Contacts of the strand formed by residues 112 - 126 (chain C) in PDB entry 1TNF
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 LYS 112 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B THR* 5.2 8.0 + - - +
73B HIS* 3.9 35.1 + - + +
102B GLN* 4.4 8.5 - - + +
103B ARG* 4.8 19.4 - - - +
68C GLY* 4.0 11.7 + - - +
104C GLU* 4.2 20.4 - - - +
106C PRO* 4.9 2.0 - - - +
109C ALA* 4.0 25.7 + - - +
110C GLU 3.5 4.1 + - - +
111C ALA* 1.3 74.5 - - - +
113C PRO* 1.3 67.7 - - + +
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Residues in contact with PRO 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B HIS* 2.7 40.2 + - + -
75B LEU* 6.0 3.6 - - + -
99B SER* 3.4 3.6 + - - -
102B GLN* 3.9 1.5 - - - +
65C LYS* 5.8 2.2 - - + -
66C GLY 3.2 13.5 - - - +
67C GLN* 3.9 15.0 - - + +
111C ALA 4.0 5.2 - - - +
112C LYS* 1.3 87.1 - - + -
114C TRP* 1.3 60.1 + - - +
115C TYR* 4.2 24.6 - - + +
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Residues in contact with TRP 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B SER* 3.4 5.4 - - - -
102B GLN* 3.1 37.5 - - - +
64C PHE* 3.9 20.2 - - + -
65C LYS* 3.7 2.1 - - - -
66C GLY* 2.8 60.7 + - - -
68C GLY 2.7 28.4 + - - -
69C CYS* 3.2 15.3 - - - -
74C VAL* 3.7 19.5 - - + -
76C LEU* 3.8 15.0 - - + -
100C PRO* 3.7 31.4 - - + -
101C CYS* 4.1 1.8 - - - -
113C PRO* 1.3 72.6 - - - +
115C TYR* 1.3 75.4 + - - +
116C GLU* 4.1 7.6 - - + +
141C TYR* 3.8 34.3 - + - -
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Residues in contact with TYR 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.4 37.9 - - + +
97B ILE* 3.0 45.4 - - + +
98B LYS* 4.0 5.7 - - - +
99B SER* 3.2 24.1 + - - +
102B GLN* 5.7 0.2 + - - -
63C LEU* 4.3 12.1 - - + -
64C PHE 3.5 6.5 - - - -
65C LYS* 4.2 11.0 - - + +
113C PRO* 4.2 20.8 - - + +
114C TRP* 1.3 85.6 - - - +
116C GLU* 1.3 72.5 + - - +
117C PRO* 4.0 2.3 - - - +
143C LEU* 3.4 31.1 - - + +
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Residues in contact with GLU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLU* 5.4 0.9 - - - +
98B LYS* 5.0 5.4 + - - +
99B SER 5.7 0.3 - - - +
102B GLN* 5.2 1.9 + - - -
63C LEU* 3.8 2.8 - - - +
64C PHE* 2.9 47.2 + - + +
76C LEU* 4.3 8.7 - - + -
98C LYS* 3.5 41.1 + - + +
99C SER 5.7 0.2 - - - -
100C PRO* 3.4 33.5 - - + +
114C TRP* 4.1 13.3 - - + +
115C TYR* 1.3 85.8 + - - +
117C PRO* 1.3 64.7 - - - +
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Residues in contact with PRO 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ALA* 4.2 21.3 - - + -
97B ILE 3.9 8.7 - - - +
98B LYS* 3.6 44.9 - - + -
118B ILE* 4.9 4.7 - - + -
61C GLN* 4.9 9.0 - - + +
62C VAL 3.5 7.2 - - - +
63C LEU* 3.7 13.7 - - + -
98C LYS* 2.9 25.8 + - - +
115C TYR 4.0 0.4 - - - +
116C GLU* 1.3 88.0 - - - +
118C ILE* 1.3 60.0 + - - +
119C TYR* 6.4 0.7 - - + -
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Residues in contact with ILE 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A PRO* 5.0 6.3 - - + -
60C SER 3.8 0.2 - - - +
61C GLN* 3.0 6.1 - - - +
62C VAL* 2.8 43.0 + - + +
64C PHE* 3.4 31.4 - - + -
77C THR 4.6 3.4 - - - +
78C HIS* 4.2 18.8 - - + +
96C ALA* 3.8 42.6 - - + +
98C LYS* 3.8 30.7 - - + +
117C PRO* 1.3 76.2 - - - +
119C TYR* 1.3 71.7 - - - +
120C LEU* 4.8 1.3 - - + -
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Residues in contact with TYR 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLN* 4.9 2.3 - - - +
117A PRO* 6.1 0.7 - - - +
119A TYR* 3.5 47.4 + + + +
57B LEU* 5.9 1.0 - - - +
119B TYR* 3.9 31.6 - + + +
121B GLY* 3.2 42.2 + - - -
59C TYR* 3.4 16.1 - - + +
60C SER 3.2 13.2 - - - -
61C GLN* 3.9 8.5 - - + +
96C ALA* 5.4 1.0 - - - +
117C PRO* 4.3 0.6 - - + -
118C ILE* 1.3 82.1 - - - +
120C LEU* 1.3 81.7 - - - +
121C GLY* 4.1 1.5 - - - -
151C TYR* 3.3 25.8 - + - -
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLN* 3.6 22.4 - - - +
119A TYR* 5.4 1.1 - - - -
59C TYR* 3.2 4.6 - - - -
60C SER 2.9 29.2 + - - +
78C HIS* 3.2 47.6 - - + +
80C ILE* 3.8 29.2 - - + +
94C LEU* 3.8 16.8 - - + -
95C SER* 3.6 29.6 - - - +
96C ALA* 4.1 6.1 - - + +
118C ILE* 4.8 2.5 - - + -
119C TYR* 1.3 87.4 - - - +
121C GLY* 1.3 57.9 + - - +
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Residues in contact with GLY 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 4.7 0.2 - - - -
119A TYR* 3.3 37.0 + - - -
151A TYR* 3.1 22.1 + - - -
57C LEU* 5.4 1.6 - - - -
58C ILE 3.3 9.2 - - - -
59C TYR* 4.2 2.9 - - - -
94C LEU* 3.5 6.4 - - - +
119C TYR* 4.1 3.4 - - - -
120C LEU* 1.3 76.7 - - - +
122C GLY* 1.3 57.1 + - - -
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Residues in contact with GLY 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR* 4.4 11.4 - - - -
119A TYR* 4.1 1.0 + - - -
151A TYR* 4.7 1.1 - - - -
56C TYR 3.6 1.4 - - - +
57C LEU* 3.5 5.2 - - - +
58C ILE* 2.8 42.0 + - - +
94C LEU* 4.2 1.3 - - - +
121C GLY* 1.3 75.6 - - - -
123C VAL* 1.3 67.8 + - - -
124C PHE* 3.7 19.7 - - - -
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Residues in contact with VAL 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A VAL* 4.7 7.2 - - + -
14A ALA 5.5 0.4 - - - +
15A HIS* 3.4 15.9 + - + +
36A LEU* 5.1 5.9 - - + +
57A LEU* 5.4 0.9 - - + -
59A TYR* 3.1 42.2 + - + +
154A ILE 5.1 1.3 - - - +
155A ILE* 4.1 30.3 - - + -
55C LEU* 4.9 11.9 - - + -
56C TYR 3.5 3.8 - - - +
57C LEU* 3.5 36.6 - - + -
122C GLY* 1.3 72.8 - - - -
124C PHE* 1.3 61.7 + - - +
157C LEU* 4.6 9.2 - - + -
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Residues in contact with PHE 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A HIS* 3.7 27.8 - + - -
34A ASN* 3.3 38.6 - - + +
36A LEU* 5.7 0.7 - - - -
151A TYR* 5.4 1.6 - + - -
55C LEU* 4.0 3.4 - - - -
56C TYR* 2.6 45.6 + - - +
58C ILE* 3.5 28.0 - - + -
93C LEU* 4.0 30.1 - - + -
94C LEU* 3.6 42.4 - - + -
122C GLY* 3.7 12.8 - - - -
123C VAL* 1.3 75.8 - - - +
125C GLN* 1.3 61.7 + - - +
126C LEU* 3.5 3.6 + - + +
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Residues in contact with GLN 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ARG* 2.7 50.9 + - - +
8A PRO* 3.1 17.9 - - - +
34A ASN* 3.6 19.9 + - - +
36A LEU* 5.0 7.6 - - + +
53C GLU* 4.4 4.2 - - - +
54C GLY 2.9 41.9 + - - +
55C LEU* 3.5 16.6 - - + +
82C ARG* 3.1 21.6 + - - +
124C PHE* 1.3 70.7 - - - +
126C LEU* 1.3 74.4 + - - +
127C GLU* 4.6 7.4 - - - +
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Residues in contact with LEU 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C VAL* 3.8 21.5 - - + -
53C GLU* 4.6 0.2 - - - -
54C GLY 2.8 13.4 + - - +
56C TYR* 3.6 44.4 - - + -
58C ILE* 4.5 8.5 - - + -
82C ARG* 3.8 18.6 - - + +
93C LEU* 5.6 0.9 - - + -
124C PHE* 3.5 4.4 + - + +
125C GLN* 1.3 97.9 + - - +
127C GLU* 1.3 65.0 + - - +
130C ASP* 3.7 27.8 - - + -
132C LEU* 3.7 34.3 - - + -
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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