Contacts of the helix formed by residues 92 - 106 (chain A) in PDB entry 5TJB
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 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A VAL* 1.3 78.5 - - - +
93A PHE* 1.3 59.1 + - - +
94A ARG* 3.6 14.9 + - - +
95A GLU* 2.7 42.5 + - - +
96A GLU* 2.9 26.2 + - - +
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Residues in contact with PHE 93 (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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92A THR* 1.3 72.6 - - - +
94A ARG* 1.3 60.2 + - - +
96A GLU* 3.2 10.0 + - + +
97A ASN* 2.7 59.6 + - - -
239A THR* 4.8 2.9 - - + -
240A ILE 4.2 7.2 - - - -
241A ASN* 3.7 44.4 - - + +
243A GLN* 3.8 22.2 - - - +
254A TYR* 3.7 48.5 - + + +
256A PHE* 4.0 7.0 - + - -
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Residues in contact with ARG 94 (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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92A THR* 3.2 12.9 + - - +
93A PHE* 1.3 81.6 - - - +
95A GLU* 1.3 89.5 + - - +
97A ASN* 3.2 4.5 + - - +
98A THR* 2.8 33.7 + - - +
254A TYR* 5.0 4.3 - - + -
256A PHE* 3.5 33.5 - - + -
276A GLU* 5.8 2.6 + - - -
277A THR* 3.1 38.7 + - - +
278A GLN* 4.2 1.1 - - - +
279A ALA* 3.7 27.4 - - + +
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 3.3 25.9 - - + +
92A THR* 2.7 46.6 + - - +
94A ARG* 1.3 102.3 + - - +
96A GLU* 1.3 65.4 + - - +
98A THR* 3.1 9.9 + - - -
99A ILE* 3.0 28.4 + - + +
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Residues in contact with GLU 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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91A VAL* 3.9 18.2 - - + +
92A THR 2.9 11.4 + - - +
93A PHE* 3.2 13.9 + - + +
95A GLU* 1.3 76.2 - - - +
97A ASN* 1.3 66.1 + - - +
99A ILE* 3.3 30.0 + - - +
100A ALA* 3.4 10.9 + - - +
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Residues in contact with ASN 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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93A PHE* 2.7 62.9 + - - -
94A ARG 3.4 8.1 - - - +
96A GLU* 1.3 79.8 - - - +
98A THR* 1.3 56.4 + - - +
100A ALA* 3.0 10.5 + - - +
101A PHE* 2.9 35.5 + - + -
147A TYR* 2.6 35.2 + - - +
239A THR* 4.8 0.7 - - - +
256A PHE* 3.6 22.0 - - + -
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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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94A ARG* 2.8 24.0 + - - +
95A GLU* 3.1 13.3 + - - -
97A ASN* 1.3 73.6 - - - +
99A ILE* 1.3 63.9 + - - +
101A PHE* 3.1 12.2 + - - +
102A ARG* 3.0 53.2 + - - +
256A PHE* 5.7 0.2 - - - -
275A LEU* 4.0 17.7 - - + +
277A THR* 2.6 32.5 + - + +
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Residues in contact with ILE 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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91A VAL* 5.2 10.3 - - + -
95A GLU* 3.0 18.8 + - + +
96A GLU* 3.6 28.5 - - - +
97A ASN 3.2 0.2 - - - -
98A THR* 1.3 75.8 - - - +
100A ALA* 1.3 65.3 + - - +
102A ARG* 3.2 27.5 + - - +
103A HIS* 3.2 33.7 + - + +
109A TYR* 5.4 4.3 - - - +
111A ASP* 4.2 8.5 - - - +
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Residues in contact with ALA 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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96A GLU 3.4 7.1 + - - +
97A ASN* 3.0 12.8 + - - +
99A ILE* 1.3 80.9 - - - +
101A PHE* 1.3 61.6 + - + +
103A HIS* 3.2 8.8 + - - +
104A LEU* 2.9 40.5 + - + +
147A TYR* 4.9 7.6 - - + +
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Residues in contact with PHE 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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97A ASN* 2.9 22.7 + - + -
98A THR* 3.1 16.4 + - - +
100A ALA* 1.3 80.3 - - + +
102A ARG* 1.3 56.3 - - - +
104A LEU* 4.5 6.7 - - + -
105A PHE* 2.8 58.6 + + + +
139A LEU* 6.3 0.2 - - + -
147A TYR* 3.6 41.5 - + - -
237A LEU* 3.6 24.2 - - + -
256A PHE* 3.9 26.7 - + + -
258A VAL* 3.9 26.5 - - + -
275A LEU* 3.7 12.6 - - + +
277A THR* 4.0 8.5 - - + -
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Residues in contact with ARG 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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95A GLU 5.2 0.2 + - - -
98A THR* 3.0 46.9 + - - +
99A ILE* 3.2 21.5 + - - +
101A PHE* 1.3 77.2 - - - +
103A HIS* 1.3 63.2 + - - +
106A LEU* 3.1 49.3 + - + +
109A TYR* 3.5 33.2 + - + +
114A ASP* 3.6 27.3 + - - -
275A LEU* 3.1 36.4 + - + +
276A GLU* 3.9 15.2 + - - -
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Residues in contact with HIS 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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99A ILE* 3.2 29.9 + - + +
100A ALA* 3.2 10.6 + - - +
102A ARG* 1.3 77.5 - - - +
104A LEU* 1.3 63.6 + - + +
106A LEU 4.0 8.5 - - - +
109A TYR* 3.5 29.5 + + - +
110A SER* 4.6 4.0 - - - -
111A ASP* 2.7 43.7 + - - -
131A HIS* 5.2 1.9 + - - -
135A GLN* 5.4 0.3 + - - -
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Residues in contact with LEU 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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100A ALA* 2.9 30.3 + - + +
101A PHE* 3.9 15.5 - - + +
103A HIS* 1.3 78.9 - - + +
105A PHE* 1.3 68.5 + - + +
131A HIS* 3.5 6.3 + - - -
135A GLN* 3.0 43.4 + - + +
139A LEU* 4.2 14.8 - - + -
142A VAL* 4.6 12.1 - - + +
143A SER* 4.1 31.9 - - - +
144A LEU 5.6 0.7 - - - +
147A TYR* 5.3 1.3 - - + -
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Residues in contact with PHE 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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101A PHE* 2.8 59.5 + + + +
104A LEU* 1.3 79.7 - - + +
106A LEU* 1.3 62.6 + - - +
107A LEU 3.7 0.9 + - - -
128A ALA 4.5 1.7 - - - +
131A HIS* 3.6 7.1 - - - -
132A ALA* 3.5 34.5 + - + +
135A GLN* 3.6 20.2 - - + -
136A TYR* 3.6 26.7 - - - -
139A LEU* 4.0 27.4 - - + -
235A PHE* 3.7 37.7 - + - -
237A LEU* 4.5 1.8 - - + -
258A VAL* 5.1 0.2 - - + -
260A ILE* 3.9 17.9 - - + -
275A LEU* 4.3 6.5 - - + -
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Residues in contact with LEU 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 ARG* 3.1 47.3 + - + +
103A HIS 4.0 8.0 - - - +
105A PHE* 1.3 79.9 - - - +
107A LEU* 1.3 66.4 + - - +
108A GLY 3.3 1.0 + - - -
109A TYR* 3.2 33.0 + - + +
117A PHE* 3.7 17.9 - - + -
131A HIS* 4.2 2.1 + - - -
260A ILE* 4.1 19.1 - - + -
262A PHE* 5.7 0.9 - - + -
273A ILE* 3.9 26.2 - - + +
274A SER* 5.2 0.9 - - - -
275A LEU* 4.2 21.5 - - + +
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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