Contacts of the helix formed by residues 114 - 125 (chain C) in PDB entry 1TTT
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 PRO 114 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C HIS* 3.0 13.7 - - + +
113C MET* 1.3 101.5 - - + +
115C GLN* 1.3 70.4 + - - +
117C ARG* 2.9 21.5 + - + +
118C GLU* 2.9 12.7 + - - +
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Residues in contact with GLN 115 (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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19C HIS* 2.8 49.5 + - - -
20C VAL* 4.1 4.4 - - - +
84C GLY 3.2 24.1 + - - +
86C ALA* 3.8 26.8 - - + +
89C ILE* 4.7 0.4 - - + -
114C PRO* 1.3 77.8 - - - +
116C THR* 1.3 60.8 + - - +
118C GLU* 3.4 25.2 - - - +
119C HIS* 2.4 59.4 + - + +
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Residues in contact with THR 116 (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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18C GLY* 4.3 8.1 - - - -
19C HIS* 3.4 26.2 + - - +
22C HIS* 4.2 8.3 + - - -
104C LEU* 4.7 10.4 - - + +
105C VAL 4.5 3.5 + - - -
106C VAL* 4.6 15.6 - - + +
112C PRO* 3.7 16.5 - - + +
113C MET 3.1 19.0 + - - +
115C GLN* 1.3 79.6 - - - +
117C ARG* 1.3 65.1 + - - +
119C HIS* 3.9 1.4 - - - +
120C ILE* 3.1 22.5 + - - +
154C VAL* 5.3 1.1 - - + -
157C LEU* 3.6 23.1 - - + -
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Residues in contact with ARG 117 (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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113C MET 3.3 5.2 + - - +
114C PRO* 2.9 11.5 + - + +
116C THR* 1.3 81.8 - - - +
118C GLU* 1.3 64.4 + - - +
120C ILE* 3.5 3.6 + - - +
121C LEU* 3.1 17.7 + - + +
157C LEU* 3.5 27.3 - - + +
160C GLN* 2.7 37.6 + - - +
161C TYR* 2.6 57.2 + - + -
323C LEU* 5.5 1.1 - - - -
326C GLU* 4.8 9.3 + - - +
327C GLU* 3.8 33.8 - - - +
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Residues in contact with GLU 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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86C ALA* 4.8 2.3 - - - +
89C ILE* 3.3 23.4 - - + +
114C PRO 2.9 11.4 + - - +
115C GLN* 3.4 26.3 - - - +
117C ARG* 1.3 75.6 - - - +
119C HIS* 1.3 56.1 + - - +
121C LEU* 2.6 29.5 + - + +
122C LEU* 2.6 24.0 + - + +
323C LEU* 6.3 1.1 - - + -
389C ARG* 2.3 36.4 + - - -
392C GLY 5.0 0.5 - - - +
393C ARG* 4.4 2.1 - - - -
394C THR* 2.8 22.7 + - + +
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Residues in contact with HIS 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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17C ILE* 3.7 19.0 - - + +
18C GLY* 2.8 48.0 + - - +
24C LYS* 5.3 0.2 - - - +
82C CYS* 5.9 0.4 - - - +
83C PRO 3.6 18.7 + - - -
84C GLY* 4.2 0.8 - - - -
89C ILE* 3.9 16.6 - - + +
92C MET* 3.3 37.4 - - + +
104C LEU* 4.9 1.1 - - + -
115C GLN* 2.4 45.8 + - + +
116C THR 3.9 2.7 - - - +
118C GLU* 1.3 65.3 - - - +
120C ILE* 1.3 63.8 + - - +
122C LEU* 4.3 0.7 - - - -
123C ALA* 2.8 27.4 + - - +
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Residues in contact with ILE 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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17C ILE* 4.9 2.9 - - + -
104C LEU* 3.7 31.2 - - + -
116C THR 3.1 13.9 + - - +
117C ARG* 3.6 5.4 - - - +
118C GLU 2.9 1.0 + - - -
119C HIS* 1.3 78.8 - - - +
121C LEU* 1.3 69.0 + - - +
123C ALA* 3.2 5.1 - - - +
124C ARG* 2.9 22.2 + - - +
131C ILE* 4.9 4.5 - - + -
154C VAL* 5.1 0.4 - - + +
157C LEU* 3.7 33.0 - - + +
158C LEU* 4.3 19.5 - - + +
161C TYR* 3.7 20.2 - - + -
163C PHE* 3.4 29.5 - - + -
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Residues in contact with LEU 121 (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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117C ARG 3.1 9.7 + - - +
118C GLU* 2.6 15.8 + - + +
120C ILE* 1.3 79.6 - - - +
122C LEU* 1.3 57.3 + - + +
124C ARG* 3.3 10.4 + - - +
125C GLN* 2.9 35.3 + - + +
161C TYR* 3.3 38.6 - - + -
321C TYR* 6.2 1.6 - - + -
323C LEU* 3.7 35.0 - - + -
394C THR* 4.2 17.9 - - + -
397C ALA* 4.0 24.7 - - + -
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Residues in contact with LEU 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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89C ILE* 3.2 39.3 - - + -
92C MET* 3.7 20.4 - - + -
93C ILE* 3.7 26.7 - - + -
118C GLU* 2.6 28.5 + - + +
121C LEU* 1.3 70.5 - - + +
123C ALA* 1.3 60.1 + - - +
125C GLN* 2.6 26.9 + - - +
126C VAL* 2.8 17.1 + - - +
387C ALA* 4.1 23.1 - - + -
389C ARG* 4.5 5.2 - - - -
394C THR* 3.9 23.3 - - + +
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Residues in contact with ALA 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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17C ILE* 4.2 15.7 - - + -
92C MET* 4.1 2.2 - - + +
96C ALA* 4.5 11.9 - - + -
102C ALA* 5.2 2.7 - - + -
119C HIS 2.8 21.7 + - - +
120C ILE* 3.2 5.8 - - - +
122C LEU* 1.3 75.2 - - - +
124C ARG* 1.3 61.7 + - - +
126C VAL* 3.4 6.7 + - - -
127C GLY 3.5 0.5 + - - -
128C VAL* 3.0 44.9 + - + +
131C ILE* 5.5 2.7 - - + -
163C PHE* 5.0 4.0 - - + -
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Residues in contact with ARG 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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120C ILE 2.9 8.3 + - - +
121C LEU* 3.5 12.7 - - - +
123C ALA* 1.3 74.8 - - - +
125C GLN* 1.3 99.1 + - - +
126C VAL 3.0 6.3 + - - -
127C GLY* 3.1 10.7 + - - -
128C VAL 4.3 5.4 - - - +
161C TYR* 3.2 31.9 + - - +
162C GLU* 3.5 21.1 + - - +
163C PHE* 3.5 25.5 - - + -
385C ARG* 3.3 51.5 + - - +
397C ALA* 5.6 0.8 - - - +
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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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121C LEU* 2.9 17.4 + - + +
122C LEU 2.6 14.2 + - - +
124C ARG* 1.3 119.0 + - - +
126C VAL* 1.3 57.5 + - - +
127C GLY 3.3 1.4 + - - -
343C TYR 5.7 0.4 - - - +
345C ARG 5.4 0.3 + - - -
385C ARG* 3.0 39.0 - - - +
386C PHE* 2.7 37.4 + - - +
387C ALA* 3.7 14.8 - - + -
397C ALA* 3.6 22.5 - - + +
398C GLY 3.1 26.1 + - - +
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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