Contacts of the helix formed by residues 98 - 110 (chain A) in PDB entry 3TNF
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 ASN 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MPD 5.9 2.2 - - + -
16A ASP* 2.7 40.6 + - - +
94A LYS* 2.8 42.5 + - - +
95A SER 4.1 2.0 - - - +
96A PHE 3.2 0.4 - - - -
97A ASP* 1.3 71.7 - - - +
99A ILE* 1.3 65.4 + - - +
100A ARG 3.1 0.7 - - - -
101A ASN* 3.0 34.4 + - + +
102A TRP* 3.0 19.4 + - + +
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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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15A GLY* 5.6 0.4 - - - -
86A LEU* 4.1 21.5 - - + +
87A VAL 3.7 31.0 - - - +
88A TYR* 3.9 20.2 - - + -
95A SER 3.7 9.8 + - - +
96A PHE* 3.1 18.3 + - + +
97A ASP 3.0 1.0 + - - -
98A ASN* 1.3 76.7 - - - +
100A ARG* 1.3 56.6 + - - +
102A TRP* 3.2 11.7 + - + -
103A ILE* 2.8 53.5 + - + +
118A ILE* 4.2 17.9 - - + -
139A LEU* 4.2 9.9 - - + -
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Residues in contact with ARG 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 PHE* 4.8 4.0 - - - -
97A ASP* 3.0 50.2 + - - +
99A ILE* 1.3 78.2 - - - +
101A ASN* 1.3 63.6 + - - +
103A ILE* 3.3 7.5 + - - +
104A ARG* 3.0 28.5 + - - +
139A LEU* 4.3 22.4 - - + +
143A TYR* 3.5 25.9 + - - +
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Residues in contact with ASN 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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1A MPD 4.0 24.5 - - + +
97A ASP 4.9 0.8 + - - -
98A ASN* 3.0 33.2 + - - +
100A ARG* 1.3 81.8 + - - +
102A TRP* 1.3 67.4 - - - +
104A ARG* 3.3 16.8 + - - +
105A ASN* 2.8 26.7 + - - +
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Residues in contact with TRP 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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1A MPD 3.6 25.7 - - + +
14A ILE* 3.3 31.6 - - + -
15A GLY* 3.7 30.7 - - - -
16A ASP* 3.0 25.8 + - - +
64A THR* 5.8 2.0 - - - -
65A ALA 5.2 3.4 - - - -
71A ARG* 3.4 46.0 - - + -
74A THR* 4.3 11.9 - - + -
78A TYR* 3.9 15.4 + - - -
86A LEU* 3.9 15.0 - - + -
95A SER 5.5 0.7 - - - -
98A ASN* 3.0 31.3 + - + +
99A ILE* 3.5 14.4 - - + +
101A ASN* 1.3 75.2 - - - +
103A ILE* 1.3 65.0 + - - +
105A ASN* 3.2 4.0 + - - +
106A ILE* 3.0 29.6 + - - +
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Residues in contact with ILE 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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86A LEU* 3.6 21.1 - - + -
99A ILE* 2.8 41.2 + - + +
100A ARG* 3.5 5.2 - - - +
102A TRP* 1.3 71.4 - - - +
104A ARG* 1.3 64.1 + - - +
106A ILE* 3.1 8.1 + - - +
107A GLU* 3.0 37.6 + - + +
116A LYS* 5.5 10.7 - - + +
118A ILE* 4.3 3.6 - - + -
139A LEU* 5.2 1.3 - - + -
143A TYR* 3.7 56.3 - - + -
145A ILE* 4.2 17.7 - - + -
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Residues in contact with ARG 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 ARG 3.0 16.7 + - - +
101A ASN* 3.3 16.5 + - - +
103A ILE* 1.3 76.7 - - - +
105A ASN* 1.3 64.1 + - - +
107A GLU* 3.0 18.3 + - - +
108A GLU* 2.8 56.7 + - + +
279B LEU* 4.2 8.7 - - - +
282B LEU* 4.6 5.6 - - + +
295B SER* 4.9 6.5 + - - -
296B LEU* 3.7 23.9 - - - +
299B GLU* 2.8 39.4 + - - -
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Residues in contact with ASN 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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1A MPD 3.4 38.8 + - + +
74A THR* 5.4 0.6 - - - +
75A THR* 3.6 19.3 - - - +
78A TYR* 2.6 43.6 + - - +
101A ASN 2.8 18.0 + - - +
102A TRP 3.4 5.2 - - - +
104A ARG* 1.3 78.6 - - - +
106A ILE* 1.3 56.4 + - - +
108A GLU* 4.3 9.6 - - - +
109A HIS* 3.1 42.4 + - - +
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Residues in contact with ILE 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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14A ILE* 3.3 28.5 - - + -
78A TYR* 3.8 26.0 - - + +
84A ILE* 3.9 22.7 - - + -
86A LEU* 3.7 19.5 - - + -
102A TRP 3.0 13.3 + - - +
103A ILE* 3.4 7.6 - - - +
105A ASN* 1.3 75.4 - - - +
107A GLU* 1.3 62.3 + - - +
110A ALA* 2.6 48.9 + - + +
111A SER 5.1 0.2 - - - +
114A VAL* 4.3 10.3 - - + -
116A LYS* 4.5 15.3 - - + +
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Residues in contact with GLU 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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103A ILE* 3.0 32.8 + - + +
104A ARG* 3.0 20.4 + - - +
106A ILE* 1.3 76.8 - - + +
108A GLU* 1.3 62.7 + - + +
109A HIS 3.6 0.2 + - - -
110A ALA 3.8 9.8 - - - +
112A ALA* 5.6 4.8 + - - +
116A LYS* 4.6 18.2 + - - +
143A TYR* 4.8 10.5 - - - -
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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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104A ARG* 2.8 59.4 + - + +
105A ASN* 4.3 5.9 - - - +
107A GLU* 1.3 78.9 - - + +
109A HIS* 1.3 87.9 + - + +
110A ALA 4.9 0.7 - - - -
278B LYS* 4.6 17.3 + - + +
279B LEU* 5.6 1.3 - - - +
282B LEU* 3.8 16.9 - - + +
299B GLU* 5.2 2.8 - - - +
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Residues in contact with HIS 109 (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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75A THR* 3.9 27.5 - - + +
78A TYR* 3.6 24.1 - - + +
79A ARG* 5.3 6.6 - - - +
105A ASN* 3.1 35.8 + - - +
106A ILE 3.1 1.8 + - - -
108A GLU* 1.3 107.3 + - + +
110A ALA* 1.3 61.6 + - - +
111A SER 4.4 0.2 + - - -
275B ASP* 4.6 17.0 + - - -
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Residues in contact with ALA 110 (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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78A TYR* 3.6 26.4 - - + +
84A ILE* 4.4 4.3 - - + -
106A ILE* 2.6 45.9 + - + +
107A GLU* 3.8 9.7 - - - +
108A GLU 4.9 0.2 - - - -
109A HIS* 1.3 75.5 - - - +
111A SER* 1.3 67.0 + - - +
112A ALA* 3.4 1.9 + - - -
114A VAL* 4.1 13.5 - - + -
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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