Contacts of the helix formed by residues 92 - 103 (chain I) 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 GLN 92 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91I LYS* 1.3 76.9 - - + +
93I GLU* 1.3 52.6 + - - +
95I GLU* 3.2 9.8 - - - +
96I ARG* 2.2 42.6 + - + +
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Residues in contact with GLU 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91I LYS* 3.3 4.9 - - + +
92I GLN* 1.3 75.8 - - - +
94I GLU* 1.3 53.5 + - - +
96I ARG* 3.2 8.0 + - - +
97I SER* 2.5 37.9 + - - -
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Residues in contact with GLU 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91I LYS 3.2 20.1 + - - +
93I GLU* 1.3 75.7 - - - +
95I GLU* 1.3 51.2 + - - +
97I SER* 2.4 28.9 + - - -
98I LYS* 2.1 80.2 + - - +
101I ASP* 4.1 10.2 - - - +
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Residues in contact with GLU 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H LEU* 4.4 13.4 - - + +
91I LYS 2.5 19.8 + - - +
92I GLN* 2.9 13.9 + - - +
94I GLU* 1.3 71.7 - - - +
96I ARG* 1.3 51.8 + - - +
98I LYS* 3.1 20.4 - - + +
99I VAL* 2.6 40.9 + - + +
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Residues in contact with ARG 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I GLN* 2.2 31.9 + - + +
93I GLU* 3.3 8.3 - - - +
95I GLU* 1.3 66.4 - - - +
97I SER* 1.3 50.0 + - - +
99I VAL* 3.0 12.3 + - - +
100I ASP* 2.7 39.8 + - - +
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Residues in contact with SER 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I GLU 2.5 16.0 + - - -
94I GLU* 2.4 48.6 + - - -
96I ARG* 1.3 68.9 - - - +
98I LYS* 1.3 51.8 + - - -
100I ASP* 2.7 13.5 + - - +
101I ASP* 2.2 52.0 + - - -
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Residues in contact with LYS 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H LEU* 4.4 18.1 - - + +
84H LYS* 5.4 7.6 - - + -
91I LYS 5.4 2.2 + - - +
94I GLU* 2.1 67.0 + - - +
95I GLU* 3.1 23.2 - - + +
97I SER* 1.3 65.6 + - - -
99I VAL* 1.3 54.1 + - - +
101I ASP* 3.6 9.0 + - - +
102I LEU* 2.7 39.7 + - - +
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Residues in contact with VAL 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H LEU* 4.5 15.3 - - + -
95I GLU 2.6 23.9 + - - +
96I ARG* 3.0 13.7 + - - +
98I LYS* 1.3 73.1 - - - +
100I ASP* 1.3 62.8 + - - +
102I LEU* 3.8 16.5 - - + +
103I ARG* 3.2 27.9 - - - +
136I LEU* 5.1 0.2 - - - +
138I PHE* 5.7 12.1 - - + -
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Residues in contact with ASP 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I ARG* 2.7 19.2 + - - +
97I SER* 2.7 19.2 + - - +
99I VAL* 1.3 74.9 - - - +
101I ASP* 1.3 68.1 + - - +
103I ARG* 3.2 28.2 + - - +
104I GLY* 5.3 0.9 - - - -
105I THR* 5.5 2.6 + - - -
82J LYS* 5.2 11.7 + - - +
84J LYS* 5.6 5.8 + - - -
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Residues in contact with ASP 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94I GLU* 4.1 11.4 - - - +
97I SER* 2.2 49.8 + - - +
98I LYS* 3.6 10.1 + - - +
100I ASP* 1.3 69.0 - - - +
102I LEU* 1.3 65.4 + - - +
103I ARG 2.9 10.2 - - - +
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Residues in contact with LEU 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H LEU* 6.1 0.9 - - + -
83H ASP* 5.4 2.2 - - + -
84H LYS* 4.2 22.2 - - + +
87H LEU* 3.6 22.7 - - + -
88H GLN* 4.2 13.2 - - + +
91H GLN* 2.8 49.8 + - - +
98I LYS 2.7 21.3 + - - +
99I VAL* 3.8 15.9 - - + +
101I ASP* 1.3 74.1 - - - +
103I ARG* 1.3 63.9 + - - +
136I LEU* 3.7 35.8 - - + +
137I SER 5.5 0.2 - - - +
153I ASN* 4.7 3.3 + - - -
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Residues in contact with ARG 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99I VAL* 3.2 30.3 - - - +
100I ASP* 3.2 19.8 + - - +
101I ASP 2.9 10.7 + - - +
102I LEU* 1.3 90.1 - - - +
104I GLY* 1.3 62.3 + - - +
107I MET* 3.0 25.9 - - - +
136I LEU* 3.6 9.4 - - + -
151I LEU* 3.0 24.8 - - - +
153I ASN* 3.8 8.0 + - - +
160I ILE* 2.5 55.0 + - + +
161I GLY* 5.4 0.8 - - - -
82J LYS* 6.0 5.5 - - - +
84J LYS* 5.9 5.9 - - - +
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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