Contacts of the helix formed by residues 98 - 112 (chain Y) in PDB entry 1T6B
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 ASP 98 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96Y THR* 3.3 5.5 + - - +
97Y GLY* 1.3 74.2 - - - +
99Y ARG* 1.3 62.5 + - - +
100Y GLY* 3.1 25.5 + - - -
101Y LYS* 3.3 37.5 + - + +
102Y ILE* 3.1 25.3 + - - +
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Residues in contact with ARG 99 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70Y ALA* 2.9 25.1 + - - +
71Y GLU* 5.0 1.2 - - - +
73Y PHE 3.2 24.5 + - - -
74Y VAL* 3.6 35.8 - - + +
75Y SER 5.1 2.3 + - - -
76Y PRO* 6.4 0.9 - - - -
78Y MET 5.6 2.6 + - - -
80Y LEU* 4.8 5.3 - - - +
97Y GLY 3.4 12.9 + - - +
98Y ASP* 1.3 71.2 + - - +
100Y GLY* 1.3 65.1 + - - +
102Y ILE* 3.4 37.9 + - - +
103Y SER* 3.1 24.6 + - - -
106Y LEU* 5.9 0.6 - - - +
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Residues in contact with GLY 100 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98Y ASP* 3.1 8.9 + - - -
99Y ARG* 1.3 75.8 - - - +
101Y LYS* 1.3 64.0 + - - +
103Y SER* 3.6 6.5 - - - -
104Y LYS* 3.0 22.9 + - - +
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Residues in contact with LYS 101 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93Y LEU* 3.6 15.5 - - + +
96Y THR* 3.4 34.1 + - + +
98Y ASP* 3.3 27.6 + - + +
99Y ARG 3.4 0.2 - - - -
100Y GLY* 1.3 74.6 - - - +
102Y ILE* 1.3 52.5 + - - +
104Y LYS* 3.2 8.5 + - - +
105Y GLY 2.8 28.9 + - - -
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Residues in contact with ILE 102 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70Y ALA* 4.3 2.7 - - + -
78Y MET 5.6 0.4 - - - +
80Y LEU* 3.7 29.2 - - + -
82Y PHE* 3.8 4.5 - - + -
93Y LEU* 3.9 17.7 - - + -
96Y THR* 3.7 21.5 - - + +
97Y GLY* 4.1 5.6 - - - -
98Y ASP 3.1 25.5 + - - +
99Y ARG* 3.7 45.8 - - - +
100Y GLY 3.3 0.4 - - - -
101Y LYS* 1.3 74.9 - - - +
103Y SER* 1.3 56.2 + - - +
105Y GLY* 2.8 6.9 + - - -
106Y LEU* 2.7 49.1 + - + +
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Residues in contact with SER 103 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99Y ARG 3.1 14.6 + - - -
100Y GLY* 3.6 7.9 - - - -
102Y ILE* 1.3 81.1 - - - +
104Y LYS* 1.3 61.1 + - - -
106Y LEU* 3.0 21.7 + - - +
107Y GLU* 3.1 24.6 + - - +
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Residues in contact with LYS 104 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100Y GLY 3.0 14.8 + - - +
101Y LYS* 3.4 11.7 - - - +
102Y ILE 3.2 0.2 - - - -
103Y SER* 1.3 71.6 - - - +
105Y GLY* 1.3 61.1 + - - +
107Y GLU* 3.4 17.3 + - - +
108Y ASP* 3.0 48.1 + - - +
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Residues in contact with GLY 105 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82Y PHE* 3.7 18.4 - - - -
92Y ILE* 3.9 1.9 - - - +
93Y LEU* 4.4 11.2 - - - +
101Y LYS 2.8 12.0 + - - -
102Y ILE 2.8 13.1 + - - -
104Y LYS* 1.3 72.0 - - - +
106Y LEU* 1.3 54.8 - - - -
108Y ASP* 3.2 13.1 - - - +
109Y LEU* 2.9 30.8 + - - +
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Residues in contact with LEU 106 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63Y TYR* 3.4 35.5 - - + +
66Y VAL* 3.9 17.5 - - + -
67Y GLN* 4.1 23.3 - - + +
70Y ALA* 4.0 19.7 - - + -
71Y GLU* 6.1 1.8 - - + -
82Y PHE* 3.6 24.9 - - + -
99Y ARG* 5.9 0.4 - - - +
102Y ILE* 2.7 25.7 + - + +
103Y SER* 3.0 12.5 + - - +
105Y GLY* 1.3 70.8 - - - +
107Y GLU* 1.3 63.8 + - - +
109Y LEU* 3.1 5.0 + - + +
110Y LYS* 2.9 26.3 + - - +
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Residues in contact with GLU 107 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63Y TYR* 4.7 5.5 + - - -
103Y SER* 3.1 26.6 + - - +
104Y LYS* 3.7 17.0 - - - +
106Y LEU* 1.3 78.9 - - - +
108Y ASP* 1.3 63.4 + - - +
110Y LYS* 3.2 21.9 + - - +
111Y ARG* 3.4 15.0 + - - +
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Residues in contact with ASP 108 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92Y ILE* 3.6 33.3 - - + +
104Y LYS* 3.0 41.3 + - - +
105Y GLY* 3.2 13.1 - - - +
106Y LEU 3.1 0.2 - - - -
107Y GLU* 1.3 74.6 - - - +
109Y LEU* 1.3 65.3 + - - +
111Y ARG* 3.0 19.1 + - - +
112Y VAL* 3.6 10.7 + - - +
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Residues in contact with LEU 109 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Y LEU* 3.9 19.1 - - + -
59Y TRP* 2.9 34.0 + - + -
63Y TYR* 3.9 12.1 - - + -
66Y VAL* 3.8 26.9 - - + -
82Y PHE* 3.7 35.7 - - + -
84Y VAL* 3.7 29.2 - - + -
92Y ILE* 4.5 7.4 - - + -
105Y GLY 2.9 14.4 + - - +
106Y LEU* 3.1 13.2 + - + +
108Y ASP* 1.3 74.4 - - - +
110Y LYS* 1.3 61.8 + - - +
111Y ARG 3.1 1.4 + - - -
112Y VAL* 3.1 11.8 + - + +
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Residues in contact with LYS 110 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Y TRP* 4.7 5.7 + - - +
60Y ILE* 5.6 10.1 - - - -
63Y TYR* 3.7 45.0 - - + +
106Y LEU 2.9 10.0 + - - +
107Y GLU* 3.4 17.5 - - - +
108Y ASP 3.1 0.4 - - - -
109Y LEU* 1.3 78.5 - - - +
111Y ARG* 1.3 59.0 + - + +
112Y VAL 3.7 4.2 + - - +
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Residues in contact with ARG 111 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648X ASP* 5.6 8.4 + - - +
649X THR* 5.2 6.9 + - - -
650X GLU* 4.7 14.3 + - - -
694X TYR* 4.6 21.0 + - - +
107Y GLU 3.5 15.7 + - - +
108Y ASP* 3.0 12.6 + - - +
110Y LYS* 1.3 78.6 - - + +
112Y VAL* 1.3 65.3 + - - +
113Y SER* 3.3 4.9 + - - -
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Residues in contact with VAL 112 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Y LYS* 3.9 35.9 - - + +
59Y TRP* 3.6 40.9 - - + +
84Y VAL* 4.5 13.0 - - + -
92Y ILE* 5.1 9.2 - - + -
108Y ASP 3.6 10.2 + - - +
109Y LEU* 3.1 23.0 + - + +
110Y LYS 4.4 1.9 - - - +
111Y ARG* 1.3 76.0 - - - +
113Y SER* 1.3 64.6 + - - +
114Y PRO* 3.6 7.2 - - - +
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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