Contacts of the helix formed by residues 83 - 97 (chain q) 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 q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102i GLU* 4.1 22.9 - - - +
49q LEU* 4.4 0.7 - - - -
74q TYR* 4.8 1.1 + - - +
80q ARG* 4.2 20.6 - - - +
81q GLN 4.6 4.5 - - - +
82q ILE* 1.3 80.8 - - - +
84q PRO* 1.3 68.3 - - + +
85q TYR* 4.6 5.6 - - + +
86q THR* 3.1 21.7 + - - +
87q LEU* 2.9 23.7 + - - +
113q ASP* 4.0 23.5 + - - +
114q PRO* 4.2 12.6 - - + -
115q LYS* 5.2 11.2 - - + +
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Residues in contact with PRO 84 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49q LEU* 3.9 26.2 - - + -
82q ILE 4.0 2.5 - - - +
83q LYS* 1.3 82.2 - - + +
85q TYR* 1.3 66.2 + - - +
87q LEU* 3.1 9.9 + - + +
88q MET* 2.9 22.3 + - - +
109q ILE* 4.7 0.8 - - + +
111q GLY 4.4 6.3 - - - -
112q LEU 4.2 16.2 - - - +
113q ASP* 4.2 8.3 - - + -
114q PRO* 3.7 17.5 - - + -
120q PHE* 3.5 36.4 - - + -
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Residues in contact with TYR 85 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100i TYR 5.4 0.4 - - - -
83q LYS* 3.4 4.7 - - + +
84q PRO* 1.3 78.8 - - - +
86q THR* 1.3 59.2 + - - +
88q MET* 3.1 30.2 + - + +
89q SER* 2.9 34.8 + - - +
120q PHE* 3.3 33.0 - + - -
132q VAL* 4.0 22.2 - - + +
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Residues in contact with THR 86 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100i TYR* 3.5 36.4 - - + -
102i GLU* 3.1 33.2 + - - +
74q TYR* 3.9 8.3 - - + +
82q ILE* 3.7 18.8 - - + -
83q LYS* 3.1 24.8 + - - +
84q PRO 3.1 0.4 - - - -
85q TYR* 1.3 75.5 - - - +
87q LEU* 1.3 59.7 + - - +
89q SER* 3.3 2.6 + - - -
90q MET* 2.9 29.8 + - - +
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Residues in contact with LEU 87 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45q MET* 4.1 19.5 - - + -
49q LEU* 3.7 35.4 - - + -
51q ILE* 5.1 3.4 - - + -
67q LEU* 4.0 29.2 - - + -
71q LEU* 4.0 23.8 - - + -
82q ILE* 3.6 7.5 - - + +
83q LYS 2.9 12.4 + - - +
84q PRO* 3.4 10.1 - - + +
86q THR* 1.3 71.7 - - - +
88q MET* 1.3 67.4 + - - +
90q MET* 3.2 6.1 + - - +
91q VAL* 2.9 25.6 + - + +
109q ILE* 3.8 19.1 - - + -
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Residues in contact with MET 88 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84q PRO 2.9 12.0 + - - +
85q TYR* 3.4 38.1 - - + +
87q LEU* 1.3 80.0 - - - +
89q SER* 1.3 64.7 + - - +
91q VAL* 3.4 3.3 + - - +
92q ALA* 2.9 27.0 + - - +
109q ILE* 3.6 9.6 - - + +
120q PHE* 4.1 2.9 - - + -
122q CYS* 3.5 41.5 - - - -
124q LEU* 3.8 8.3 - - + +
130q PRO* 3.5 35.2 - - + -
131q MET 4.3 0.2 - - - -
132q VAL* 3.9 12.1 - - + -
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Residues in contact with SER 89 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98i LEU 5.6 0.3 - - - +
99i VAL 3.5 12.0 - - - +
100i TYR 3.8 11.6 + - - -
101i GLN* 3.5 36.4 + - - +
85q TYR* 2.9 18.1 + - - -
86q THR 3.7 4.3 - - - -
87q LEU 3.3 0.2 - - - -
88q MET* 1.3 87.0 - - - +
90q MET* 1.3 57.7 + - - +
92q ALA* 3.3 7.6 + - - +
93q ASN* 3.0 24.3 + - - +
130q PRO* 6.4 0.2 - - - -
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Residues in contact with MET 90 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99i VAL* 3.9 11.8 + - + +
100i TYR* 3.0 44.2 - - + +
67q LEU* 4.2 13.7 - - + -
70q ARG* 4.4 30.8 + - + +
71q LEU* 4.1 8.7 - - - -
74q TYR* 4.2 14.1 - - + -
82q ILE* 3.6 27.4 - - + -
86q THR 2.9 13.3 + - - +
87q LEU* 3.4 15.9 - - - +
89q SER* 1.3 74.9 - - - +
91q VAL* 1.3 64.9 + - - +
93q ASN* 3.3 6.2 + - - +
94q LEU* 3.0 22.3 + - + +
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Residues in contact with VAL 91 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51q ILE* 4.0 10.8 - - + -
63q VAL* 5.3 3.1 - - + -
67q LEU* 3.6 34.8 - - + -
87q LEU* 2.9 22.7 + - + +
88q MET 3.7 4.3 - - - +
90q MET* 1.3 71.7 - - - +
92q ALA* 1.3 66.7 + - - +
94q LEU* 3.2 12.5 + - + +
95q LEU* 2.9 44.0 + - + +
107q PRO* 4.0 18.6 - - + -
109q ILE* 4.4 6.5 - - + -
124q LEU* 4.1 8.5 - - + -
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Residues in contact with ALA 92 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54p MET* 4.2 10.5 - - + +
88q MET 2.9 14.6 + - - +
89q SER* 3.4 12.6 - - - +
90q MET 3.3 0.2 - - - -
91q VAL* 1.3 77.9 - - - +
93q ASN* 1.3 63.3 + - - +
95q LEU* 3.3 2.3 + - - +
96q TYR* 3.0 25.3 + - - +
124q LEU* 3.6 14.5 - - + +
128q GLY* 3.4 25.1 - - - +
130q PRO* 4.9 8.1 - - + -
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Residues in contact with ASN 93 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98i LEU* 4.8 5.0 - - - +
99i VAL* 4.0 35.5 - - + +
54p MET* 4.5 13.6 - - + +
70q ARG* 3.2 25.5 - - - +
89q SER 3.0 13.9 + - - +
90q MET* 3.5 10.1 - - - +
92q ALA* 1.3 77.4 - - - +
94q LEU* 1.3 61.9 + - - +
96q TYR* 3.2 2.8 + - - +
97q GLU* 3.0 41.3 + - - +
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Residues in contact with LEU 94 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63q VAL* 4.0 34.3 - - + +
66q ARG* 4.0 35.2 - - + +
67q LEU* 4.1 12.3 - - + +
70q ARG* 3.8 37.9 - - - +
90q MET 3.0 9.7 + - - +
91q VAL* 3.2 14.3 + - + +
93q ASN* 1.3 81.4 - - - +
95q LEU* 1.3 73.1 + - + +
97q GLU* 3.7 16.1 + - - +
98q LYS 4.5 0.2 + - - -
103q TYR* 4.4 15.4 - - + -
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Residues in contact with LEU 95 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63q VAL* 4.1 9.4 - - + -
91q VAL* 2.9 35.4 + - + +
94q LEU* 1.3 88.5 - - + +
96q TYR* 1.3 66.0 + - - +
98q LYS* 3.1 22.5 + - - +
102q PRO* 5.2 0.9 - - - +
103q TYR* 4.3 12.5 + - + -
105q THR* 4.0 21.8 - - + +
107q PRO* 4.0 15.7 - - + -
124q LEU* 4.4 0.9 - - + -
125q ASP 3.6 23.1 - - - +
126q LEU 3.7 18.4 - - - +
127q ILE* 4.1 7.1 - - - +
128q GLY* 3.7 16.4 - - - +
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Residues in contact with TYR 96 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50p ALA* 4.2 8.3 - - + -
51p ASP* 3.3 34.1 + - - -
54p MET* 3.8 45.9 - - + +
55p THR* 5.4 1.0 + - - -
86p MET* 5.6 4.6 - - + +
94p ILE* 4.2 17.8 - - - +
92q ALA 3.0 15.8 + - - +
93q ASN 3.9 2.5 - - - +
95q LEU* 1.3 72.8 - - - +
97q GLU* 1.3 65.5 + - - +
98q LYS 3.0 2.2 - - - -
99q ARG* 3.1 42.0 + - + +
127q ILE* 3.3 23.1 + - + +
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Residues in contact with GLU 97 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70q ARG* 2.7 36.0 + - - -
93q ASN* 3.0 36.3 + - - +
94q LEU 3.7 11.5 - - - +
95q LEU 3.1 0.8 - - - -
96q TYR* 1.3 77.7 - - - +
98q LYS* 1.3 66.1 + - + +
99q ARG* 3.3 2.8 + - - +
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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