9 + - - +
92c ALA* 3.0 26.9 + - - +
109c ILE* 3.7 11.1 - - + +
120c PHE* 4.0 2.5 - - + -
122c CYS* 3.5 40.8 - - - -
124c LEU* 3.8 7.7 - - + +
130c PRO* 3.7 33.4 - - + -
132c VAL* 3.8 13.0 - - + -
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Residues in contact with SER 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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99C VAL 3.7 11.6 - - - +
100C TYR 3.8 19.6 + - - -
101C GLN* 3.7 22.4 - - - +
85c TYR* 3.0 17.3 + - - -
86c THR 3.8 1.8 - - - -
87c LEU 3.3 0.2 - - - -
88c MET* 1.3 86.8 - - - +
90c MET* 1.3 61.1 + - - +
92c ALA* 3.3 8.4 + - - +
93c ASN* 3.0 23.9 + - - +
130c PRO* 6.3 0.4 - - - -
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Residues in contact with MET 90 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C VAL* 4.1 10.2 + - + -
100C TYR* 3.2 37.2 - - + +
67c LEU* 4.1 20.9 - - + -
70c ARG* 4.1 31.5 + - + +
71c LEU* 4.2 10.8 - - - -
74c TYR* 4.3 17.3 - - + -
82c ILE* 3.7 20.2 - - + -
86c THR 2.9 17.1 + - - +
87c LEU* 3.4 14.4 - - - +
89c SER* 1.3 73.4 - - - +
91c VAL* 1.3 65.4 + - - +
93c ASN* 3.3 6.2 + - - +
94c LEU* 3.0 21.7 + - - +
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Residues in contact with VAL 91 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51c ILE* 4.0 11.0 - - + -
63c VAL* 5.3 7.6 - - + -
67c LEU* 3.6 37.5 - - + -
87c LEU* 2.9 19.1 + - + +
88c MET 3.7 6.7 - - - +
90c MET* 1.3 72.7 - - - +
92c ALA* 1.3 66.7 + - - +
94c LEU* 3.1 6.0 + - + +
95c LEU* 2.9 32.6 + - + +
107c PRO* 3.8 30.3 - - + -
109c ILE* 4.1 8.3 - - + -
124c LEU* 4.2 8.1 - - + -
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Residues in contact with ALA 92 (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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54b MET* 4.9 9.6 - - + -
88c MET 3.0 14.6 + - - +
89c SER* 3.5 12.8 - - - +
90c MET 3.3 0.2 - - - -
91c VAL* 1.3 75.6 - - - +
93c ASN* 1.3 62.5 + - - +
95c LEU* 3.3 2.3 + - - +
96c TYR* 3.0 26.8 + - - +
124c LEU* 3.6 15.7 - - + +
127c ILE 4.2 2.1 - - - +
128c GLY* 3.6 23.0 - - - +
130c PRO* 5.2 7.4 - - + -
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Residues in contact with ASN 93 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LEU 4.8 2.9 - - - +
99C VAL* 4.0 41.3 - - + +
54b MET* 4.6 16.6 - - + +
70c ARG* 3.2 17.0 - - - +
89c SER 3.0 13.0 + - - +
90c MET* 3.5 8.5 - - - +
91c VAL 3.2 0.2 - - - -
92c ALA* 1.3 77.1 - - - +
94c LEU* 1.3 63.0 + - - +
96c TYR* 3.3 2.8 + - - +
97c GLU* 3.1 50.5 + - - +
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Residues in contact with LEU 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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63c VAL* 4.1 40.2 - - + +
66c ARG* 3.9 36.1 - - + +
67c LEU* 4.2 10.8 - - + +
70c ARG* 3.8 40.6 - - - +
90c MET 3.0 11.3 + - - +
91c VAL* 3.1 10.7 + - + +
93c ASN* 1.3 82.7 - - - +
95c LEU* 1.3 65.3 + - + +
97c GLU* 3.6 16.9 + - - +
98c LYS* 4.4 0.3 + - - +
103c TYR* 4.2 16.5 - - + -
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Residues in contact with LEU 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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63c VAL* 4.1 9.6 - - + -
91c VAL* 2.9 36.0 + - + +
92c ALA 3.7 3.4 - - - +
94c LEU* 1.3 76.2 - - + +
96c TYR* 1.3 62.4 + - - +
98c LYS* 3.1 27.0 + - - +
99c ARG* 3.9 0.9 + - - -
102c PRO* 5.3 1.4 - - - +
103c TYR* 4.0 23.3 - - + -
105c THR* 4.1 20.9 - - + +
107c PRO* 3.9 14.8 - - + -
124c LEU* 4.4 1.8 - - + -
125c ASP 3.6 22.9 - - - +
126c LEU 3.7 20.6 - - - +
127c ILE* 4.4 2.3 - - - +
128c GLY* 3.9 15.5 - - - +
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Residues in contact with TYR 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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50b ALA* 4.4 7.2 - - + -
51b ASP* 2.9 37.5 + - - +
54b MET* 3.8 49.0 - - + +
55b THR* 5.4 0.3 + - - -
94b ILE* 4.5 14.1 - - + +
92c ALA 3.0 17.6 + - - +
93c ASN 3.9 2.9 - - - +
95c LEU* 1.3 72.0 - - - +
97c GLU* 1.3 65.5 + - - +
98c LYS 3.0 2.2 - - - -
99c ARG* 3.1 42.9 + - + +
127c ILE* 3.2 23.3 - - + +
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Residues in contact with GLU 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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70c ARG* 2.7 35.7 + - - -
93c ASN* 3.1 35.6 + - - +
94c LEU* 3.6 12.5 - - - +
95c LEU 3.1 0.6 - - - -
96c TYR* 1.3 76.6 - - - +
98c LYS* 1.3 68.2 + - + +
99c ARG 3.4 1.7 + - - -
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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