Contacts of the helix formed by residues 108 - 122 (chain B) in PDB entry 3TQS
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 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B ASN 4.1 4.7 - - - +
107B LEU* 1.3 86.5 - - + +
109B TYR* 1.3 60.9 + - - +
110B ASN* 3.2 20.4 + - - +
111B ILE* 3.5 22.9 + - + +
112B SER* 2.7 27.4 + - - -
134B GLN* 5.6 1.6 - - + +
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Residues in contact with TYR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LEU 3.9 0.6 + - - -
108B PRO* 1.3 71.4 - - - +
110B ASN* 1.3 65.3 + - + +
112B SER* 3.1 22.2 + - - -
113B THR 4.4 1.4 + - - -
134B GLN* 3.1 42.2 - - + +
136B GLU* 3.2 32.3 - - + +
137B VAL* 3.5 22.2 - - + -
140B ARG* 3.0 34.9 + - - -
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Residues in contact with ASN 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PRO* 3.4 19.1 - - - +
109B TYR* 1.3 82.4 - - + +
111B ILE* 1.3 77.6 + - - +
114B PRO* 3.8 12.4 - - - +
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Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ILE* 6.1 2.0 - - + -
87B ALA* 6.2 2.5 - - + -
88B LEU* 4.3 24.7 - - + -
107B LEU* 4.7 8.7 - - + -
108B PRO* 3.7 33.0 - - + +
109B TYR 3.3 0.2 - - - -
110B ASN* 1.3 95.9 + - - +
112B SER* 1.3 60.1 + - - +
114B PRO* 3.4 13.0 - - + -
115B LEU* 2.8 45.3 + - + +
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Residues in contact with SER 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 4.0 11.2 + - - +
108B PRO 2.7 22.4 + - - -
109B TYR* 3.1 16.2 + - - -
110B ASN 3.5 0.2 - - - -
111B ILE* 1.3 77.6 - - - +
113B THR* 1.3 63.3 + - - +
115B LEU* 4.0 0.9 - - - +
116B LEU* 3.0 32.9 + - - +
133B LEU* 3.8 21.1 - - - +
134B GLN 5.5 0.2 + - - -
137B VAL* 4.1 27.1 - - - +
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Residues in contact with THR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR 4.4 1.4 + - - -
112B SER* 1.3 79.2 - - - +
114B PRO* 1.3 71.1 - - + +
116B LEU* 3.2 4.5 + - - +
117B PHE* 2.9 57.6 + - + +
137B VAL* 5.5 0.2 - - - +
140B ARG* 4.2 12.7 + - - +
152B ARG* 5.7 3.4 - - - +
153B LEU* 3.7 29.6 - - + +
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Residues in contact with PRO 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 3.6 18.3 - - + +
110B ASN 3.8 9.4 - - - +
111B ILE* 3.3 31.4 - - + +
113B THR* 1.3 96.4 - - + +
115B LEU* 1.3 59.8 + - - +
117B PHE* 3.6 6.5 + - + +
118B HIS* 3.1 23.7 + - - +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 3.9 25.6 - - + -
87B ALA* 3.5 36.8 - - + +
88B LEU* 3.4 12.0 - - + +
92B PHE* 5.1 0.2 - - + -
107B LEU* 3.4 41.5 - - + -
111B ILE* 2.8 32.6 + - + +
112B SER 4.1 1.6 - - - +
114B PRO* 1.3 71.2 - - - +
116B LEU* 1.3 65.1 + - - +
118B HIS* 3.2 5.4 + - + +
119B LEU* 3.0 38.2 + - + +
131B PHE* 5.0 0.9 - - + -
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LEU* 5.3 5.6 - - + -
112B SER* 3.0 25.9 + - - +
113B THR* 3.7 3.1 - - - +
115B LEU* 1.3 75.4 - - - +
117B PHE* 1.3 59.2 + - + +
119B LEU* 3.1 8.4 + - + +
120B PHE* 2.8 47.2 + - + -
129B MSE 4.6 2.5 - - - -
131B PHE* 3.8 34.5 - - + -
133B LEU* 4.8 13.0 - - + -
137B VAL* 5.2 2.5 - - + -
141B ILE* 3.7 32.5 - - + -
153B LEU* 4.3 6.7 - - + -
187B LEU* 4.1 20.4 - - + -
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Residues in contact with PHE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B THR* 2.9 38.0 + - + +
114B PRO* 3.9 6.5 - - + +
116B LEU* 1.3 78.0 - - + +
118B HIS* 1.3 62.9 + - - +
120B PHE* 3.3 22.5 + + - +
121B SER* 3.0 21.7 + - - -
152B ARG* 3.7 46.7 - - + -
153B LEU* 4.0 22.7 - - + -
156B MSE 3.7 35.4 - - + -
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Residues in contact with HIS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ALA 3.2 23.1 - - - -
88B LEU* 3.3 24.2 + - - +
89B GLN* 4.2 7.2 - - - -
90B PHE 2.8 26.2 + - - -
92B PHE* 4.1 9.6 - + - -
114B PRO 3.1 19.0 + - - +
115B LEU* 3.4 8.7 - - + +
117B PHE* 1.3 77.4 - - - +
119B LEU* 1.3 61.0 + - - +
121B SER* 2.5 30.2 + - - -
122B GLN* 3.2 31.4 + - - +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ILE* 4.8 1.1 - - + -
92B PHE* 3.6 43.5 - - + -
103B VAL* 4.5 7.9 - - + -
115B LEU* 3.0 28.8 + - + +
116B LEU* 3.1 10.5 + - - +
118B HIS* 1.3 75.8 - - - +
120B PHE* 1.3 59.7 + - - +
122B GLN* 2.9 21.5 + - - -
123B ILE* 3.1 13.0 + - - -
126B ILE* 3.6 26.4 - - + +
129B MSE 3.9 16.2 - - - -
131B PHE* 3.6 35.9 - - + -
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Residues in contact with PHE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 2.8 33.1 + - + -
117B PHE* 3.5 31.4 - + - +
119B LEU* 1.3 79.1 - - + +
121B SER* 1.3 61.7 + - - +
122B GLN 3.0 1.3 + - - -
123B ILE* 3.2 32.0 + - + +
129B MSE 4.3 11.0 - - + -
156B MSE 4.3 1.1 - - + -
157B ALA* 3.6 39.7 - - + -
160B PHE* 3.5 48.7 - + + -
161B CYS* 3.9 19.3 - - - -
187B LEU* 4.1 15.5 - - + -
200B LEU* 5.9 0.5 - - - +
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Residues in contact with SER 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B PHE 3.0 12.4 + - - -
118B HIS* 2.5 30.3 + - - -
120B PHE* 1.3 76.3 - - - +
122B GLN* 1.3 67.4 + - - +
123B ILE 3.6 0.6 + - - -
124B HIS* 4.9 4.2 + - - -
160B PHE* 5.6 1.8 - - - -
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Residues in contact with GLN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B PHE 3.3 9.4 + - - -
91B ASP* 3.9 13.1 + - - +
92B PHE* 2.9 38.6 + - + +
93B SER* 4.1 1.8 + - - -
118B HIS* 3.2 34.8 - - - +
119B LEU* 2.9 11.5 + - - +
121B SER* 1.3 89.6 + - - +
123B ILE* 1.3 55.9 + - - +
124B HIS* 3.2 15.7 - - + -
125B CYS* 2.9 36.4 + - + +
126B ILE* 4.2 3.5 - - + +
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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