Contacts of the helix formed by residues 114 - 125 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A HIS* 3.8 9.2 - - - +
113A MET* 1.3 100.1 - - + +
115A GLN* 1.3 77.2 + - - +
116A THR 2.8 5.2 - - - -
117A ARG* 2.8 19.7 + - + +
118A GLU* 2.9 12.3 + - - +
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Residues in contact with GLN 115 (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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19A HIS* 2.9 45.8 + - + -
20A VAL* 5.0 1.8 - - - +
84A GLY 3.5 24.4 + - - +
86A ALA* 3.8 22.9 - - + +
89A ILE* 4.3 4.5 - - + -
114A PRO* 1.3 80.8 - - - +
116A THR* 1.3 59.5 + - - +
118A GLU* 3.2 27.8 - - - +
119A HIS* 2.7 59.8 + - + +
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Residues in contact with THR 116 (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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19A HIS* 3.6 21.7 + - - +
22A HIS* 4.5 4.2 + - - -
104A LEU* 4.3 18.0 - - + +
105A VAL 5.4 0.2 + - - -
106A VAL* 4.0 26.0 - - + +
112A PRO* 3.7 15.2 - - + +
113A MET 2.8 33.2 + - - -
114A PRO 2.8 0.4 - - - -
115A GLN* 1.3 79.0 - - - +
117A ARG* 1.3 66.7 + - - +
119A HIS* 3.9 1.0 - - - +
120A ILE* 3.2 24.0 + - + +
154A VAL* 5.3 2.9 - - + -
157A LEU* 4.5 8.5 - - + -
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Residues in contact with ARG 117 (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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113A MET 3.3 3.2 + - - +
114A PRO* 2.8 12.0 + - + +
116A THR* 1.3 82.1 - - - +
118A GLU* 1.3 65.6 + - + +
120A ILE* 3.0 16.2 + - - +
121A LEU* 3.0 12.9 + - + +
157A LEU* 4.0 28.8 - - + +
160A GLN* 3.0 33.1 + - - +
161A TYR* 2.5 50.9 + - + +
323A LEU* 5.9 0.9 - - + -
326A GLU* 4.6 8.0 + - - +
327A GLU* 3.6 40.5 - - - +
328A GLY* 5.4 0.2 - - - -
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Residues in contact with GLU 118 (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 ALA* 4.8 2.8 - - - +
89A ILE* 3.6 12.2 - - + +
114A PRO 2.9 10.2 + - - +
115A GLN* 3.2 30.0 - - - +
117A ARG* 1.3 84.5 - - + +
119A HIS* 1.3 52.4 + - - +
121A LEU* 3.6 5.2 - - + +
122A LEU* 2.6 49.0 + - + +
389A ARG* 2.4 35.7 + - - -
392A GLY 4.9 0.9 - - - +
393A ARG* 4.6 1.4 - - - -
394A THR* 2.8 24.5 + - + +
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Residues in contact with HIS 119 (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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17A ILE* 3.5 22.6 - - + -
18A GLY 3.0 41.7 + - - +
24A LYS* 5.5 0.2 - - - +
83A PRO 3.6 20.1 + - - -
84A GLY* 3.7 3.0 - - - -
89A ILE* 3.5 29.4 - - + +
92A MET* 3.2 30.5 - - + +
104A LEU* 4.8 1.3 - - + -
115A GLN* 2.7 34.6 + - + +
116A THR 3.9 2.5 - - - +
118A GLU* 1.3 70.6 - - - +
120A ILE* 1.3 61.9 + - - +
123A ALA* 2.8 34.2 + - - +
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Residues in contact with ILE 120 (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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17A ILE* 4.9 1.3 - - - +
104A LEU* 4.0 25.1 - - + -
116A THR* 3.2 15.2 + - + +
117A ARG 3.0 8.6 + - - +
119A HIS* 1.3 82.5 - - - +
121A LEU* 1.3 62.8 + - - +
123A ALA* 3.4 6.4 + - - +
124A ARG 3.3 14.6 + - - -
131A ILE* 4.5 5.6 - - + -
154A VAL* 5.0 0.9 - - + +
157A LEU* 4.3 18.6 - - + -
158A LEU* 3.3 37.7 - - + -
161A TYR* 4.1 16.2 - - + -
163A PHE* 3.5 31.7 - - + -
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Residues in contact with LEU 121 (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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117A ARG* 3.0 9.3 + - + +
118A GLU* 3.8 8.3 - - + +
120A ILE* 1.3 80.3 - - - +
122A LEU* 1.3 73.1 + - + +
124A ARG* 3.3 9.0 + - - +
125A GLN* 3.1 36.3 + - + +
161A TYR* 3.2 41.1 - - + -
321A TYR* 6.3 0.2 - - + -
323A LEU* 4.1 22.4 - - + -
387A ALA* 6.2 0.2 - - + -
394A THR* 3.7 30.3 - - + -
397A ALA* 4.2 15.3 - - + -
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Residues in contact with LEU 122 (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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89A ILE* 3.6 33.4 - - + -
92A MET* 4.0 11.2 - - + -
93A ILE* 4.2 21.1 - - + +
96A ALA* 5.5 0.4 - - - -
118A GLU* 2.6 49.4 + - + +
119A HIS 3.9 2.7 - - - +
121A LEU* 1.3 79.9 - - + +
123A ALA* 1.3 63.4 + - - +
125A GLN* 3.1 4.9 + - + +
126A VAL* 3.1 23.3 + - - +
387A ALA* 3.9 27.4 - - + -
389A ARG* 4.5 1.6 - - - -
394A THR* 3.9 20.4 - - + +
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Residues in contact with ALA 123 (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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17A ILE* 4.4 17.0 - - + -
92A MET* 4.5 0.8 - - + +
96A ALA* 4.4 14.1 - - + -
119A HIS 2.8 21.5 + - - +
120A ILE* 3.5 7.4 - - - +
122A LEU* 1.3 72.4 - - - +
124A ARG* 1.3 58.8 - - - +
126A VAL* 2.9 17.2 + - - -
127A GLY 3.1 0.9 + - - -
128A VAL* 3.0 44.7 + - + +
131A ILE* 4.9 2.7 - - + -
163A PHE* 4.8 4.3 - - + -
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Residues in contact with ARG 124 (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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120A ILE 3.3 4.6 + - - +
121A LEU* 3.3 11.2 + - - +
123A ALA* 1.3 77.6 - - - +
125A GLN* 1.3 95.4 + - - +
126A VAL 2.8 9.5 + - - -
127A GLY* 3.0 13.2 + - - -
128A VAL 4.1 5.8 - - - +
161A TYR* 3.2 34.3 + - - -
162A GLU* 3.5 21.9 + - - +
163A PHE* 3.5 24.7 - - + -
385A ARG* 3.8 47.0 + - - +
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Residues in contact with GLN 125 (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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121A LEU* 3.1 20.2 + - + +
122A LEU* 3.1 7.1 + - - +
124A ARG* 1.3 110.6 + - - +
126A VAL* 1.3 63.9 + - + +
127A GLY 3.5 0.2 - - - -
345A ARG 5.4 0.2 + - - -
385A ARG* 3.5 42.2 - - - +
386A PHE* 3.1 33.5 + - - +
387A ALA* 4.0 13.7 - - + -
397A ALA* 3.6 25.6 - - + +
398A GLY 3.5 16.2 + - - +
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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