Contacts of the helix formed by residues 94 - 108 (chain A) in PDB entry 6TT8
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 THR 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A LEU* 4.6 16.8 - - + -
92A ALA* 4.0 0.2 - - - +
93A TRP* 1.3 81.3 - - - +
95A ASP* 1.3 65.5 + - - +
96A ASP* 4.1 8.7 + - - +
97A GLN* 3.2 29.7 + - - +
98A THR* 2.8 26.7 + - - -
127A GLY 3.3 8.3 - - - -
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Residues in contact with ASP 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A THR* 1.3 72.2 - - - +
96A ASP* 1.3 59.5 + - - +
98A THR 3.3 0.5 + - - -
99A ALA* 2.9 26.6 + - - +
127A GLY 3.1 12.4 + - - +
128A GLY* 3.2 12.8 - - - -
129A MET 3.4 0.3 + - - -
130A ASP* 3.0 22.6 + - - +
131A ALA* 2.9 41.1 + - + +
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Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A THR* 3.2 8.6 - - - +
95A ASP* 1.3 79.0 - - - +
97A GLN* 1.3 64.0 + - + +
99A ALA* 3.0 18.5 + - - +
100A GLN* 2.9 43.9 + - - +
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Residues in contact with GLN 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ASP* 4.6 15.3 + - + +
49A LEU* 3.6 19.5 - - + +
63A SER* 3.3 22.3 - - - -
64A TYR 2.8 28.9 + - - +
65A LEU* 4.9 3.9 - - - +
92A ALA* 3.6 13.9 - - + -
93A TRP* 3.4 21.7 + - - +
94A THR* 3.2 18.7 + - - +
95A ASP 3.4 0.2 - - - -
96A ASP* 1.3 77.4 - - + +
98A THR* 1.3 61.9 + - - +
100A GLN* 3.1 21.6 + - - +
101A ILE* 3.2 15.1 + - - +
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Residues in contact with THR 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A THR* 4.0 12.3 - - + -
92A ALA* 3.0 19.6 + - - +
94A THR 2.8 22.1 + - - -
95A ASP 3.5 5.4 - - - -
97A GLN* 1.3 76.7 - - - +
99A ALA* 1.3 62.8 + - - +
101A ILE* 3.1 24.3 + - + +
102A LEU* 3.2 14.1 + - + +
128A GLY* 3.2 30.0 - - - +
131A ALA* 4.2 3.8 - - + -
132A LEU* 3.9 21.1 - - + -
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ASP 2.9 14.1 + - - +
96A ASP* 3.0 14.3 + - - +
98A THR* 1.3 76.1 - - - +
100A GLN* 1.3 57.5 + - + +
102A LEU* 3.2 17.2 + - + +
103A ASN* 3.0 27.1 + - - +
131A ALA* 4.4 6.7 - - + +
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Residues in contact with GLN 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 3.4 26.7 - - + +
47A GLY* 4.4 2.9 - - - -
48A ASP* 3.7 28.1 + - - +
49A LEU* 3.4 24.8 - - + +
51A PHE* 4.9 0.7 - - - -
96A ASP* 2.9 33.7 + - - +
97A GLN* 3.3 14.3 - - - +
99A ALA* 1.3 76.2 - - + +
101A ILE* 1.3 59.2 + - - +
103A ASN* 3.1 10.6 + - - +
104A TRP* 2.9 24.7 + - - +
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Residues in contact with ILE 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 3.6 13.5 - - + -
51A PHE* 3.9 14.8 - - + -
61A HIS* 3.6 36.8 - - + +
79A ILE* 3.8 28.7 - - + -
88A VAL* 5.1 8.1 - - + -
90A ASP 5.5 0.4 - - - +
91A THR* 4.8 1.6 - - - -
92A ALA* 4.0 13.0 - - + +
97A GLN 3.3 11.2 - - - +
98A THR* 3.1 26.2 + - + +
100A GLN* 1.3 76.9 - - - +
102A LEU* 1.3 59.2 + - + +
104A TRP* 3.1 2.9 + - - +
105A ILE* 2.9 40.1 + - + +
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A VAL* 5.1 5.2 - - + -
98A THR* 3.2 16.8 + - + +
99A ALA* 3.2 15.4 + - + +
101A ILE* 1.3 77.9 - - + +
103A ASN* 1.3 61.2 + - - +
105A ILE* 3.5 12.9 + - + +
106A LYS* 3.1 23.6 + - - +
113A VAL* 4.2 14.4 - - + -
131A ALA* 4.3 8.1 - - + +
132A LEU* 4.1 21.3 - - + -
135A ALA* 3.9 27.4 - - + -
137A ILE* 3.7 21.1 - - + -
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Residues in contact with ASN 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 4.3 14.2 - - + -
99A ALA 3.0 14.0 + - - +
100A GLN* 3.3 13.3 - - - +
102A LEU* 1.3 75.2 - - - +
104A TRP* 1.3 59.1 + - - +
106A LYS* 3.3 9.2 + - - +
107A GLN* 2.8 32.3 + - - +
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Residues in contact with TRP 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLN* 3.2 23.5 + - - +
46A PHE* 3.8 36.5 - + + -
51A PHE* 3.7 45.2 - + + -
59A TRP* 3.5 42.6 - + + -
79A ILE* 4.1 19.7 - - + -
100A GLN 2.9 12.2 + - - +
101A ILE 3.4 7.2 - - - +
103A ASN* 1.3 74.9 - - - +
105A ILE* 1.3 63.4 + - + +
107A GLN* 3.4 6.4 - - - +
108A GLU* 2.8 60.0 + - + +
109A ILE* 4.2 17.5 - - + -
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ILE* 4.0 17.0 - - + -
86A VAL* 3.7 24.2 - - + -
88A VAL* 3.9 29.4 - - + -
101A ILE* 2.9 29.7 + - + +
102A LEU* 3.6 12.8 - - + +
104A TRP* 1.3 86.2 - - + +
106A LYS* 1.3 51.7 + - - +
109A ILE* 2.9 16.6 + - + +
110A ASN 2.7 29.1 + - - -
111A LEU 3.5 21.1 - - - +
113A VAL* 3.9 14.4 - - + -
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Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LEU 3.1 17.1 + - - +
103A ASN* 3.6 10.8 - - - +
105A ILE* 1.3 77.6 - - - +
107A GLN* 1.3 65.0 + - - +
110A ASN* 2.7 56.9 + - - +
111A LEU 4.8 5.2 - - - +
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Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLN* 5.2 4.6 - - - +
46A PHE* 3.2 36.5 - - + -
103A ASN* 2.8 19.2 + - - +
104A TRP* 3.0 7.2 + - - +
106A LYS* 1.3 80.9 - - - +
108A GLU* 1.3 90.7 + - - +
110A ASN* 4.8 2.6 + - - +
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Residues in contact with GLU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLN* 4.9 10.1 + - - -
104A TRP* 2.8 54.7 + - + +
107A GLN* 1.3 102.8 + - - +
109A ILE* 1.3 70.4 + - + +
110A ASN* 3.4 2.3 - - - +
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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